From ef788a1ae0adba6933af8c4a4bcd9441361b36fd Mon Sep 17 00:00:00 2001 From: Jannik Buhr Date: Fri, 1 Mar 2024 15:11:42 +0100 Subject: [PATCH 1/8] refactor: address "possibly unbound" code paths in radical migration analysis --- .../analyse_kimmdy_migration.py | 46 ++++++++++--------- 1 file changed, 24 insertions(+), 22 deletions(-) diff --git a/guide/tutorials/analyse-extended-simulations/analyse_kimmdy_migration.py b/guide/tutorials/analyse-extended-simulations/analyse_kimmdy_migration.py index b8a4b70a..4b2a09ad 100644 --- a/guide/tutorials/analyse-extended-simulations/analyse_kimmdy_migration.py +++ b/guide/tutorials/analyse-extended-simulations/analyse_kimmdy_migration.py @@ -26,6 +26,7 @@ def get_inbetween(p1, p2, val): interactions = json.load(json_file) # %% +rgb = None if analysis_type == "quantitative": rgb = np.tile(np.asarray([0.62, 0.59, 0.98]), (len(interactions.keys()), 1)) elif analysis_type == "max_rate": @@ -51,6 +52,8 @@ def get_inbetween(p1, p2, val): min_count = np.min(counts) if not manual_max_count: max_count = np.max(counts) + else: + max_count = manual_max_count norm_counts = (counts - min_count) / (max_count - min_count) print(f"min count: {min_count}, max count: {max_count}") @@ -62,7 +65,6 @@ def get_inbetween(p1, p2, val): # Get RGB values for the normalized counts rgb = [np.asarray(cmap(value)[:3]) for value in norm_counts] -# breakpoint() # %% radius = 10 counter = 0 @@ -78,29 +80,29 @@ def get_inbetween(p1, p2, val): p1 = get_inbetween(a1, a2, 0.1) p2 = get_inbetween(a1, a2, 0.9) - if do_arrow: + if do_arrow and rgb: p1_far = get_inbetween(a1, a2, 0.18) - cylinder = ( - [cgo.CYLINDER] - + p1_far.tolist() - + p_cap.tolist() - + [radius] - + rgb[counter].tolist() - + rgb[counter].tolist() - ) - head = ( - [cgo.CONE] - + p_cap.tolist() - + p2.tolist() - + [radius * 2, 0.0] - + rgb[counter].tolist() - + rgb[counter].tolist() - + [1.0, 0.0] - ) - # cmd.load_cgo(cylinder,f"cylinder{i}") - cmd.load_cgo(cylinder + head, f"cylinder{k}") - counter += 1 + cylinder = ( + [cgo.CYLINDER] + + p1_far.tolist() + + p_cap.tolist() + + [radius] + + rgb[counter].tolist() + + rgb[counter].tolist() + ) + head = ( + [cgo.CONE] + + p_cap.tolist() + + p2.tolist() + + [radius * 2, 0.0] + + rgb[counter].tolist() + + rgb[counter].tolist() + + [1.0, 0.0] + ) + # cmd.load_cgo(cylinder,f"cylinder{i}") + cmd.load_cgo(cylinder + head, f"cylinder{k}") + counter += 1 print(f"Loading geometry file") cmd.load(geometry_path.as_posix()) print("Changing default settings") From a04dfc22d9bcad54e1f1f5080cd457e4371af939 Mon Sep 17 00:00:00 2001 From: Jannik Buhr Date: Fri, 1 Mar 2024 15:21:39 +0100 Subject: [PATCH 2/8] fix: null-check --- src/kimmdy/analysis.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/kimmdy/analysis.py b/src/kimmdy/analysis.py index 17c6245a..0a724da8 100644 --- a/src/kimmdy/analysis.py +++ b/src/kimmdy/analysis.py @@ -587,6 +587,7 @@ def reaction_participation(dir: str, open_plot: bool = False): for recipes in run_dir.glob("*decide_recipe/recipes.csv"): # get picked recipe rc, picked_rp = RecipeCollection.from_csv(recipes) + assert picked_rp, f"No picked recipe found in {recipes}." # get involved atoms reaction_atom_ids = set() for step in picked_rp.recipe_steps: From 347a0929c367c5025689a96a6fd300d342b0d1c8 Mon Sep 17 00:00:00 2001 From: Jannik Buhr Date: Fri, 1 Mar 2024 15:34:33 +0100 Subject: [PATCH 3/8] fix: discover correct gromacs data dir for gmx compiled from source --- src/kimmdy/utils.py | 9 +++++++-- tests/test_topology.py | 8 ++++++++ 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/src/kimmdy/utils.py b/src/kimmdy/utils.py index 560a8b96..e12c1740 100644 --- a/src/kimmdy/utils.py +++ b/src/kimmdy/utils.py @@ -292,18 +292,23 @@ def get_gmx_dir(gromacs_alias: str = "gmx") -> Optional[Path]: logger.warning("GROMACS not found.") return None + from_source = False gmx_prefix = None for l in r.stderr.splitlines(): if l.startswith("Data prefix:"): gmx_prefix = Path(l.split()[2]) + if "(source tree)" in l: + from_source = True break if gmx_prefix is None: logger.warning("GROMACS data directory not found in gromacs message.") return None - gmx_dir = Path(gmx_prefix) / "share" / "gromacs" - return gmx_dir + if from_source: + return Path(gmx_prefix) / "share" + else: + return Path(gmx_prefix) / "share" / "gromacs" def check_gmx_version(config): diff --git a/tests/test_topology.py b/tests/test_topology.py index c6090914..abd605d0 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -15,6 +15,8 @@ ) import logging +from kimmdy.utils import get_gmx_dir + @pytest.fixture(scope="module") def filedir() -> Path: @@ -109,6 +111,12 @@ def random_topology_and_break(draw): break_this = draw(st.sampled_from(list(top.bonds.keys()))) return (top, break_this) +class TestGMX: + def test_gmx_dir_is_found(self): + gmx = get_gmx_dir() + assert gmx + assert Path(gmx).is_dir() + class TestMatch: @pytest.fixture From 0bebb4721659454fdbf71364d15a43a17a584f61 Mon Sep 17 00:00:00 2001 From: Jannik Buhr Date: Mon, 4 Mar 2024 10:45:15 +0100 Subject: [PATCH 4/8] sort imports --- src/kimmdy/analysis.py | 25 +++++++++++++------------ src/kimmdy/cmd.py | 27 ++++++++++++++------------- src/kimmdy/config.py | 15 +++++++++------ src/kimmdy/coordinates.py | 21 +++++++++++---------- src/kimmdy/kmc.py | 10 ++++++---- src/kimmdy/parsing.py | 12 ++++++------ src/kimmdy/plugins.py | 7 ++++--- src/kimmdy/recipe.py | 11 ++++++----- src/kimmdy/runmanager.py | 25 ++++++++++++++----------- src/kimmdy/schema.py | 7 ++++--- src/kimmdy/tasks.py | 7 ++++--- src/kimmdy/tools.py | 11 +++++------ src/kimmdy/utils.py | 18 ++++++++++-------- tests/test_topology.py | 18 ++++++++++-------- 14 files changed, 116 insertions(+), 98 deletions(-) diff --git a/src/kimmdy/analysis.py b/src/kimmdy/analysis.py index cd8cd102..aa597e81 100644 --- a/src/kimmdy/analysis.py +++ b/src/kimmdy/analysis.py @@ -2,24 +2,25 @@ For command line usage, run `kimmdy-analysis -h`. """ -from typing import Optional, Union -from pathlib import Path -import MDAnalysis as mda +import argparse +import json import subprocess as sp -import matplotlib.pyplot as plt -import matplotlib.patches as mpatches +from datetime import datetime +from pathlib import Path +from typing import Optional, Union + import matplotlib as mpl -import seaborn.objects as so +import matplotlib.patches as mpatches +import matplotlib.pyplot as plt +import MDAnalysis as mda +import pandas as pd import seaborn as sns -import argparse +import seaborn.objects as so from seaborn import axes_style -import pandas as pd -from datetime import datetime -import json -from kimmdy.utils import run_shell_cmd from kimmdy.parsing import read_json, write_json -from kimmdy.recipe import RecipeCollection, Break, Bind, Place, Relax +from kimmdy.recipe import Bind, Break, Place, RecipeCollection +from kimmdy.utils import run_shell_cmd def get_analysis_dir(dir: Path) -> Path: diff --git a/src/kimmdy/cmd.py b/src/kimmdy/cmd.py index 27354742..6a3838ee 100644 --- a/src/kimmdy/cmd.py +++ b/src/kimmdy/cmd.py @@ -4,27 +4,28 @@ """ import argparse +import logging +import logging.config +import os +import sys +import textwrap from os import chmod from pathlib import Path -import textwrap from typing import Optional + import dill -import logging -import logging.config -from kimmdy.config import Config -from kimmdy.runmanager import RunManager + from kimmdy.assets.templates import jobscript -from kimmdy.utils import longFormatter -from kimmdy.plugins import discover_plugins +from kimmdy.config import Config from kimmdy.plugins import ( - reaction_plugins, + broken_parameterization_plugins, broken_reaction_plugins, + discover_plugins, parameterization_plugins, - broken_parameterization_plugins, + reaction_plugins, ) -import importlib.resources as pkg_resources -import sys -import os +from kimmdy.runmanager import RunManager +from kimmdy.utils import longFormatter if sys.version_info > (3, 10): from importlib_metadata import version @@ -258,9 +259,9 @@ def _run(args: argparse.Namespace): if args.callgraph: try: from pycallgraph2 import PyCallGraph - from pycallgraph2.output import GraphvizOutput from pycallgraph2.config import Config as Vis_conf from pycallgraph2.globbing_filter import GlobbingFilter + from pycallgraph2.output import GraphvizOutput except ImportError as e: logger.error( "pycallgraph2 needed for call visualization. Get it with `pip install pycallgraph2`" diff --git a/src/kimmdy/config.py b/src/kimmdy/config.py index 03f97fd8..8f059494 100644 --- a/src/kimmdy/config.py +++ b/src/kimmdy/config.py @@ -4,19 +4,22 @@ """ from __future__ import annotations + import shutil -from pprint import pformat, pprint +from pathlib import Path +from pprint import pformat from typing import Any, Optional + import yaml -from pathlib import Path + from kimmdy.plugins import ( - reaction_plugins, + broken_parameterization_plugins, broken_reaction_plugins, parameterization_plugins, - broken_parameterization_plugins, + reaction_plugins, ) -from kimmdy.schema import Sequence, get_combined_scheme -from kimmdy.utils import get_gmx_dir, check_file_exists, check_gmx_version +from kimmdy.schema import get_combined_scheme +from kimmdy.utils import check_file_exists, check_gmx_version, get_gmx_dir class Config: diff --git a/src/kimmdy/coordinates.py b/src/kimmdy/coordinates.py index b45c7c04..7720f0d8 100644 --- a/src/kimmdy/coordinates.py +++ b/src/kimmdy/coordinates.py @@ -1,31 +1,32 @@ """coordinate, topology and plumed modification functions""" import logging -from typing import Optional, Union from copy import deepcopy -import MDAnalysis as mda from pathlib import Path +from typing import Optional, Union + +import MDAnalysis as mda import numpy as np -from kimmdy.tasks import TaskFiles -from kimmdy.parsing import read_plumed, write_plumed from kimmdy.constants import REACTIVE_MOLECULEYPE +from kimmdy.parsing import read_plumed, write_plumed from kimmdy.recipe import Place -from kimmdy.topology.topology import MoleculeType, Topology -from kimmdy.topology.ff import FF +from kimmdy.tasks import TaskFiles from kimmdy.topology.atomic import ( - Bond, Angle, + Bond, Dihedral, DihedralType, - ProperDihedralId, + Exclusion, ImproperDihedralId, - MultipleDihedrals, Interaction, InteractionType, InteractionTypes, - Exclusion, + MultipleDihedrals, + ProperDihedralId, ) +from kimmdy.topology.ff import FF +from kimmdy.topology.topology import MoleculeType, Topology from kimmdy.topology.utils import match_atomic_item_to_atomic_type logger = logging.getLogger(__name__) diff --git a/src/kimmdy/kmc.py b/src/kimmdy/kmc.py index ebb17120..c1f7d7b1 100644 --- a/src/kimmdy/kmc.py +++ b/src/kimmdy/kmc.py @@ -8,13 +8,15 @@ and because we have one reactant molecule """ -from typing import Optional import logging -import numpy as np -from itertools import pairwise from dataclasses import dataclass, field +from itertools import pairwise +from typing import Optional + +import numpy as np from numpy.random import default_rng -from kimmdy.recipe import RecipeCollection, Recipe + +from kimmdy.recipe import Recipe, RecipeCollection @dataclass diff --git a/src/kimmdy/parsing.py b/src/kimmdy/parsing.py index b39679c1..929f0aec 100644 --- a/src/kimmdy/parsing.py +++ b/src/kimmdy/parsing.py @@ -2,14 +2,14 @@ All read_<...> and write_<...> functions. """ -import os -import logging import json -import numpy as np -from pathlib import Path -from typing import Optional, Union +import logging +import os from itertools import takewhile -from typing import TypedDict +from pathlib import Path +from typing import Optional, TypedDict, Union + +import numpy as np from kimmdy.utils import get_gmx_dir diff --git a/src/kimmdy/plugins.py b/src/kimmdy/plugins.py index edbbc6e3..dcfe959d 100644 --- a/src/kimmdy/plugins.py +++ b/src/kimmdy/plugins.py @@ -4,15 +4,16 @@ """ from __future__ import annotations -from typing import TYPE_CHECKING -from abc import ABC, abstractmethod + import logging import sys +from abc import ABC, abstractmethod +from typing import TYPE_CHECKING if TYPE_CHECKING: - from kimmdy.runmanager import RunManager from kimmdy.config import Config from kimmdy.recipe import RecipeCollection + from kimmdy.runmanager import RunManager from kimmdy.tasks import TaskFiles from kimmdy.topology.topology import Topology diff --git a/src/kimmdy/recipe.py b/src/kimmdy/recipe.py index c4ea8c10..0440eaee 100644 --- a/src/kimmdy/recipe.py +++ b/src/kimmdy/recipe.py @@ -2,15 +2,16 @@ """ from __future__ import annotations -from typing import TYPE_CHECKING, Callable, Optional +import csv +import logging from abc import ABC +from copy import copy from dataclasses import dataclass, field from pathlib import Path -import logging -from copy import copy +from typing import TYPE_CHECKING, Callable, Optional + import dill -import csv import numpy as np logger = logging.getLogger(__name__) @@ -527,8 +528,8 @@ def plot(self, outfile, highlight_r=None, highlight_t=None): """ import matplotlib.pyplot as plt - import seaborn as sns import numpy as np + import seaborn as sns self.aggregate_reactions() cumprob = self.calc_cumprob() diff --git a/src/kimmdy/runmanager.py b/src/kimmdy/runmanager.py index ef65b995..901fc7ff 100644 --- a/src/kimmdy/runmanager.py +++ b/src/kimmdy/runmanager.py @@ -6,32 +6,35 @@ """ from __future__ import annotations + import logging -from pathlib import Path -from copy import copy, deepcopy -import dill import queue +import time +from copy import copy, deepcopy +from datetime import timedelta from enum import Enum, auto from functools import partial -from datetime import timedelta +from pathlib import Path +from pprint import pformat from typing import Optional + +import dill + from kimmdy.config import Config +from kimmdy.coordinates import break_bond_plumed, merge_top_slow_growth, place_atom +from kimmdy.kmc import KMCResult, extrande, extrande_mod, frm, rf_kmc from kimmdy.parsing import read_top, write_json, write_top from kimmdy.plugins import ( BasicParameterizer, + ReactionPlugin, parameterization_plugins, reaction_plugins, - ReactionPlugin, ) -from kimmdy.recipe import CustomTopMod, RecipeCollection, Break, Bind, Place, Relax -from kimmdy.utils import run_gmx, truncate_sim_files -from kimmdy.coordinates import place_atom, break_bond_plumed, merge_top_slow_growth +from kimmdy.recipe import Bind, Break, CustomTopMod, Place, RecipeCollection, Relax from kimmdy.tasks import Task, TaskFiles, get_plumed_out -from pprint import pformat from kimmdy.topology.topology import Topology from kimmdy.topology.utils import get_is_reactive_predicate_f -import time -from kimmdy.kmc import KMCResult, rf_kmc, extrande, frm, extrande_mod +from kimmdy.utils import run_gmx, truncate_sim_files logger = logging.getLogger(__name__) diff --git a/src/kimmdy/schema.py b/src/kimmdy/schema.py index e4a992a9..b08ddad9 100644 --- a/src/kimmdy/schema.py +++ b/src/kimmdy/schema.py @@ -11,17 +11,18 @@ - required """ -import json import importlib.resources as pkg_resources +import json import logging -from kimmdy.plugins import reaction_plugins # needed for eval of type_scheme from schema # don't remove even if lsp says it's unused -import kimmdy import pathlib from pathlib import Path +import kimmdy +from kimmdy.plugins import reaction_plugins + logger = logging.getLogger(__name__) diff --git a/src/kimmdy/tasks.py b/src/kimmdy/tasks.py index c0339447..00629acc 100644 --- a/src/kimmdy/tasks.py +++ b/src/kimmdy/tasks.py @@ -3,11 +3,12 @@ output paths and the Task class for steps in the runmanager. """ +import logging +import shutil from dataclasses import dataclass, field from pathlib import Path -import shutil from typing import Any, Callable, Optional -import logging + from kimmdy.parsing import read_plumed from kimmdy.utils import longFormatter @@ -144,7 +145,7 @@ def __init__( logger.debug(f"Init task {self.name}\tkwargs: {self.kwargs}\tOut: {self.out}") - def __call__(self) -> TaskFiles: + def __call__(self) -> Optional[TaskFiles]: if self.out is not None: self.kwargs.update({"files": create_task_directory(self.runmng, self.out)}) diff --git a/src/kimmdy/tools.py b/src/kimmdy/tools.py index 6c4a530b..42ab819c 100644 --- a/src/kimmdy/tools.py +++ b/src/kimmdy/tools.py @@ -2,16 +2,15 @@ Standalone tools that are complementary to KIMMDY. """ -from pathlib import Path -import shutil import argparse -from typing import Optional import json +import shutil +from pathlib import Path +from typing import Optional -from kimmdy.topology.topology import Topology from kimmdy.parsing import read_top, write_top -from kimmdy.plugins import parameterization_plugins -from kimmdy.plugins import discover_plugins +from kimmdy.plugins import discover_plugins, parameterization_plugins +from kimmdy.topology.topology import Topology def build_examples(restore: str): diff --git a/src/kimmdy/utils.py b/src/kimmdy/utils.py index e12c1740..8b093fd4 100644 --- a/src/kimmdy/utils.py +++ b/src/kimmdy/utils.py @@ -3,17 +3,19 @@ """ from __future__ import annotations -import subprocess as sp -import numpy as np -import re + import logging -from typing import Optional, TYPE_CHECKING +import re +import subprocess as sp from pathlib import Path +from typing import TYPE_CHECKING, Optional + +import numpy as np if TYPE_CHECKING: + from kimmdy.parsing import Plumed_dict from kimmdy.tasks import TaskFiles from kimmdy.topology.topology import Topology - from kimmdy.parsing import Plumed_dict logger = logging.getLogger(__name__) @@ -41,7 +43,7 @@ def format(self, record): return result -# input/output utility functions +### IO utility functions ### def run_shell_cmd(s, cwd=None) -> sp.CompletedProcess: @@ -75,7 +77,7 @@ def check_file_exists(p: Path): raise LookupError(m) -# reaction plugin building blocks +### reaction plugin building blocks ### def get_atomnrs_from_plumedid( @@ -278,7 +280,7 @@ def morse_transition_rate( return k, fs -# GROMACS related functions +### GROMACS related functions ### def get_gmx_dir(gromacs_alias: str = "gmx") -> Optional[Path]: diff --git a/tests/test_topology.py b/tests/test_topology.py index abd605d0..2cdfbafd 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -1,20 +1,21 @@ +import logging from copy import deepcopy from pathlib import Path -import pytest + import numpy as np +import pytest +from hypothesis import HealthCheck, Phase, given, settings +from hypothesis import strategies as st -from kimmdy.parsing import read_top, TopologyDict -from kimmdy.recipe import Break, Bind -from hypothesis import Phase, given, settings, HealthCheck, strategies as st -from kimmdy.topology.topology import REACTIVE_MOLECULEYPE, Topology +from kimmdy.parsing import TopologyDict, read_top +from kimmdy.recipe import Bind, Break from kimmdy.topology.atomic import * +from kimmdy.topology.topology import REACTIVE_MOLECULEYPE, Topology from kimmdy.topology.utils import ( + get_protein_section, get_reactive_section, match_atomic_item_to_atomic_type, - get_protein_section, ) -import logging - from kimmdy.utils import get_gmx_dir @@ -111,6 +112,7 @@ def random_topology_and_break(draw): break_this = draw(st.sampled_from(list(top.bonds.keys()))) return (top, break_this) + class TestGMX: def test_gmx_dir_is_found(self): gmx = get_gmx_dir() From 0bc1db3f32f0864fa545545aa49dab139e5311db Mon Sep 17 00:00:00 2001 From: Jannik Buhr Date: Tue, 5 Mar 2024 15:12:08 +0100 Subject: [PATCH 5/8] refactor(recipe): make BondOperation and Place regular classes instead of dataclasses --- src/kimmdy/analysis.py | 6 +- src/kimmdy/config.py | 5 +- src/kimmdy/coordinates.py | 22 +++--- src/kimmdy/kmc.py | 12 +++ src/kimmdy/parsing.py | 16 ++-- src/kimmdy/plugins.py | 4 +- src/kimmdy/recipe.py | 161 ++++++++++++++++++++++++++++++-------- tests/test_recipe.py | 19 +++-- 8 files changed, 180 insertions(+), 65 deletions(-) diff --git a/src/kimmdy/analysis.py b/src/kimmdy/analysis.py index aa597e81..4e68277f 100644 --- a/src/kimmdy/analysis.py +++ b/src/kimmdy/analysis.py @@ -396,9 +396,9 @@ def radical_migration( picked_recipes = {} for recipes in run_dir.glob("*decide_recipe/recipes.csv"): task_nr = int(recipes.parents[0].stem.split(sep="_")[0]) - rc, picked_recipe = RecipeCollection.from_csv(recipes) + _, picked_recipe = RecipeCollection.from_csv(recipes) picked_recipes[task_nr] = picked_recipe - sorted_recipes = [val for key, val in sorted(picked_recipes.items())] + sorted_recipes = [v for _, v in sorted(picked_recipes.items())] for sorted_recipe in sorted_recipes: connectivity_difference = {} @@ -598,7 +598,7 @@ def reaction_participation(dir: str, open_plot: bool = False): reaction_count = {"overall": 0} for recipes in run_dir.glob("*decide_recipe/recipes.csv"): # get picked recipe - rc, picked_rp = RecipeCollection.from_csv(recipes) + _, picked_rp = RecipeCollection.from_csv(recipes) assert picked_rp, f"No picked recipe found in {recipes}." # get involved atoms reaction_atom_ids = set() diff --git a/src/kimmdy/config.py b/src/kimmdy/config.py index 8f059494..6d44307d 100644 --- a/src/kimmdy/config.py +++ b/src/kimmdy/config.py @@ -328,9 +328,10 @@ def _validate(self, section: str = "config"): ) name = self.out.name.split("_") out_end = name[-1] - out_start = "_".join(name[:-1]) if out_end.isdigit(): - self.out = self.out.with_name(f"{out_start}_{int(out_end)+1:03}") + self.out = self.out.with_name( + f"{'_'.join(name[:-1])}_{int(out_end)+1:03}" + ) else: self.out = self.out.with_name(self.out.name + "_001") diff --git a/src/kimmdy/coordinates.py b/src/kimmdy/coordinates.py index 7720f0d8..be101a19 100644 --- a/src/kimmdy/coordinates.py +++ b/src/kimmdy/coordinates.py @@ -195,8 +195,12 @@ def merge_dihedrals( parameterizedB = None # construct parameterized Dihedral - if parameterizedA and parameterizedB: + if parameterizedA is not None and parameterizedB is not None: # same + + assert type(parameterizedA) == Dihedral or type(parameterizedA) == DihedralType + assert type(parameterizedB) == Dihedral or type(parameterizedB) == DihedralType + dihedralmerge = Dihedral( *dihedral_key, funct=funct, @@ -207,8 +211,9 @@ def merge_dihedrals( c4=parameterizedB.c1, c5=parameterizedB.periodicity, ) - elif parameterizedA: + elif parameterizedA is not None: # breaking + assert type(parameterizedA) == Dihedral or type(parameterizedA) == DihedralType dihedralmerge = Dihedral( *dihedral_key, funct=funct, @@ -219,8 +224,9 @@ def merge_dihedrals( c4="0.00", c5=parameterizedA.periodicity, ) - elif parameterizedB: + elif parameterizedB is not None: # binding + assert type(parameterizedB) == Dihedral or type(parameterizedB) == DihedralType dihedralmerge = Dihedral( *dihedral_key, funct="9", @@ -242,14 +248,10 @@ def merge_top_moleculetypes_slow_growth( molA: MoleculeType, molB: MoleculeType, ff: FF, - focus_nr: Optional[list[str]] = None, ) -> MoleculeType: """Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation""" hyperparameters = {"morse_well_depth": 300} # [kJ mol-1] - # TODO: - # think about how to bring focus_nr into this - # atoms for nr in molA.atoms.keys(): atomA = molA.atoms[nr] @@ -520,9 +522,7 @@ def merge_top_moleculetypes_slow_growth( return molB -def merge_top_slow_growth( - topA: Topology, topB: Topology, focus_nr: Optional[list[str]] = None -) -> Topology: +def merge_top_slow_growth(topA: Topology, topB: Topology) -> Topology: """Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation. @@ -531,7 +531,7 @@ def merge_top_slow_growth( molA = topA.moleculetypes[REACTIVE_MOLECULEYPE] molB = topB.moleculetypes[REACTIVE_MOLECULEYPE] - molB = merge_top_moleculetypes_slow_growth(molA, molB, topB.ff, focus_nr) + molB = merge_top_moleculetypes_slow_growth(molA, molB, topB.ff) return topB diff --git a/src/kimmdy/kmc.py b/src/kimmdy/kmc.py index c1f7d7b1..2921e04c 100644 --- a/src/kimmdy/kmc.py +++ b/src/kimmdy/kmc.py @@ -235,6 +235,10 @@ def extrande_mod( f"\t\texpected tau: {expected_tau}" ) + b = None + tau = None + l = None + t_max = None for cr_boarders, cr_rates, cr_recipes in zip( pairwise(boarders), rate_windows, recipe_windows ): @@ -262,6 +266,9 @@ def extrande_mod( if chosen_recipe is not None: break + if None in [b, tau, l, t_max]: + logger.error(f"Extrande calculation failed, some variables are None.") + if chosen_recipe is None: logger.info( f"No reaction was chosen\naccepted: 0, rejected: {rejected}, extra: {n_extra}" @@ -343,6 +350,8 @@ def extrande( ) n_extra = 0 + tau = None + l = None while t < t_max: crr_window_idx = np.searchsorted(boarders, t, side="right") - 1 # only 0 rates left -> skip to end @@ -390,6 +399,9 @@ def extrande( f"{n_extra} extra reactions performed during extrande KMC calculation. Try increasing tau_scale" ) + if None in [tau, l]: + logger.error(f"Extrande calculation failed, some variables are None.") + if chosen_recipe is None: logger.info( f"No reaction was chosen\naccepted: 0, rejected: 1, extra: {n_extra}" diff --git a/src/kimmdy/parsing.py b/src/kimmdy/parsing.py index 929f0aec..6607017f 100644 --- a/src/kimmdy/parsing.py +++ b/src/kimmdy/parsing.py @@ -524,15 +524,15 @@ def read_distances_dat(distances_dat: Path) -> dict: class JSONEncoder(json.JSONEncoder): """Encoder that enables writing JSONs with numpy types.""" - def default(self, obj): - if isinstance(obj, np.integer): - return int(obj) - elif isinstance(obj, np.floating): - return float(obj) - elif isinstance(obj, np.ndarray): - return obj.tolist() + def default(self, o): + if isinstance(o, np.integer): + return int(o) + elif isinstance(o, np.floating): + return float(o) + elif isinstance(o, np.ndarray): + return o.tolist() else: - return super(JSONEncoder, self).default(obj) + return super(JSONEncoder, self).default(o) def write_json( diff --git a/src/kimmdy/plugins.py b/src/kimmdy/plugins.py index dcfe959d..66dea168 100644 --- a/src/kimmdy/plugins.py +++ b/src/kimmdy/plugins.py @@ -106,8 +106,8 @@ def parameterize_topology(self, current_topology: Topology) -> Topology: class BasicParameterizer(Parameterizer): """reconstruct base force field state""" - def parameterize_topology(self, current_topology: Topology) -> None: + def parameterize_topology(self, current_topology: Topology) -> Topology: """Do nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology """ - pass + return current_topology diff --git a/src/kimmdy/recipe.py b/src/kimmdy/recipe.py index 0440eaee..95a2341f 100644 --- a/src/kimmdy/recipe.py +++ b/src/kimmdy/recipe.py @@ -7,7 +7,7 @@ import logging from abc import ABC from copy import copy -from dataclasses import dataclass, field +from dataclasses import dataclass from pathlib import Path from typing import TYPE_CHECKING, Callable, Optional @@ -37,10 +37,11 @@ class Relax(RecipeStep): """ -@dataclass class Place(RecipeStep): """Change topology and/or coordinates to place an atom. + Either provide the index (ix_to_place) or the ID (id_to_place) of the atom to place. + Parameters ---------- new_coords : @@ -54,13 +55,43 @@ class Place(RecipeStep): Index of atom to place. 1-based """ - new_coords: tuple[float, float, float] - ix_to_place: Optional[int] = None - id_to_place: Optional[str] = None + def __init__( + self, + new_coords: tuple[float, float, float], + ix_to_place: Optional[int] = None, + id_to_place: Optional[str] = None, + ): + """Create a new Place RecipeStep instance. - _ix_to_place: Optional[int] = field(init=False, repr=False, default=None) + of the first and second atom, either the id (1-based, str) or ix + (0-based, int) can be given. If both are given, the ix is used. - def __post_init__(self): + Parameters + ---------- + new_coords : + New xyz coordinates for atom to place to. Valid for the end point of the recipe timespan. + ix_to_place : + The index of the atom. zero-based, by default None + id_to_place : + The ID of the atom. one-based, by default None + + Raises + ------ + ValueError + If neither an index nor an ID is provided for any of the atoms. + """ + self.new_coords = new_coords + self._ix_to_place: int + if id_to_place is not None: + if type(id_to_place) is not str: + raise ValueError(f"atom_id_1 is {type(id_to_place)}, should be str.") + self._ix_to_place = int(id_to_place) - 1 + if ix_to_place is not None: + if type(ix_to_place) is not int: + raise ValueError(f"atom_ix_1 is {type(ix_to_place)}, should be int.") + self._ix_to_place = ix_to_place + if id_to_place is not None and ix_to_place is not None: + logger.warning(f"Both atom_ix_1 and atom_id_1 are given, using atom_ix_1.") if self._ix_to_place is None: raise ValueError("id_ or ix_ to_place must be provided!") @@ -77,8 +108,6 @@ def ix_to_place(self, value: Optional[int]): @property def id_to_place(self) -> Optional[str]: - if self._ix_to_place is None: - return None return str(self._ix_to_place + 1) @id_to_place.setter @@ -88,12 +117,33 @@ def id_to_place(self, value: Optional[str]): assert isinstance(value, str), f"id_to_place is {type(value)}, should be str." self._ix_to_place = int(value) - 1 + def __eq__(self, other): + """Two Placements are equal if their atom indices are equal and they have the same new coordinates.""" + + if not isinstance(other, Place) or type(self) != type(other): + logger.warning( + f"Comparing RecipeSteps with different types: {type(self)} and {type(other)}. Returning False." + ) + return False + return ( + self._ix_to_place == other._ix_to_place + and self.new_coords == other.new_coords + ) + + def __hash__(self): + return hash((self._ix_to_place, self.new_coords, type(self).__name__)) + + def __repr__(self): + return f"{type(self).__name__}(ix_to_place={self._ix_to_place}, new_coords={self.new_coords})" + + def __str__(self): + return f"{type(self).__name__}({self._ix_to_place}, {self.new_coords})" + -@dataclass class BondOperation(RecipeStep): """Handle a bond operation on the recipe step. - This class takes in either zero-based indices or one-base IDs for two atoms + This class takes in either zero-based indices or one-base IDs for two atoms. Parameters ---------- @@ -117,27 +167,57 @@ class BondOperation(RecipeStep): """ - atom_ix_1: Optional[int] = None - atom_ix_2: Optional[int] = None - atom_id_1: Optional[str] = None - atom_id_2: Optional[str] = None + def __init__( + self, + atom_ix_1: Optional[int] = None, + atom_ix_2: Optional[int] = None, + atom_id_1: Optional[str] = None, + atom_id_2: Optional[str] = None, + ): + """Create a new BondOperation instance. - _atom_ix_1: int = field(init=False, repr=False, default=None) - _atom_ix_2: int = field(init=False, repr=False, default=None) + of the first and second atom, either the id (1-based, str) or ix + (0-based, int) can be given. If both are given, the ix is used. - def __post_init__(self): - e = "" - if not (isinstance(self.atom_ix_1, int) or isinstance(self.atom_id_1, str)): - e += "Exactly on of atom_ix_1 and atom_id_1 must be given!\n" - if not (isinstance(self.atom_ix_2, int) or isinstance(self.atom_id_2, str)): - e += "Exactly on of atom_ix_2 and atom_id_2 must be given!\n" - if len(e) > 0: - raise ValueError(e) + Parameters + ---------- + atom_ix_1 : int, optional + The index of the first atom. zero-based, by default None + atom_ix_2 : int, optional + The index of the second atom. zero-based, by default None + atom_id_1 : str, optional + The ID of the first atom. one-based, by default None + atom_id_2 : str, optional + The ID of the second atom. one-based, by default None + + Raises + ------ + ValueError + If neither an index nor an ID is provided for any of the atoms. + """ + self._atom_ix_1: int + self._atom_ix_2: int + if atom_id_1 is not None: + if type(atom_id_1) is not str: + raise ValueError(f"atom_id_1 is {type(atom_id_1)}, should be str.") + self._atom_ix_1 = int(atom_id_1) - 1 + if atom_id_2 is not None: + if type(atom_id_2) is not str: + raise ValueError(f"atom_id_2 is {type(atom_id_2)}, should be str.") + self._atom_ix_2 = int(atom_id_2) - 1 + if atom_ix_1 is not None: + if type(atom_ix_1) is not int: + raise ValueError(f"atom_ix_1 is {type(atom_ix_1)}, should be int.") + self._atom_ix_1 = atom_ix_1 + if atom_ix_2 is not None: + if type(atom_ix_2) is not int: + raise ValueError(f"atom_ix_2 is {type(atom_ix_2)}, should be int.") + self._atom_ix_2 = atom_ix_2 + if atom_ix_1 is not None and atom_id_1 is not None: + logger.warning(f"Both atom_ix_1 and atom_id_1 are given, using atom_ix_1.") @property def atom_id_1(self) -> str: - if self._atom_ix_1 is None: - return None return str(self._atom_ix_1 + 1) @atom_id_1.setter @@ -160,8 +240,6 @@ def atom_ix_1(self, value: int): @property def atom_id_2(self) -> str: - if self._atom_ix_2 is None: - return None return str(self._atom_ix_2 + 1) @atom_id_2.setter @@ -182,6 +260,27 @@ def atom_ix_2(self, value: int): assert isinstance(value, int), f"atom_ix_2 is {type(value)}, should be int." self._atom_ix_2 = value + def __eq__(self, other): + """Two BondOperations are equal if their atom indices are equal and they are of the same type.""" + + if not isinstance(other, BondOperation) or type(self) != type(other): + logger.warning( + f"Comparing RecipeSteps with different types: {type(self)} and {type(other)}. Returning False." + ) + return False + return ( + self._atom_ix_1 == other._atom_ix_1 and self._atom_ix_2 == other._atom_ix_2 + ) + + def __hash__(self): + return hash((self._atom_ix_1, self._atom_ix_2, type(self).__name__)) + + def __repr__(self): + return f"{type(self).__name__}(atom_ix_1={self._atom_ix_1}, atom_ix_2={self._atom_ix_2})" + + def __str__(self): + return f"{type(self).__name__}({self._atom_ix_1}, {self._atom_ix_2})" + class Break(BondOperation): """Change topology to break a bond @@ -423,10 +522,10 @@ def from_csv(cls, path: Path): with open(path, "r") as f: reader = csv.reader(f) - header = next(reader) # Skip the header row + _ = next(reader) # Skip the header row picked_rp = None for row in reader: - index_s, picked_s, recipe_steps_s, timespans_s, rates_s = row + _, picked_s, recipe_steps_s, timespans_s, rates_s = row picked = eval(picked_s) recipe_steps = eval(recipe_steps_s) diff --git a/tests/test_recipe.py b/tests/test_recipe.py index 8322107b..23a270f8 100644 --- a/tests/test_recipe.py +++ b/tests/test_recipe.py @@ -1,9 +1,12 @@ -from hypothesis import given, strategies as st -from kimmdy import recipe import csv -import pytest from dataclasses import asdict +import pytest +from hypothesis import given +from hypothesis import strategies as st + +from kimmdy import recipe + ## Test RecipeSteps # tests with random inputs @@ -78,10 +81,10 @@ def test_bo_initialization_unequal(): def test_bo_initialization_wrong_type(): # Should raise an error because initialization is with the wrong type - with pytest.raises(AssertionError): - recipe.BondOperation("1", "2") - with pytest.raises(AssertionError): - recipe.BondOperation(atom_id_1=0, atom_id_2=1) + with pytest.raises(ValueError): + recipe.BondOperation("1", "2") # type: ignore + with pytest.raises(ValueError): + recipe.BondOperation(atom_id_1=0, atom_id_2=1) # type: ignore @given( @@ -126,7 +129,7 @@ def test_place_initialization(): with pytest.raises(TypeError): recipe.Place(ix_to_place=1) - with pytest.raises(AssertionError): + with pytest.raises(ValueError): recipe.Place(id_to_place=1, new_coords=(0, 0, 0)) From 0f39b879ab13fa521b24a1ead21d2dda13c7dc74 Mon Sep 17 00:00:00 2001 From: Jannik Buhr Date: Wed, 6 Mar 2024 16:12:19 +0100 Subject: [PATCH 6/8] squiggly lines begone --- .../change_crosslink_atom_names.py | 4 +- src/kimmdy/recipe.py | 22 +++----- src/kimmdy/runmanager.py | 13 +++-- src/kimmdy/schema.py | 2 +- src/kimmdy/tools.py | 4 +- src/kimmdy/topology/topology.py | 51 +++++++++++-------- src/kimmdy/utils.py | 2 +- 7 files changed, 51 insertions(+), 47 deletions(-) diff --git a/guide/tutorials/colbuilder-files/change_crosslink_atom_names.py b/guide/tutorials/colbuilder-files/change_crosslink_atom_names.py index 648f4a80..a4388ccf 100644 --- a/guide/tutorials/colbuilder-files/change_crosslink_atom_names.py +++ b/guide/tutorials/colbuilder-files/change_crosslink_atom_names.py @@ -3,8 +3,8 @@ def main(run_info): from functions_v4 import get_data_from_file, store_linelist_to_file # Extracting data - top_all, top_array = get_data_from_file(run_info["path_top_file"]) - gro_all, gro_array = get_data_from_file(run_info["path_gro_file"]) + top_all, _ = get_data_from_file(run_info["path_top_file"]) + gro_all, _ = get_data_from_file(run_info["path_gro_file"]) # Dictionaries of corsslinks LYX = {"CB": "CBYX", "CG": "CGYX", "CD": "CDYX", "CE": "CEYX"} diff --git a/src/kimmdy/recipe.py b/src/kimmdy/recipe.py index 95a2341f..9fdb222d 100644 --- a/src/kimmdy/recipe.py +++ b/src/kimmdy/recipe.py @@ -362,17 +362,6 @@ def copy(self): list(self.timespans), ) - def calc_averages(self, window_size: int): - """Calulate average rates over some window size - - Parameters - ---------- - window_size : int - Size of the window to average over, - -1 to average over whole available range. - """ - raise NotImplementedError("calc_averages not implemented yet") - def combine_with(self, other: Recipe): """Combines this Recipe with another with the same RecipeSteps. @@ -613,7 +602,12 @@ def calc_ratesum(self) -> tuple[list, list, list]: return boarders, rate_windows, recipe_windows - def plot(self, outfile, highlight_r=None, highlight_t=None): + def plot( + self, + outfile, + highlight_r: Optional[Recipe] = None, + highlight_t: Optional[float] = None, + ): """Plot reaction rates over time Parameters @@ -637,7 +631,7 @@ def plot(self, outfile, highlight_r=None, highlight_t=None): for i, r in enumerate(self.recipes): recipe_steps[i] = r.recipe_steps - idxs = np.argsort(cumprob)[-8:] + idxs = list(np.argsort(cumprob)[-8:]) ref = np.empty((1,), dtype=object) if highlight_r is not None: ref[0] = highlight_r.recipe_steps @@ -672,7 +666,7 @@ def plot(self, outfile, highlight_r=None, highlight_t=None): plt.axvline(highlight_t, color="red") for r_i, re in enumerate(recipes): name = re.get_recipe_name() - if name == highlight_r.get_recipe_name(): + if highlight_r is not None and name == highlight_r.get_recipe_name(): name_to_args[name]["linestyle"] = "-." name_to_args[name]["linewidth"] = 2.2 diff --git a/src/kimmdy/runmanager.py b/src/kimmdy/runmanager.py index 901fc7ff..d97b0577 100644 --- a/src/kimmdy/runmanager.py +++ b/src/kimmdy/runmanager.py @@ -57,7 +57,7 @@ class State(Enum): DONE = auto() -def get_existing_files(config: Config, section: str = "root") -> dict: +def get_existing_files(config: Config) -> dict: """Initialize latest_files with every existing file defined in config""" file_d = {} attr_names = config.get_attributes() @@ -79,7 +79,7 @@ def get_existing_files(config: Config, section: str = "root") -> dict: file_d[key] = attr elif isinstance(attr, Config): - file_d.update(get_existing_files(attr, attr_name)) + file_d.update(get_existing_files(attr)) return file_d @@ -318,7 +318,8 @@ def __next__(self): f"Finished task: {task.name} after " f"{timedelta(seconds=(time.time() - current_time))}" ) - self._discover_output_files(task.name, files) + if files is not None: + self._discover_output_files(task.name, files) def _discover_output_files( self, taskname: str, files: TaskFiles @@ -608,7 +609,8 @@ def _apply_recipe(self, files: TaskFiles) -> TaskFiles: logger.info(f"Starting task: {task.name} with args: {task.kwargs}") place_files = task() logger.info(f"Finished task: {task.name}") - self._discover_output_files(task.name, place_files) + if place_files is not None: + self._discover_output_files(task.name, place_files) elif isinstance(step, Relax): logger.info("Starting relaxation md as part of reaction..") @@ -632,7 +634,8 @@ def _apply_recipe(self, files: TaskFiles) -> TaskFiles: logger.info(f"Starting task: {task.name} with args: {task.kwargs}") md_files = task() logger.info(f"Finished task: {task.name}") - self._discover_output_files(task.name, md_files) + if md_files is not None: + self._discover_output_files(task.name, md_files) elif isinstance(step, CustomTopMod): step.f(self.top) diff --git a/src/kimmdy/schema.py b/src/kimmdy/schema.py index b08ddad9..2eba57bf 100644 --- a/src/kimmdy/schema.py +++ b/src/kimmdy/schema.py @@ -59,7 +59,7 @@ def __repr__(self): def load_kimmdy_schema() -> dict: """Return the schema for the config file""" path = pkg_resources.files(kimmdy) / "kimmdy-yaml-schema.json" - with path.open("rt") as f: + with path.open("r") as f: schema = json.load(f) return schema diff --git a/src/kimmdy/tools.py b/src/kimmdy/tools.py index 42ab819c..3f89f3fd 100644 --- a/src/kimmdy/tools.py +++ b/src/kimmdy/tools.py @@ -161,7 +161,7 @@ def modify_top( # radicals != None -> iterate over rad_str.split, can be empty rad_str = None if radicals is not None: - rad_str = " ".join(radicals) + rad_str = " ".join([str(r) for r in radicals]) elif not search_amber_rad: rad_str = "" @@ -221,7 +221,7 @@ def modify_top( print("Done") # deal with gro file - if gro: + if gro_path is not None and gro_out is not None: if removeH: print("Writing gro..", end="") with open(gro_path, "r") as f: diff --git a/src/kimmdy/topology/topology.py b/src/kimmdy/topology/topology.py index 5b288160..1d7e14e1 100644 --- a/src/kimmdy/topology/topology.py +++ b/src/kimmdy/topology/topology.py @@ -1,42 +1,45 @@ -from kimmdy.constants import ATOMTYPE_BONDORDER_FLAT +import logging +import textwrap +from copy import copy, deepcopy +from itertools import permutations +from pathlib import Path +from typing import Callable, Optional, Union + +from kimmdy.constants import ( + ATOM_ID_FIELDS, + ATOMTYPE_BONDORDER_FLAT, + REACTIVE_MOLECULEYPE, + RESNR_ID_FIELDS, +) from kimmdy.parsing import TopologyDict +from kimmdy.plugins import BasicParameterizer, Parameterizer +from kimmdy.recipe import Bind, Break, RecipeStep from kimmdy.topology.atomic import ( + Angle, Atom, Bond, - Pair, - Angle, Dihedral, + DihedralRestraint, + Exclusion, MultipleDihedrals, + Pair, PositionRestraint, - DihedralRestraint, ResidueImproperSpec, Settle, - Exclusion, ) +from kimmdy.topology.ff import FF from kimmdy.topology.utils import ( + attributes_to_list, get_moleculetype_atomics, get_moleculetype_header, - attributes_to_list, + get_residue_fragments, get_top_section, + increment_field, is_not_solvent_or_ion, set_moleculetype_atomics, set_top_section, - get_residue_fragments, ) -from kimmdy.topology.ff import FF -from kimmdy.plugins import BasicParameterizer, Parameterizer -from itertools import permutations, combinations -import textwrap -import logging -from typing import Optional -from copy import copy, deepcopy -from pathlib import Path -from kimmdy.constants import ATOM_ID_FIELDS, RESNR_ID_FIELDS, REACTIVE_MOLECULEYPE -from typing import Callable, Union - from kimmdy.utils import TopologyAtomAddress -from kimmdy.topology.utils import increment_field -from kimmdy.recipe import RecipeStep, Bind, Break logger = logging.getLogger("kimmdy.topology") @@ -475,6 +478,9 @@ def _regenerate_topology_from_bound_to(self, ff): for atom in self.atoms.values(): impropers = self._get_atom_improper_dihedrals(atom.nr, ff) for key, improper in impropers: + periodicity = "" + if improper.c2 is not None: + periodicity = improper.c2 self.improper_dihedrals[key] = MultipleDihedrals( *key, "4", @@ -484,7 +490,7 @@ def _regenerate_topology_from_bound_to(self, ff): "4", c0=improper.c0, c1=improper.c1, - periodicity=improper.c2, + periodicity=periodicity, ) }, ) @@ -554,7 +560,8 @@ def reindex_atomnrs(self) -> dict[str, str]: continue # do pairs before the dihedrals are updated - if pair := self.pairs.pop((dihedrals.ai, dihedrals.al), False): + pair = self.pairs.pop((dihedrals.ai, dihedrals.al), None) + if pair is not None: pair_ai = update_map.get(pair.ai) pair_aj = update_map.get(pair.aj) diff --git a/src/kimmdy/utils.py b/src/kimmdy/utils.py index 8b093fd4..fdf21ac3 100644 --- a/src/kimmdy/utils.py +++ b/src/kimmdy/utils.py @@ -168,7 +168,7 @@ def get_edissoc_from_atomnames( try: E_dis = edissoc[residue][frozenset(atomnames)] - except KeyError as e: + except KeyError: # continue with guessed edissoc logger.warning( f"Did not find dissociation energy for atomtypes {atomnames}, residue {residue} in edissoc file, using standard value of 400.0" From e54549e9cefac884dc2621d28e2134f1a799b929 Mon Sep 17 00:00:00 2001 From: Jannik Buhr Date: Wed, 6 Mar 2024 16:45:01 +0100 Subject: [PATCH 7/8] minor fixes --- tests/test_parsing.py | 9 ++++++--- tests/test_recipe.py | 4 ++-- tests/test_topology.py | 16 ++++++++++------ 3 files changed, 18 insertions(+), 11 deletions(-) diff --git a/tests/test_parsing.py b/tests/test_parsing.py index 4a892114..c3ef6223 100644 --- a/tests/test_parsing.py +++ b/tests/test_parsing.py @@ -1,12 +1,14 @@ import re import string -import pytest -from hypothesis import settings, HealthCheck, given, strategies as st from pathlib import Path +import pytest +from hypothesis import HealthCheck, given, settings +from hypothesis import strategies as st + from kimmdy import parsing -from kimmdy.utils import get_gmx_dir from kimmdy.constants import AA3 +from kimmdy.utils import get_gmx_dir ## test topology parser @@ -40,6 +42,7 @@ def test_doubleparse_urea(arranged_tmp_path): def test_ff_includes_with_gmxdir(arranged_tmp_path): top_dict = parsing.read_top(Path("urea.top")) gmx_dir = get_gmx_dir("gmx") + assert gmx_dir is not None, "gmx dir not found" tip3_dict = parsing.read_top(gmx_dir / "top" / "amber99.ff" / "tip3p.itp") assert top_dict["atomtypes"] diff --git a/tests/test_recipe.py b/tests/test_recipe.py index 23a270f8..02520c66 100644 --- a/tests/test_recipe.py +++ b/tests/test_recipe.py @@ -128,9 +128,9 @@ def test_place_initialization(): assert m2 != m3 with pytest.raises(TypeError): - recipe.Place(ix_to_place=1) + recipe.Place(ix_to_place=1) # type: ignore with pytest.raises(ValueError): - recipe.Place(id_to_place=1, new_coords=(0, 0, 0)) + recipe.Place(id_to_place=1, new_coords=(0, 0, 0)) # type: ignore def test_relax_initialization(): diff --git a/tests/test_topology.py b/tests/test_topology.py index 2cdfbafd..2616fdf2 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -331,7 +331,8 @@ def test_del_atom_hexala(self, hexala_top_fix, atomindex): for a_del in angles_to_delete: assert None in [update.get(a) for a in a_del] for a_up in angles_to_update: - new = top.angles[tuple([update.get(a) for a in a_up])] + k1, k2, k3 = [update[a] for a in a_up] + new = top.angles[k1, k2, k3] old = hexala_top_fix.angles[a_up] assert old.ai == rev_update.get(new.ai) assert old.aj == rev_update.get(new.aj) @@ -341,7 +342,8 @@ def test_del_atom_hexala(self, hexala_top_fix, atomindex): for pd_del in pd_to_delete: assert None in tuple([update.get(a) for a in pd_del]) for pd_up in pd_to_update: - new = top.proper_dihedrals[tuple([update.get(a) for a in pd_up])] + k1, k2, k3, k4 = [update[a] for a in pd_up] + new = top.proper_dihedrals[k1, k2, k3, k4] old = hexala_top_fix.proper_dihedrals[pd_up] assert old.ai == rev_update.get(new.ai) assert old.aj == rev_update.get(new.aj) @@ -360,7 +362,8 @@ def test_del_atom_hexala(self, hexala_top_fix, atomindex): for id_del in id_to_delete: assert None in tuple([update.get(a) for a in id_del]) for id_up in id_to_update: - new = top.improper_dihedrals[tuple([update.get(a) for a in id_up])] + k1, k2, k3, k4 = [update[a] for a in id_up] + new = top.improper_dihedrals[k1, k2, k3, k4] old = hexala_top_fix.improper_dihedrals[id_up] assert old.ai == rev_update.get(new.ai) assert old.aj == rev_update.get(new.aj) @@ -637,9 +640,10 @@ def test_top_update_dict(self, raw_hexala_top_fix): assert raw["moleculetype_Protein"]["content"][0] == ["Protein", "3"] assert top.top["moleculetype_Reactive"]["content"][0] == ["Reactive", "3"] for section in ["atoms", "bonds", "angles", "dihedrals", "pairs"]: - top.top["moleculetype_Reactive"]["subsections"][section]["content"] == raw[ - "moleculetype_Protein" - ]["subsections"][section]["content"] + assert ( + top.top["moleculetype_Reactive"]["subsections"][section]["content"] + == raw["moleculetype_Protein"]["subsections"][section]["content"] + ) def test_top_properties(self, hexala_top_fix): top = deepcopy(hexala_top_fix) From 5f089e81fcd6c0d5d299322fd8a255337367cd3b Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 6 Mar 2024 15:48:04 +0000 Subject: [PATCH 8/8] chore(docs): render docs --- _reference/analysis.qmd | 28 +- _reference/coordinates.qmd | 4 +- _reference/recipe.qmd | 65 +- _reference/runmanager.qmd | 2 +- docs/_reference/analysis.html | 68 +- docs/_reference/coordinates.html | 4 +- docs/_reference/recipe.html | 80 +-- docs/_reference/runmanager.html | 2 +- docs/guide/explanation/index.html | 2 +- docs/guide/how-to/index.html | 10 +- docs/guide/tutorials/getting-started.html | 2 +- docs/guide/tutorials/index.html | 6 +- docs/listings.json | 12 +- docs/search.json | 782 +++++++++++----------- docs/sitemap.xml | 144 ++-- 15 files changed, 619 insertions(+), 592 deletions(-) diff --git a/_reference/analysis.qmd b/_reference/analysis.qmd index f3b755c9..7c7292a5 100644 --- a/_reference/analysis.qmd +++ b/_reference/analysis.qmd @@ -17,23 +17,25 @@ For command line usage, run `kimmdy-analysis -h`. | [plot_energy](#kimmdy.analysis.plot_energy) | Plot GROMACS energy for a KIMMDY run. | | [plot_rates](#kimmdy.analysis.plot_rates) | Plot rates of all possible reactions for each 'decide_recipe' step. | | [plot_runtime](#kimmdy.analysis.plot_runtime) | Plot runtime of all tasks. | +| [radical_migration](#kimmdy.analysis.radical_migration) | Plot population of radicals for a KIMMDY run. | | [radical_population](#kimmdy.analysis.radical_population) | Plot population of radicals for a KIMMDY run. | | [reaction_participation](#kimmdy.analysis.reaction_participation) | Plot runtime of all tasks. | ### concat_traj { #kimmdy.analysis.concat_traj } -`analysis.concat_traj(dir, filetype, steps, open_vmd=False)` +`analysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)` Find and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected. #### Parameters -| Name | Type | Description | Default | -|------------|-------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|------------| -| `dir` | [str](`str`) | Directory to search for subdirectories | _required_ | -| `steps` | [Union](`typing.Union`)\[[list](`list`)\[[str](`str`)\], [str](`str`)\] | List of steps e.g. ["equilibrium", "production"]. Or a string "all" to return all subdirectories | _required_ | -| `open_vmd` | [bool](`bool`) | Open concatenated trajectory in VMD | `False` | +| Name | Type | Description | Default | +|----------------|-------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|------------| +| `dir` | [str](`str`) | Directory to search for subdirectories | _required_ | +| `steps` | [Union](`typing.Union`)\[[list](`list`)\[[str](`str`)\], [str](`str`)\] | List of steps e.g. ["equilibrium", "production"]. Or a string "all" to return all subdirectories | _required_ | +| `open_vmd` | [bool](`bool`) | Open concatenated trajectory in VMD | `False` | +| `output_group` | [Optional](`typing.Optional`)\[[str](`str`)\] | index group for output. Default is "Protein" for xtc and "System" for trr. | `None` | ### entry_point_analysis { #kimmdy.analysis.entry_point_analysis } @@ -129,6 +131,20 @@ Plot runtime of all tasks. | `datefmt` | [str](`str`) | Date format in the KIMMDY logfile | _required_ | | `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False` | +### radical_migration { #kimmdy.analysis.radical_migration } + +`analysis.radical_migration(dirs, type='qualitative', cutoff=1)` + +Plot population of radicals for a KIMMDY run. + +#### Parameters + +| Name | Type | Description | Default | +|----------|--------------------------------|--------------------------------------------------------------------------------------------|-----------------| +| `dirs` | [list](`list`)\[[str](`str`)\] | KIMMDY run directories to be analysed. | _required_ | +| `type` | [str](`str`) | How to analyse radical migration. Available are 'qualitative','occurence' and 'min_rate'", | `'qualitative'` | +| `cutoff` | [int](`int`) | Ignore migration between two atoms if it happened less often than the specified value. | `1` | + ### radical_population { #kimmdy.analysis.radical_population } `analysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)` diff --git a/_reference/coordinates.qmd b/_reference/coordinates.qmd index 7ff60b97..2e018300 100644 --- a/_reference/coordinates.qmd +++ b/_reference/coordinates.qmd @@ -58,13 +58,13 @@ Merge one to two Dihedrals or -Types into a Dihedral in free-energy syntax ### merge_top_moleculetypes_slow_growth { #kimmdy.coordinates.merge_top_moleculetypes_slow_growth } -`coordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff, focus_nr=None)` +`coordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)` Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation ### merge_top_slow_growth { #kimmdy.coordinates.merge_top_slow_growth } -`coordinates.merge_top_slow_growth(topA, topB, focus_nr=None)` +`coordinates.merge_top_slow_growth(topA, topB)` Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation. diff --git a/_reference/recipe.qmd b/_reference/recipe.qmd index 8b54ad97..69b34e2a 100644 --- a/_reference/recipe.qmd +++ b/_reference/recipe.qmd @@ -20,35 +20,35 @@ Contains the Reaction Recipe, RecipeStep and RecipeCollection. ### Bind { #kimmdy.recipe.Bind } -`recipe.Bind()` +`recipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)` Change topology to form a bond #### Parameters -| Name | Type | Description | Default | -|-------------|--------------|-----------------------------------------------------------|------------| -| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None | _required_ | -| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | _required_ | -| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None | _required_ | -| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None | _required_ | +| Name | Type | Description | Default | +|-------------|--------------|-----------------------------------------------------------|-----------| +| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None | `None` | +| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | `None` | +| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None | `None` | +| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None | `None` | ### BondOperation { #kimmdy.recipe.BondOperation } -`recipe.BondOperation(_atom_ix_1=field(init=False, repr=False, default=None), _atom_ix_2=field(init=False, repr=False, default=None))` +`recipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)` Handle a bond operation on the recipe step. -This class takes in either zero-based indices or one-base IDs for two atoms +This class takes in either zero-based indices or one-base IDs for two atoms. #### Parameters -| Name | Type | Description | Default | -|-------------|--------------|-----------------------------------------------------------|------------| -| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None | _required_ | -| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | _required_ | -| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None | _required_ | -| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None | _required_ | +| Name | Type | Description | Default | +|-------------|--------------|-----------------------------------------------------------|-----------| +| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None | `None` | +| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | `None` | +| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None | `None` | +| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None | `None` | #### Raises @@ -62,18 +62,18 @@ Internally, this class stores the atom indices and converts IDs to indices as ne ### Break { #kimmdy.recipe.Break } -`recipe.Break()` +`recipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)` Change topology to break a bond #### Parameters -| Name | Type | Description | Default | -|-------------|--------------|-----------------------------------------------------------|------------| -| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None | _required_ | -| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | _required_ | -| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None | _required_ | -| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None | _required_ | +| Name | Type | Description | Default | +|-------------|--------------|-----------------------------------------------------------|-----------| +| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None | `None` | +| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | `None` | +| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None | `None` | +| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None | `None` | ### CustomTopMod { #kimmdy.recipe.CustomTopMod } @@ -89,17 +89,19 @@ A custom recipe step that can be used to define a custom topology modification. ### Place { #kimmdy.recipe.Place } -`recipe.Place(new_coords, _ix_to_place=field(init=False, repr=False, default=None))` +`recipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)` Change topology and/or coordinates to place an atom. +Either provide the index (ix_to_place) or the ID (id_to_place) of the atom to place. + #### Parameters | Name | Type | Description | Default | |---------------|--------------------------------------------------------------------------|-------------------------------------------------------------------------------------------|------------| | `new_coords` | [tuple](`tuple`)\[[float](`float`), [float](`float`), [float](`float`)\] | New xyz coordinates for atom to place to. Valid for the end point of the recipe timespan. | _required_ | -| `ix_to_place` | [int](`int`) | Index of atom to place. 0-based. | _required_ | -| `id_to_place` | [str](`str`) | Index of atom to place. 1-based | _required_ | +| `ix_to_place` | [int](`int`) | Index of atom to place. 0-based. | `None` | +| `id_to_place` | [str](`str`) | Index of atom to place. 1-based | `None` | ### Recipe { #kimmdy.recipe.Recipe } @@ -121,22 +123,9 @@ product state from the educt state. | Name | Description | | --- | --- | -| [calc_averages](#kimmdy.recipe.Recipe.calc_averages) | Calulate average rates over some window size | | [check_consistency](#kimmdy.recipe.Recipe.check_consistency) | Run consistency checks for correct size of variables | | [combine_with](#kimmdy.recipe.Recipe.combine_with) | Combines this Recipe with another with the same RecipeSteps. | -##### calc_averages { #kimmdy.recipe.Recipe.calc_averages } - -`recipe.Recipe.calc_averages(window_size)` - -Calulate average rates over some window size - -###### Parameters - -| Name | Type | Description | Default | -|---------------|--------------|-------------------------------------------------------------------------------|------------| -| `window_size` | [int](`int`) | Size of the window to average over, -1 to average over whole available range. | _required_ | - ##### check_consistency { #kimmdy.recipe.Recipe.check_consistency } `recipe.Recipe.check_consistency()` diff --git a/_reference/runmanager.qmd b/_reference/runmanager.qmd index d52899ff..f50412f7 100644 --- a/_reference/runmanager.qmd +++ b/_reference/runmanager.qmd @@ -82,6 +82,6 @@ one of IDLE, MD, REACTION, SETUP, DONE. ### get_existing_files { #kimmdy.runmanager.get_existing_files } -`runmanager.get_existing_files(config, section='root')` +`runmanager.get_existing_files(config)` Initialize latest_files with every existing file defined in config \ No newline at end of file diff --git a/docs/_reference/analysis.html b/docs/_reference/analysis.html index 75eb9245..08fe1d9a 100644 --- a/docs/_reference/analysis.html +++ b/docs/_reference/analysis.html @@ -483,14 +483,18 @@

On this page

-
  • radical_population +
  • radical_migration
    • -
  • reaction_participation +
  • radical_population
    • +
  • reaction_participation +
    • @@ -548,10 +552,14 @@

    Functions

    Plot runtime of all tasks. -radical_population +radical_migration Plot population of radicals for a KIMMDY run. +radical_population +Plot population of radicals for a KIMMDY run. + + reaction_participation Plot runtime of all tasks. @@ -559,7 +567,7 @@

    Functions

    concat_traj

    -

    analysis.concat_traj(dir, filetype, steps, open_vmd=False)

    +

    analysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)

    Find and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.

    Parameters

    @@ -591,6 +599,12 @@

    Parameters

    Open concatenated trajectory in VMD False + +output_group +Optional[str] +index group for output. Default is “Protein” for xtc and “System” for trr. +None +
    @@ -812,12 +826,50 @@

    Parameters

    +
    +

    radical_migration

    +

    analysis.radical_migration(dirs, type='qualitative', cutoff=1)

    +

    Plot population of radicals for a KIMMDY run.

    +
    +

    Parameters

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameTypeDescriptionDefault
    dirslist[str]KIMMDY run directories to be analysed.required
    typestrHow to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,'qualitative'
    cutoffintIgnore migration between two atoms if it happened less often than the specified value.1
    +
    +

    radical_population

    analysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)

    Plot population of radicals for a KIMMDY run.

    -
    -

    Parameters

    +
    +

    Parameters

    @@ -872,8 +924,8 @@

    Parameters

    reaction_participation

    analysis.reaction_participation(dir, open_plot=False)

    Plot runtime of all tasks.

    -
    -

    Parameters

    +
    +

    Parameters

    diff --git a/docs/_reference/coordinates.html b/docs/_reference/coordinates.html index 4307f800..da7775f2 100644 --- a/docs/_reference/coordinates.html +++ b/docs/_reference/coordinates.html @@ -576,12 +576,12 @@

    merge_d

    merge_top_moleculetypes_slow_growth

    -

    coordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff, focus_nr=None)

    +

    coordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)

    Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation

    merge_top_slow_growth

    -

    coordinates.merge_top_slow_growth(topA, topB, focus_nr=None)

    +

    coordinates.merge_top_slow_growth(topA, topB)

    Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation.

    TODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.

    diff --git a/docs/_reference/recipe.html b/docs/_reference/recipe.html index 897abf34..57061871 100644 --- a/docs/_reference/recipe.html +++ b/docs/_reference/recipe.html @@ -480,7 +480,6 @@

    On this page

  • Parameters
  • Methods
    • @@ -564,7 +563,7 @@

    Classes

    Bind

    -

    recipe.Bind()

    +

    recipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)

    Change topology to form a bond

    Parameters

    @@ -582,25 +581,25 @@

    Parameters

    atom_ix_1 int The index of the first atom. zero-based, by default None -required +None atom_ix_2 int The index of the second atom. zero-based, by default None -required +None atom_id_1 str The ID of the first atom. one-based, by default None -required +None atom_id_2 str The ID of the second atom. one-based, by default None -required +None @@ -608,9 +607,9 @@

    Parameters

    BondOperation

    -

    recipe.BondOperation(_atom_ix_1=field(init=False, repr=False, default=None), _atom_ix_2=field(init=False, repr=False, default=None))

    +

    recipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)

    Handle a bond operation on the recipe step.

    -

    This class takes in either zero-based indices or one-base IDs for two atoms

    +

    This class takes in either zero-based indices or one-base IDs for two atoms.

    Parameters

    @@ -627,25 +626,25 @@

    Parameters

    - + - + - + - +
    atom_ix_1 int The index of the first atom. zero-based, by default NonerequiredNone
    atom_ix_2 int The index of the second atom. zero-based, by default NonerequiredNone
    atom_id_1 str The ID of the first atom. one-based, by default NonerequiredNone
    atom_id_2 str The ID of the second atom. one-based, by default NonerequiredNone
    @@ -674,7 +673,7 @@

    Notes

    Break

    -

    recipe.Break()

    +

    recipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)

    Change topology to break a bond

    Parameters

    @@ -692,25 +691,25 @@

    Parameters

    atom_ix_1 int The index of the first atom. zero-based, by default None -required +None atom_ix_2 int The index of the second atom. zero-based, by default None -required +None atom_id_1 str The ID of the first atom. one-based, by default None -required +None atom_id_2 str The ID of the second atom. one-based, by default None -required +None @@ -744,8 +743,9 @@

    Parameters

    Place

    -

    recipe.Place(new_coords, _ix_to_place=field(init=False, repr=False, default=None))

    +

    recipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)

    Change topology and/or coordinates to place an atom.

    +

    Either provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.

    Parameters

    @@ -768,13 +768,13 @@

    Parameters

    - + - +
    ix_to_place int Index of atom to place. 0-based.requiredNone
    id_to_place str Index of atom to place. 1-basedrequiredNone
    @@ -828,45 +828,15 @@

    Methods

    -calc_averages -Calulate average rates over some window size - - check_consistency Run consistency checks for correct size of variables - + combine_with Combines this Recipe with another with the same RecipeSteps. -
    -
    calc_averages
    -

    recipe.Recipe.calc_averages(window_size)

    -

    Calulate average rates over some window size

    -
    -
    Parameters
    - - - - - - - - - - - - - - - - - -
    NameTypeDescriptionDefault
    window_sizeintSize of the window to average over, -1 to average over whole available range.required
    -
    -
    check_consistency

    recipe.Recipe.check_consistency()

    @@ -876,8 +846,8 @@
    che
    combine_with

    recipe.Recipe.combine_with(other)

    Combines this Recipe with another with the same RecipeSteps.

    -
    -
    Parameters
    +
    +
    Parameters
    @@ -1014,8 +984,8 @@
    fr
    plot

    recipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)

    Plot reaction rates over time

    -
    -
    Parameters
    +
    +
    Parameters
    diff --git a/docs/_reference/runmanager.html b/docs/_reference/runmanager.html index bd2142a3..68fc24c3 100644 --- a/docs/_reference/runmanager.html +++ b/docs/_reference/runmanager.html @@ -649,7 +649,7 @@

    Functions

    get_existing_files

    -

    runmanager.get_existing_files(config, section='root')

    +

    runmanager.get_existing_files(config)

    Initialize latest_files with every existing file defined in config

    diff --git a/docs/guide/explanation/index.html b/docs/guide/explanation/index.html index 11dfda2d..bd292ffc 100644 --- a/docs/guide/explanation/index.html +++ b/docs/guide/explanation/index.html @@ -537,7 +537,7 @@

    Explanations

    - + Visualize Topologies diff --git a/docs/guide/how-to/index.html b/docs/guide/how-to/index.html index c5bd9900..0696cb1d 100644 --- a/docs/guide/how-to/index.html +++ b/docs/guide/how-to/index.html @@ -537,7 +537,7 @@

    How-To

    - + Contribute @@ -545,7 +545,7 @@

    How-To

      - + Examples @@ -553,7 +553,7 @@

    How-To

      - + High Performance Computing @@ -561,7 +561,7 @@

    How-To

      - + Install Machine Learning Plugins @@ -569,7 +569,7 @@

    How-To

      - + Reaction only diff --git a/docs/guide/tutorials/getting-started.html b/docs/guide/tutorials/getting-started.html index 0aadb78b..90decd3d 100644 --- a/docs/guide/tutorials/getting-started.html +++ b/docs/guide/tutorials/getting-started.html @@ -603,7 +603,7 @@

    Setup the Simulation<

    Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.

    diff --git a/docs/guide/tutorials/index.html b/docs/guide/tutorials/index.html index aa2fe573..a5b905ec 100644 --- a/docs/guide/tutorials/index.html +++ b/docs/guide/tutorials/index.html @@ -507,7 +507,7 @@

    Tutorials

    -
    +

    @@ -539,7 +539,7 @@

    -
    +

    @@ -571,7 +571,7 @@

    -
    +

     

    diff --git a/docs/listings.json b/docs/listings.json index 6f9d901e..92ab3a37 100644 --- a/docs/listings.json +++ b/docs/listings.json @@ -1,10 +1,8 @@ [ { - "listing": "/guide/tutorials/index.html", + "listing": "/guide/explanation/index.html", "items": [ - "/guide/tutorials/getting-started.html", - "/guide/tutorials/colbuilder.html", - "/guide/tutorials/write-plugin.html" + "/guide/explanation/topology.html" ] }, { @@ -18,9 +16,11 @@ ] }, { - "listing": "/guide/explanation/index.html", + "listing": "/guide/tutorials/index.html", "items": [ - "/guide/explanation/topology.html" + "/guide/tutorials/getting-started.html", + "/guide/tutorials/colbuilder.html", + "/guide/tutorials/write-plugin.html" ] } ] \ No newline at end of file diff --git a/docs/search.json b/docs/search.json index 5054a1de..152638c6 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1,94 +1,115 @@ [ { - "objectID": "guide/explanation/topology.html", - "href": "guide/explanation/topology.html", - "title": "Visualize Topologies", + "objectID": "guide/explanation/index.html", + "href": "guide/explanation/index.html", + "title": "Explanations", "section": "", - "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n \n\n1 CT\n\n 1 CT \n\n2 HC\n\n 2 HC \n\n1 CT–2 HC\n\n \n\n3 HC\n\n 3 HC \n\n1 CT–3 HC\n\n \n\n4 HC\n\n 4 HC \n\n1 CT–4 HC\n\n \n\n5 C\n\n 5 C \n\n1 CT–5 C\n\n \n\n6 O\n\n 6 O \n\n5 C–6 O\n\n \n\n7 N\n\n 7 N \n\n5 C–7 N\n\n \n\n8 H\n\n 8 H \n\n7 N–8 H\n\n \n\n9 CT\n\n 9 CT \n\n7 N–9 CT\n\n \n\n10 CT\n\n 10 CT \n\n9 CT–10 CT\n\n \n\n14 C\n\n 14 C \n\n9 CT–14 C\n\n \n\n11 HC\n\n 11 HC \n\n10 CT–11 HC\n\n \n\n12 HC\n\n 12 HC \n\n10 CT–12 HC\n\n \n\n13 HC\n\n 13 HC \n\n10 CT–13 HC\n\n \n\n15 O\n\n 15 O \n\n14 C–15 O\n\n \n\n16 N\n\n 16 N \n\n14 C–16 N\n\n \n\n17 H\n\n 17 H \n\n16 N–17 H\n\n \n\n18 CT\n\n 18 CT \n\n16 N–18 CT\n\n \n\n19 H1\n\n 19 H1 \n\n18 CT–19 H1\n\n \n\n20 H1\n\n 20 H1 \n\n18 CT–20 H1\n\n \n\n21 H1\n\n 21 H1 \n\n18 CT–21 H1\n\n \n\n\nFigure 1: A diagram of the Ala topology" + "text": "Pages that help you understand the inner workings of KIMMDY\n\n\n\n\n\n\n \n \n \n Order By\n Default\n \n Title\n \n \n Author\n \n \n \n \n \n \n \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nVisualize Topologies\n\n\n \n\n\n\n\n\nNo matching items\n\n Back to top" }, { - "objectID": "guide/explanation/topology.html#capped-alanine-with-a-radical", - "href": "guide/explanation/topology.html#capped-alanine-with-a-radical", - "title": "Visualize Topologies", + "objectID": "guide/tutorials/getting-started.html", + "href": "guide/tutorials/getting-started.html", + "title": "Get Started", "section": "", - "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n \n\n1 CT\n\n 1 CT \n\n2 HC\n\n 2 HC \n\n1 CT–2 HC\n\n \n\n3 HC\n\n 3 HC \n\n1 CT–3 HC\n\n \n\n4 HC\n\n 4 HC \n\n1 CT–4 HC\n\n \n\n5 C\n\n 5 C \n\n1 CT–5 C\n\n \n\n6 O\n\n 6 O \n\n5 C–6 O\n\n \n\n7 N\n\n 7 N \n\n5 C–7 N\n\n \n\n8 H\n\n 8 H \n\n7 N–8 H\n\n \n\n9 CT\n\n 9 CT \n\n7 N–9 CT\n\n \n\n10 CT\n\n 10 CT \n\n9 CT–10 CT\n\n \n\n14 C\n\n 14 C \n\n9 CT–14 C\n\n \n\n11 HC\n\n 11 HC \n\n10 CT–11 HC\n\n \n\n12 HC\n\n 12 HC \n\n10 CT–12 HC\n\n \n\n13 HC\n\n 13 HC \n\n10 CT–13 HC\n\n \n\n15 O\n\n 15 O \n\n14 C–15 O\n\n \n\n16 N\n\n 16 N \n\n14 C–16 N\n\n \n\n17 H\n\n 17 H \n\n16 N–17 H\n\n \n\n18 CT\n\n 18 CT \n\n16 N–18 CT\n\n \n\n19 H1\n\n 19 H1 \n\n18 CT–19 H1\n\n \n\n20 H1\n\n 20 H1 \n\n18 CT–20 H1\n\n \n\n21 H1\n\n 21 H1 \n\n18 CT–21 H1\n\n \n\n\nFigure 1: A diagram of the Ala topology" + "text": "In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water." }, { - "objectID": "guide/explanation/topology.html#multiple-molecules", - "href": "guide/explanation/topology.html#multiple-molecules", - "title": "Visualize Topologies", - "section": "Multiple molecules", - "text": "Multiple molecules\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n \n\n1 C\n\n 1 C \n\n2 O\n\n 2 O \n\n1 C–2 O\n\n \n\n3 N\n\n 3 N \n\n1 C–3 N\n\n \n\n6 N\n\n 6 N \n\n1 C–6 N\n\n \n\n4 H\n\n 4 H \n\n3 N–4 H\n\n \n\n5 H\n\n 5 H \n\n3 N–5 H\n\n \n\n7 H\n\n 7 H \n\n6 N–7 H\n\n \n\n8 H\n\n 8 H \n\n6 N–8 H\n\n \n\n\nFigure 2: Topology of one molecule of urea\n\n\n\n\nWhen we want to run reactions within molecules that are either separate moleculetypes or multiples of the same moleculetype, KIMMDY can combine those into a single moleculetype and make multiples explicit.\ni.e. if we have a topology with two molecules of urea defined as:\n[ system ]\nUrea in Water\n\n[ molecules ]\n;molecule name nr.\nUrea 2\nSOL 1000\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea-times-2.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-2-top.dot\")\n\nWe end up with\n\n\n\n\n\n\n\n\nG\n\n \n\n1 C\n\n 1 C \n\n2 O\n\n 2 O \n\n1 C–2 O\n\n \n\n3 N\n\n 3 N \n\n1 C–3 N\n\n \n\n6 N\n\n 6 N \n\n1 C–6 N\n\n \n\n4 H\n\n 4 H \n\n3 N–4 H\n\n \n\n5 H\n\n 5 H \n\n3 N–5 H\n\n \n\n7 H\n\n 7 H \n\n6 N–7 H\n\n \n\n8 H\n\n 8 H \n\n6 N–8 H\n\n \n\n9 C\n\n 9 C \n\n10 O\n\n 10 O \n\n9 C–10 O\n\n \n\n11 N\n\n 11 N \n\n9 C–11 N\n\n \n\n14 N\n\n 14 N \n\n9 C–14 N\n\n \n\n12 H\n\n 12 H \n\n11 N–12 H\n\n \n\n13 H\n\n 13 H \n\n11 N–13 H\n\n \n\n15 H\n\n 15 H \n\n14 N–15 H\n\n \n\n16 H\n\n 16 H \n\n14 N–16 H\n\n \n\n\nFigure 3: A diagram of the two urea molecules topology\n\n\n\n\nThis way, explicit atom numbers match up with the atom numbers in the coordinate file (or rather, line numbers - 2, since the numbers in the actual atomnr column can overflow due to the fixed-width file format)." + "objectID": "guide/tutorials/getting-started.html#installation", + "href": "guide/tutorials/getting-started.html#installation", + "title": "Get Started", + "section": "Installation", + "text": "Installation\n\nPrerequisites\n\npython3.9 or higher\ngromacs (tested with version 2021.4, gmx should be available in the PATH)\n\nOptional:\n\nplumed-patched version of gromacs (for the homolysis reaction).\n\n\n\n\n\n\n\n\n\n\n\nIf you plan to use our machine-learning plugins, take a look at the full installation instruction\n\n\nLet’s first create a directory and a virtual environment for kimmdy:\nmkdir kimmdy-tutorial\ncd kimmdy-tutorial\npython -m venv .venv\nsource .venv/bin/activate\nTo install KIMMDY, the builtin reaction plugins and the analysis tools use\npip install kimmdy[reactions,analysis]" }, { - "objectID": "guide/references/cmd_ref.html", - "href": "guide/references/cmd_ref.html", - "title": "CLI Arguments", - "section": "", - "text": "The prefered method of starting a KIMMDY run is via the command line, though Python entry points are supported as well." + "objectID": "guide/tutorials/getting-started.html#setup-the-simulation", + "href": "guide/tutorials/getting-started.html#setup-the-simulation", + "title": "Get Started", + "section": "Setup the Simulation", + "text": "Setup the Simulation\nDownload and unzip the input files to this directory.\nwget https://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started-files/setup.zip\nunzip setup.zip\nThe kimmdy.yml file should look like this:\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow.mdp'\nchanger:\n coordinates:\n md: 'relax' \nreactions:\n hat_reaction:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions\n\nOur starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.\n \n \n \nStart the KIMMDY run with the kimmdy command:" }, { - "objectID": "guide/references/cmd_ref.html#kimmdy", - "href": "guide/references/cmd_ref.html#kimmdy", - "title": "CLI Arguments", - "section": "KIMMDY", - "text": "KIMMDY\n\n!kimmdy --help\n\nusage: kimmdy [-h] [--input INPUT] [--checkpoint CHECKPOINT]\n [--loglevel LOGLEVEL] [--logfile LOGFILE] [--show-plugins]\n [--generate-jobscript] [--version] [--debug] [--callgraph]\n\nWelcome to KIMMDY. `kimmdy` runs KIMMDY, further tools are available as\n`kimmdy-...` commands. These are `-analysis`, `-modify-top` and `-build-\nexamples`. Access their help with `kimmdy-... -h.`\n\noptions:\n -h, --help show this help message and exit\n --input INPUT, -i INPUT\n Kimmdy input file. Default `kimmdy.yml`\n --checkpoint CHECKPOINT, -c CHECKPOINT\n File path of a kimmdy.cpt file to restart KIMMDY from\n a checkpoint. If a directory is given, the file\n kimmdy.cpt in that directory is used.\n --loglevel LOGLEVEL, -l LOGLEVEL\n logging level (CRITICAL, ERROR, WARNING, INFO, DEBUG)\n --logfile LOGFILE, -f LOGFILE\n logfile\n --show-plugins List available plugins\n --generate-jobscript Instead of running KIMMDY directly, generate at\n jobscript.sh for slurm HPC clusters.You can then run\n this jobscript with sbatch jobscript.sh\n --version show program's version number and exit\n --debug on error, drop into debugger\n --callgraph Generate visualization of function calls. Mostly\n useful for debugging and documentation." + "objectID": "guide/tutorials/getting-started.html#run-the-simulation", + "href": "guide/tutorials/getting-started.html#run-the-simulation", + "title": "Get Started", + "section": "Run the Simulation", + "text": "Run the Simulation\nkimmdy\nYou can also run kimmdy directly from python with\nfrom kimmdy.cmd import kimmdy_run\nkimmdy_run()\n\n\n\n\n\n\nTip\n\n\n\nKIMMDY parses your topology to generate its internal representation and writes out a new topology to be used in future steps. This topology includes everything gromacs needs to run the simulation, including forcefield parameters. KIMMDY combines all moleculetypes that are meant to take part in reactions into one moleculetype named “Reactive”. It also makes multiples explicit (e.g. 10 molecules of a peptide), such that each reactive atom has a unique representation. You can always find this topology in the output directory for the kimmdy setup task, e.g. alanine_hat_000/0_setup/<name-of-your-top.top. By default, everything that is not a solvent or ion is considered reactive. To exclude or include certain moleculetypes from this (e.g. in a lipid bilayer simulation), check out the topology.reactive options in the input file documentation. You can find another example of merging topologies in the topology explanation." }, { - "objectID": "guide/references/cmd_ref.html#analysis", - "href": "guide/references/cmd_ref.html#analysis", - "title": "CLI Arguments", - "section": "Analysis", - "text": "Analysis\n\n!kimmdy-analysis --help\n\nusage: kimmdy-analysis [-h] module ...\n\nWelcome to the KIMMDY analysis module. Use this module to analyse existing\nKIMMDY runs.\n\npositional arguments:\n module\n trjcat Concatenate trajectories of a KIMMDY run\n energy Plot GROMACS energy for a KIMMDY run\n radical_population\n Plot population of radicals for one or multiple KIMMDY\n run(s)\n rates Plot rates of all possible reactions after a MD run.\n Rates must have been saved!\n runtime Plot runtime of the tasks of a kimmdy run.\n\noptions:\n -h, --help show this help message and exit" + "objectID": "guide/tutorials/getting-started.html#analyse-the-simulation", + "href": "guide/tutorials/getting-started.html#analyse-the-simulation", + "title": "Get Started", + "section": "Analyse the Simulation", + "text": "Analyse the Simulation\nConcatenate the trajectories from the individual steps into one for viewing:\nkimmdy-analysis trjcat alanine_hat_000 --open-vmd\nCheck the energy of the system:\nkimmdy-analysis energy alanine_hat_000 --open-plot --terms Potential Kinetic\n\n\n\nEnergy plot\n\n\nVisualize where the radicals end up:\nkimmdy-analysis radical_population alanine_hat_000 --open-plot --open-vmd\nIn VMD, color the atoms by beta factor to show the radical occupancy.\n\n\n\nVMD representation settings\n\n\n\n\n\nRadical population plot\n\n\nPlot the reaction rates:\nkimmdy-analysis rates alanine_hat_000\nIn the alanine_hat_000/analysis directory you will then find a plot of rates for each possible reaction at every step they were queried, e.g.\n\n\n\nReaction rates plot\n\n\nOr do all of the above directly from python:\nfrom kimmdy.analysis import concat_trj, plot_energy, radical_population, plot_rates\nconcat_trj('alanine_hat_000', open_vmd=True)\nplot_energy('alanine_hat_000', terms=['Potential', 'Kinetic'], open_plot=True)\nradical_population('alanine_hat_000', open_plot=True, open_vmd=True)\nplot_rates('alanine_hat_000')\nCongratulations, you have successfully run your first KIMMDY simulation!" }, { - "objectID": "guide/references/cmd_ref.html#remove-hydrogen", - "href": "guide/references/cmd_ref.html#remove-hydrogen", - "title": "CLI Arguments", - "section": "Remove Hydrogen", - "text": "Remove Hydrogen\nThis module builds or restores the example directory in the package.\n\n!kimmdy-modify-top --help\n\nusage: kimmdy-modify-top [-h] [-p] [-r REMOVEH [REMOVEH ...]] [-c GROFILE]\n [-t RESIDUETYPES] [-x RADICALS]\n top out\n\nWelcome to the KIMMDY modify top module\n\npositional arguments:\n top GROMACS top file\n out Output top file name\n\noptions:\n -h, --help show this help message and exit\n -p, --parameterize Parameterize topology with grappa. (default: False)\n -r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]\n Remove one or more hydrogens by atom nrs in the top\n file. (default: None)\n -c GROFILE, --grofile GROFILE\n If necessary, also apply actions on gro file to create\n a compatible gro/top file pair. (default: None)\n -t RESIDUETYPES, --residuetypes RESIDUETYPES\n GROMACS style residuetypes file. Necessary for\n parameterization with non-amber atom types. (default:\n None)\n -x RADICALS, --radicals RADICALS\n Radicals in the system PRIOR to removing hydrogens\n with the removeH option. (default: )" + "objectID": "guide/tutorials/getting-started.html#next-steps", + "href": "guide/tutorials/getting-started.html#next-steps", + "title": "Get Started", + "section": "Next steps", + "text": "Next steps\n\nLearn more about the kimmdy.yml input file\nRun KIMMDY with a collagen fibril from Colbuilder\nWrite your own reaction plugin\nDiscover more plugins by looking for the kimmdy tag on GitHub" }, { - "objectID": "guide/references/cmd_ref.html#examples", - "href": "guide/references/cmd_ref.html#examples", - "title": "CLI Arguments", - "section": "Examples", - "text": "Examples\nThis module builds or restores the example directory in the package.\n\n!kimmdy-build-examples --help\n\nusage: kimmdy-build-examples [-h] [-r [RESTORE]]\n\nBuild examples for KIMMDY.\n\noptions:\n -h, --help show this help message and exit\n -r [RESTORE], --restore [RESTORE]\n Overwrite input files in existing example directories,\n use keyword 'hard' to also delete output files." + "objectID": "guide/tutorials/write-plugin.html", + "href": "guide/tutorials/write-plugin.html", + "title": "Write a Reaction Plugin", + "section": "", + "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions." }, { - "objectID": "guide/how-to/reaction_only.html", - "href": "guide/how-to/reaction_only.html", - "title": "Reaction only", + "objectID": "guide/tutorials/write-plugin.html#creating-a-github-repository", + "href": "guide/tutorials/write-plugin.html#creating-a-github-repository", + "title": "Write a Reaction Plugin", "section": "", - "text": "You might want to apply a KIMMDY reaction to an already existing simulation. Here are some important points for doing so." + "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions." }, { - "objectID": "guide/how-to/reaction_only.html#kimmdy-yaml", - "href": "guide/how-to/reaction_only.html#kimmdy-yaml", - "title": "Reaction only", - "section": "KIMMDY yaml", - "text": "KIMMDY yaml\nIf you want to start your sequence of tasks with a reaction, you have to give KIMMDY a trajectory. This, you do with the trr key in the kimmdy.yml file." + "objectID": "guide/tutorials/write-plugin.html#adding-the-functionality-of-the-plugin", + "href": "guide/tutorials/write-plugin.html#adding-the-functionality-of-the-plugin", + "title": "Write a Reaction Plugin", + "section": "Adding the functionality of the plugin", + "text": "Adding the functionality of the plugin\n\nMain code\nA reaction plugin has to be a derived class from the ReactionPlugin base class. Such a class has the attributes name, runmng and config and the method get_recipe_collection, which takes a TaskFiles object as argument and returns a RecipeCollection.\nThe name is a simple string and may be useful for logging. runmng is the central RunManager of a kimmdy run and has plenty of useful attributes for your plugin, especially the system Topology, which can be accessed via self.runmg.top. config contains the reaction plugin configuration as specified in the kimmdy configuration file (typically named kimmdy.yml). A RecipeCollection contains Recipes with predefined RecipeSteps that can be used to define the modification to the system for the reaction. A Recipe also contains the rates of the specified reaction and the timespans during which the corresponding rates are valid. An example plugin can be seen below.\n\n\nPlugin main code (reaction.py)\nfrom kimmdy.recipe import (\n Bind,\n Recipe,\n RecipeCollection,\n)\nfrom kimmdy.plugins import ReactionPlugin\nfrom kimmdy.tasks import TaskFiles\nfrom kimmdy.utils import (\n get_atomnrs_from_plumedid,\n)\nfrom kimmdy.parsing import (\n read_plumed,\n read_distances_dat,\n)\n\n\nclass BindReaction(ReactionPlugin):\n \"\"\"Reaction to bind two particles if they are in proximity\n \"\"\"\n\n def get_recipe_collection(self, files: TaskFiles):\n logger = files.logger\n logger.debug(\"Getting recipe for reaction: Bind\")\n\n # get cutoff distance from config, unit is [nm]\n cutoff = self.config.distance\n\n # Initialization of objects from files\n distances = read_distances_dat(files.input[\"plumed_out\"])\n plumed = read_plumed(files.input[\"plumed\"])\n\n recipes = []\n # check distances file for values lower than the cutoff\n for plumedid, dists in distances.items():\n if plumedid == \"time\":\n continue\n # checks only last frame\n if dists[-1] < cutoff:\n # get atomnrs from plumedid \n atomnrs = get_atomnrs_from_plumedid(plumedid, plumed)\n recipes.append(\n Recipe(\n recipe_steps=[\n Bind(atom_id_1=atomnrs[0], atom_id_2=atomnrs[1]),\n ],\n rates=[1],\n timespans=[(distances[\"time\"][0], distances[\"time\"][-1])],\n )\n )\n\n return RecipeCollection(recipes)\n\n\n\n\nConfiguration file schema\nA plugin defines which variables it needs in a schema. The schema can contain default values and types of these variables. For a Kimmdy run, reaction plugin variables are defined in the configuration file (kimmdy.yml). An example schema can be seen below.\n\n\nPlugin schema (kimmdy-yaml-schema.json)\n\n\n\nkimmdy-yaml-schema.json\n\n{\n \"$schema\": \"https://json-schema.org/draft/2020-12/schema\",\n \"type\": \"object\",\n \"$id\": \"bind-config\",\n \"description\": \"Settings for bind reactions\",\n \"additionalProperties\": false,\n \"properties\": {\n \"distance\": {\n \"description\": \"Cutoff distance for two particles to bind [nm]\",\n \"type\": \"float\",\n \"pytype\": \"float\"\n },\n \"kmc\": {\n \"description\": \"KMC algorithm for this reaction.\",\n \"type\": \"string\",\n \"pytype\": \"str\",\n \"enum\": [\"rfkmc\", \"frm\", \"extrande\"],\n \"default\": \"rfkmc\"\n }\n },\n \"required\": [\"distance\"]\n}" }, { - "objectID": "guide/how-to/reaction_only.html#pre-averaged-plumed-input", - "href": "guide/how-to/reaction_only.html#pre-averaged-plumed-input", - "title": "Reaction only", - "section": "Pre-averaged plumed input", - "text": "Pre-averaged plumed input\nSometimes it is handy to pre-compute the averages of the distances plumed recordes. Usually, the plumed output (distances.dat) contains one line per timestep, each line starting with the time.\nIf you calculate the averages yourself, you end up having only one line, but need to tell KIMMDY how long the timeframe was, which was averaged. To do this, make sure to write the duration of your averaged simulation in the time field like this for a 10ps simulation:\n#! FIELDS time d0 d1 d2 d3 d4\n10.000000 0.142401 0.151588 0.143725 0.156734 0.152581\nYou still need the plumed config file, even if KIMMDY does not execute plumed in the current example, as KIMMDY reads the filename of the plumed output from the plumed config." + "objectID": "guide/tutorials/write-plugin.html#making-a-python-package", + "href": "guide/tutorials/write-plugin.html#making-a-python-package", + "title": "Write a Reaction Plugin", + "section": "Making a python package", + "text": "Making a python package\nIt is necessary to make the plugin a python package to interface with Kimmdy. For this, package setup configuration files are necessary, for example setup.py and setup.cfg. In setup.cfg dependencies can be specified, which will be installed alongside the plugin. The interface with kimmdy is specified in the [options.entry_points] section. This section needs to refer to the class we created in the plugin main code and assign it to kimmdy.reaction_plugins, i.e. kimmdy.reaction_plugins = bind = <path>.<to>.<main file>:<ClassName>. Also, the directory containing the source code (typically src) is defined in [options.packages.find]. An example for setup.py and setup.cfg can be found below.\n\n\nsetup.py\nfrom setuptools import setup\n\nsetup()\n\n\n\n\nsetup.cfg\n\n\n\nsetup.cfg\n\n[metadata]\nname = kimmdy-reactions\nversion = 0.1\nlicense = GPL-3.0 \ndescription = Reaction template for KIMMDY\nlong_description = file: README.md\nauthor = Eric Hartmann\nauthor_email = eric.Hartmann@h-its.org\nclassifiers=\n Programming Language :: Python :: 3\n License :: OSI Approved :: MIT License\n Operating System :: OS Independent\n\n[options]\npackages = find:\npackage_dir =\n =src\ninclude_package_data = True\ninstall_requires =\n MDAnalysis\n\npython_requires = >= 3.9\n\n[options.packages.find]\nwhere=src\n\n[options.entry_points]\nkimmdy.reaction_plugins =\n bind = bind.reaction:BindReaction\n\n\nThe main code and configuration schema file should then be moved to the specified source directory in a directory that has the name of the reaction plugin, i.e. src/<plugin name>/.\n\n\n\n\n\n\nTip\n\n\n\nBy adding the kimmdy tag on GitHub you can make your plugin discoverable by other users. It will show up in this list" }, { - "objectID": "guide/how-to/contribute.html", - "href": "guide/how-to/contribute.html", - "title": "Contribute", + "objectID": "guide/tutorials/write-plugin.html#improving-code-quality-and-reproducibility", + "href": "guide/tutorials/write-plugin.html#improving-code-quality-and-reproducibility", + "title": "Write a Reaction Plugin", + "section": "Improving code quality and reproducibility", + "text": "Improving code quality and reproducibility\nAdding tests will help in ensuring the plugin is working as expected. An example would help users to understand what your plugin does." + }, + { + "objectID": "guide/references/input.html", + "href": "guide/references/input.html", + "title": "Input File", "section": "", - "text": "KIMMDY uses conventional commits and semantic versioning, automated via release please.\nIf a PR adds multiple commits, we use the squash and merge option to keep the commit history clean. If a PR unavoidably contains changes the message can be edited before merging to ensure release please picks up all changes.\nThe following example message (first line is the title in the GitHub UI, the rest is the body in the window below):\nGenerates the following changelog:" + "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml > Schema Store: Enable." }, { - "objectID": "guide/how-to/contribute.html#local-testing", - "href": "guide/how-to/contribute.html#local-testing", - "title": "Contribute", - "section": "Local testing", - "text": "Local testing\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, easiest option is with github cli\n\ninstall github cli (gh)\ngh extension install https://github.com/nektos/gh-act\n\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\n\ncustomize which python versions to test in tox.ini\nhtml coverage report is exported into artifacts" + "objectID": "guide/references/input.html#autocompletion", + "href": "guide/references/input.html#autocompletion", + "title": "Input File", + "section": "", + "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml > Schema Store: Enable." + }, + { + "objectID": "guide/references/input.html#all-options", + "href": "guide/references/input.html#all-options", + "title": "Input File", + "section": "All Options", + "text": "All Options\nThe following is a list of the options that can be set in the kimmdy.yml file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a .. * denotes an arbitrary name for a section. The key for a section is bold.\n\n\nTable 1: KIMMDY options\n\n\n\n\n\n\n\n\n\nOption\nDescription\nType\nDefault\n\n\n\n\n\ndryrun\nDon’t run the actual simulations, just print the tasks\nbool\nFalse\n\n\n\nwrite_checkpoint\nWrite checkpoints to continue a KIMMDY run from. Default True\nbool\nTrue\n\n\n\ncwd\nWorking directory. Default is current working directory\nPath\n\n\n\n\nname\nUsed for output folder if out is not specified\nstr\nkimmdy\n\n\n\nout\nOutput folder\nPath\n\n\n\n\nlog\nSettings for logging\n\n\n\n\n\nmax_tasks\nMaximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit.\nint\n0\n\n\n\nmax_hours\nStop KIMMDY after max_hours hours. Set this lower than the limit of your HPC cluster for use with a re-submit jobscript. 0 Means no limit.\nint\n0\n\n\n\nkmc\nKMC algorithm overwrite. Should be set by the reactions, but can be changed here.\nstr\n\n\n\n\ntau_scale\nScaling parameter for tau in the extrande kmc algorithm.\nfloat\n1.0\n\n\n\ntop\nTopology file\nPath\ntopol.top\n\n\n\ntopology\nSettings for handling the topology file.\n\n\n\n\n\ntopology.reactive.include\nExplicitly include a moleculetype or list of moleculetypes as a space-separated string.\nstr\n\n\n\n\ntopology.reactive.exclude\nExplicitly exclude a moleculetype or a list as a space-separated string. For example the lipid moleculetype in a bilayer simulation e.g. DPPC POPC'\nstr\n\n\n\n\ngro\nCoordinate file\nPath\nconf.gro\n\n\n\nndx\nGromaxs index file\nPath\nindex.ndx\n\n\n\ngromacs_alias\nGromacs alias. e.g. gmx or mpirun gmx_mpi\nstr\ngmx\n\n\n\ngmx_mdrun_flags\nFlags passed to gmx mdrun. Default -maxh 24 -dlb yes\nstr\n-maxh 24 -dlb yes\n\n\n\nff\nForce field directory (looks for .ff in cwd if not set)\nPath\n*.ff\n\n\n\nplumed\n.dat file containing plumed config\nPath\n\n\n\n\ntpr\n.tpr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\ntrr\n.trr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\nmds\nSettings for MD steps, e.g. mdp files, plumed files, etc.\n\n\n\n\n\nmds.*.mdp\nMDP file for the MD step\nPath\n\n\n\n\nmds.*.use_plumed\nWhether plumed should be used for this run or not\nbool\nFalse\n\n\n\nchanger\nSettings for applying a reaction recipe\n\n\n\n\n\nchanger.coordinates.md\nMD step from the ‘mds’ section that is used for relaxation MDs\nstr\n\n\n\n\nchanger.coordinates.slow_growth\nWhether the chosen MD step is a slow growth/free-energy simulation\nbool\nFalse\n\n\n\nchanger.topology.parameterization\nParameterization scheme that is used on the topology file after changes to it\nstr\nbasic\n\n\n\nsequence\nList of tasks. Each task can be a string (the name of the task) or an object with the task name and a multiplicity mult: <int>\nSequence\n\n\n\n\nreactions\nSettings for reactions\n\n\n\n\n\nplot_rates\nPlot the reaction rates during the reactions step\nbool\nTrue\n\n\n\nsave_recipes\nSave recipes as csv during the reactions step\nbool\nTrue" + }, + { + "objectID": "guide/references/input.html#example-kimmdy.yml-files", + "href": "guide/references/input.html#example-kimmdy.yml-files", + "title": "Input File", + "section": "Example kimmdy.yml Files", + "text": "Example kimmdy.yml Files\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow.mdp'\nchanger:\n coordinates:\n md: 'relax' \nreactions:\n hat_reaction:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions" }, { "objectID": "guide/how-to/install-ml-plugins.html", @@ -105,102 +126,102 @@ "text": "Complete Installation with ML Plugins\nconda is required for this installation to access the tensorflow and openmm packages. Solving the dependencies of the environment can overflow memory on the original conda solver. So we change the solver to the new libmamba. We also add the conda-forge channel to access the openmm package.\nconda install -n base conda-libmamba-solver\nconda config --set solver libmamba\nconda config --append channels conda-forge\nCreate a new environment.\nconda create -n kimmdy_full python=3.10 tensorflow==2.10 openmm\nconda activate kimmdy_full\nClone all repositories and install them in editable mode for development.\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ngit clone git@github.com:hits-mbm-dev/HAT_reaction_plugin.git\ngit clone git@github.com:hits-mbm-dev/grappa.git\n\npushd kimmdy\n# installs kimmdy, kimmdy-reactions and kimmdy-grappa\npip install -r requirements.txt\npopd\n\npushd HAT_reaction_plugin\npip install -r requirements.txt\npopd\n\npushd grappa\npip install -e .\npopd\n\nPotential problems when running\n\nopenmm can’t find the correct libstdc++.so.6\n\nsymlink system libstdc++.so.6 to the conda libstdc++.so.6\n\n\npushd $CONDA_PREFIX/lib\nmv libstdc++.so.6 libstdc++.so.6.old\nln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 libstdc++.so.6\npopd" }, { - "objectID": "guide/tutorials/getting-started.html", - "href": "guide/tutorials/getting-started.html", - "title": "Get Started", + "objectID": "guide/how-to/hcp.html", + "href": "guide/how-to/hcp.html", + "title": "High Performance Computing", "section": "", - "text": "In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water." + "text": "You need an installation of python (>= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same as --from-latest-checkpoint\nkimmdy -c" }, { - "objectID": "guide/tutorials/getting-started.html#installation", - "href": "guide/tutorials/getting-started.html#installation", - "title": "Get Started", - "section": "Installation", - "text": "Installation\n\nPrerequisites\n\npython3.9 or higher\ngromacs (tested with version 2021.4, gmx should be available in the PATH)\n\nOptional:\n\nplumed-patched version of gromacs (for the homolysis reaction).\n\n\n\n\n\n\n\n\n\n\n\nIf you plan to use our machine-learning plugins, take a look at the full installation instruction\n\n\nLet’s first create a directory and a virtual environment for kimmdy:\nmkdir kimmdy-tutorial\ncd kimmdy-tutorial\npython -m venv .venv\nsource .venv/bin/activate\nTo install KIMMDY, the builtin reaction plugins and the analysis tools use\npip install kimmdy[reactions,analysis]" + "objectID": "guide/how-to/hcp.html#setup", + "href": "guide/how-to/hcp.html#setup", + "title": "High Performance Computing", + "section": "", + "text": "You need an installation of python (>= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same as --from-latest-checkpoint\nkimmdy -c" }, { - "objectID": "guide/tutorials/getting-started.html#setup-the-simulation", - "href": "guide/tutorials/getting-started.html#setup-the-simulation", - "title": "Get Started", - "section": "Setup the Simulation", - "text": "Setup the Simulation\nDownload and unzip the input files to this directory.\nwget https://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started-files/setup.zip\nunzip setup.zip\nThe kimmdy.yml file should look like this:\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow.mdp'\nchanger:\n coordinates:\n md: 'relax' \nreactions:\n hat_reaction:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions\n\nOur starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.\n \n \n \nStart the KIMMDY run with the kimmdy command:" + "objectID": "guide/how-to/contribute.html", + "href": "guide/how-to/contribute.html", + "title": "Contribute", + "section": "", + "text": "KIMMDY uses conventional commits and semantic versioning, automated via release please.\nIf a PR adds multiple commits, we use the squash and merge option to keep the commit history clean. If a PR unavoidably contains changes the message can be edited before merging to ensure release please picks up all changes.\nThe following example message (first line is the title in the GitHub UI, the rest is the body in the window below):\nGenerates the following changelog:" }, { - "objectID": "guide/tutorials/getting-started.html#run-the-simulation", - "href": "guide/tutorials/getting-started.html#run-the-simulation", - "title": "Get Started", - "section": "Run the Simulation", - "text": "Run the Simulation\nkimmdy\nYou can also run kimmdy directly from python with\nfrom kimmdy.cmd import kimmdy_run\nkimmdy_run()\n\n\n\n\n\n\nTip\n\n\n\nKIMMDY parses your topology to generate its internal representation and writes out a new topology to be used in future steps. This topology includes everything gromacs needs to run the simulation, including forcefield parameters. KIMMDY combines all moleculetypes that are meant to take part in reactions into one moleculetype named “Reactive”. It also makes multiples explicit (e.g. 10 molecules of a peptide), such that each reactive atom has a unique representation. You can always find this topology in the output directory for the kimmdy setup task, e.g. alanine_hat_000/0_setup/<name-of-your-top.top. By default, everything that is not a solvent or ion is considered reactive. To exclude or include certain moleculetypes from this (e.g. in a lipid bilayer simulation), check out the topology.reactive options in the input file documentation. You can find another example of merging topologies in the topology explanation." + "objectID": "guide/how-to/contribute.html#local-testing", + "href": "guide/how-to/contribute.html#local-testing", + "title": "Contribute", + "section": "Local testing", + "text": "Local testing\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, easiest option is with github cli\n\ninstall github cli (gh)\ngh extension install https://github.com/nektos/gh-act\n\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\n\ncustomize which python versions to test in tox.ini\nhtml coverage report is exported into artifacts" }, { - "objectID": "guide/tutorials/getting-started.html#analyse-the-simulation", - "href": "guide/tutorials/getting-started.html#analyse-the-simulation", - "title": "Get Started", - "section": "Analyse the Simulation", - "text": "Analyse the Simulation\nConcatenate the trajectories from the individual steps into one for viewing:\nkimmdy-analysis trjcat alanine_hat_000 --open-vmd\nCheck the energy of the system:\nkimmdy-analysis energy alanine_hat_000 --open-plot --terms Potential Kinetic\n\n\n\nEnergy plot\n\n\nVisualize where the radicals end up:\nkimmdy-analysis radical_population alanine_hat_000 --open-plot --open-vmd\nIn VMD, color the atoms by beta factor to show the radical occupancy.\n\n\n\nVMD representation settings\n\n\n\n\n\nRadical population plot\n\n\nPlot the reaction rates:\nkimmdy-analysis rates alanine_hat_000\nIn the alanine_hat_000/analysis directory you will then find a plot of rates for each possible reaction at every step they were queried, e.g.\n\n\n\nReaction rates plot\n\n\nOr do all of the above directly from python:\nfrom kimmdy.analysis import concat_trj, plot_energy, radical_population, plot_rates\nconcat_trj('alanine_hat_000', open_vmd=True)\nplot_energy('alanine_hat_000', terms=['Potential', 'Kinetic'], open_plot=True)\nradical_population('alanine_hat_000', open_plot=True, open_vmd=True)\nplot_rates('alanine_hat_000')\nCongratulations, you have successfully run your first KIMMDY simulation!" + "objectID": "_reference/utils.html", + "href": "_reference/utils.html", + "title": "utils", + "section": "", + "text": "utils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nk_0\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\nkT\nfloat\nConstant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.\n2.479\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" }, { - "objectID": "guide/tutorials/getting-started.html#next-steps", - "href": "guide/tutorials/getting-started.html#next-steps", - "title": "Get Started", - "section": "Next steps", - "text": "Next steps\n\nLearn more about the kimmdy.yml input file\nRun KIMMDY with a collagen fibril from Colbuilder\nWrite your own reaction plugin\nDiscover more plugins by looking for the kimmdy tag on GitHub" + "objectID": "_reference/utils.html#attributes", + "href": "_reference/utils.html#attributes", + "title": "utils", + "section": "", + "text": "Name\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology." }, { - "objectID": "guide/tutorials/index.html", - "href": "guide/tutorials/index.html", - "title": "Tutorials", + "objectID": "_reference/utils.html#functions", + "href": "_reference/utils.html#functions", + "title": "utils", "section": "", - "text": "Tutorials to help you get familiar with KIMMDY.\n\n\n\n\n\n\n\n\n \n\n\n\n\nGet Started\n\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\n\n\nJannik Buhr\n\n\n\n\n\n\n \n\n\n\n\nRun KIMMDY from Colbuilder fibril\n\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\n \n\n\n\n\nWrite a Reaction Plugin\n\n\n\n\n\n\n\ndeveloper\n\n\n\n\nIn this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.\n\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\nNo matching items\n\n Back to top" + "text": "Name\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nk_0\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\nkT\nfloat\nConstant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.\n2.479\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" }, { - "objectID": "_reference/schema.html", - "href": "_reference/schema.html", - "title": "schema", + "objectID": "_reference/index.html", + "href": "_reference/index.html", + "title": "References", "section": "", - "text": "schema\nHandle the schema for the config file. To be used by the config module to validate the config file and set defaults for the Config object.\nReserved keywords: - pytype - default - description - type - required\n\n\n\n\n\nName\nDescription\n\n\n\n\nSequence\nA sequence of tasks.\n\n\n\n\n\nschema.Sequence(self, tasks)\nA sequence of tasks.\nTasks can be grouped together by using a dictionary with the following keys: - mult: number of times to repeat the tasks - tasks: list of tasks to repeat\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\ntasks\n\nlist of tasks\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nconvert_schema_to_dict\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\nflatten_scheme\nRecursively get properties and their desicripions from the scheme\n\n\ngenerate_markdown_table\nGenerate markdown table from scheme\n\n\nget_combined_scheme\nReturn the schema for the config file.\n\n\nload_kimmdy_schema\nReturn the schema for the config file\n\n\nload_plugin_schemas\nReturn the schemas for the reaction plugins known to kimmdy\n\n\nprune\nRemove empty dicts from a nested dict\n\n\n\n\n\nschema.convert_schema_to_dict(dictionary)\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndictionary\ndict\ndictionary from a raw json schema\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnested dictionary where each leaf entry is a dictionary with the\n“pytype”, “default” and “description” keys.\n\n\n\n\n\n\n\nschema.flatten_scheme(scheme, section='')\nRecursively get properties and their desicripions from the scheme\n\n\n\nschema.generate_markdown_table(scheme, append=False)\nGenerate markdown table from scheme\nUsed in documentation generation.\n\n\n\nschema.get_combined_scheme()\nReturn the schema for the config file.\nNested scheme where each leaf entry is a dictionary with the “pytype”, “default” and “description”. Contains the schema for the main kimmdy config file and all the plugins known at runtime.\n\n\n\nschema.load_kimmdy_schema()\nReturn the schema for the config file\n\n\n\nschema.load_plugin_schemas()\nReturn the schemas for the reaction plugins known to kimmdy\n\n\n\nschema.prune(d)\nRemove empty dicts from a nested dict" + "text": "Options of the main KIMMDY input file\n\n\n\nArguments of all KIMMDY parts.\n\n\n\nStart KIMMDY from a python script or the command line\n\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\n\n\n\n\nTopology modules\n\n\n\ntopology.topology\n\n\n\ntopology.ff\n\n\n\ntopology.utils\n\n\n\ntopology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc.\n\n\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n\n\nModules\n\n\n\nanalysis\nAnalysis tools for KIMMDY runs.\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\nconfig\nRead and validate kimmdy.yml configuration files\n\n\nconstants\nComstants used throughout KIMMDY\n\n\ncoordinates\ncoordinate, topology and plumed modification functions\n\n\nkmc\nKinetic Monte Carlo (KMC) classes and functions.\n\n\nparsing\nAll read_<…> and write_<…> functions.\n\n\nplugins\nPlugin base classes and basic instances thereof.\n\n\nrecipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\nrunmanager\nThe Runmanager is the main entry point of the program.\n\n\nschema\nHandle the schema for the config file.\n\n\ntasks\nThe tasks module holds the TaskFiles class which organizes input and\n\n\ntools\nStandalone tools that are complementary to KIMMDY.\n\n\nutils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\n\nReaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY\n\n\n\nhomolysis.reaction.Homolysis\nHomolytic bond breaking leading to 2 radicals.\n\n\nhat_naive.reaction.NaiveHAT\nNaive HAT reaction, selects hydrogens at random\n\n\ndummyreaction.reaction.DummyReaction\nDummy reaction, returns empty RecipeCollection" }, { - "objectID": "_reference/schema.html#classes", - "href": "_reference/schema.html#classes", - "title": "schema", + "objectID": "_reference/index.html#input-file", + "href": "_reference/index.html#input-file", + "title": "References", "section": "", - "text": "Name\nDescription\n\n\n\n\nSequence\nA sequence of tasks.\n\n\n\n\n\nschema.Sequence(self, tasks)\nA sequence of tasks.\nTasks can be grouped together by using a dictionary with the following keys: - mult: number of times to repeat the tasks - tasks: list of tasks to repeat\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\ntasks\n\nlist of tasks" + "text": "Options of the main KIMMDY input file" }, { - "objectID": "_reference/schema.html#functions", - "href": "_reference/schema.html#functions", - "title": "schema", + "objectID": "_reference/index.html#command-line-interface", + "href": "_reference/index.html#command-line-interface", + "title": "References", "section": "", - "text": "Name\nDescription\n\n\n\n\nconvert_schema_to_dict\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\nflatten_scheme\nRecursively get properties and their desicripions from the scheme\n\n\ngenerate_markdown_table\nGenerate markdown table from scheme\n\n\nget_combined_scheme\nReturn the schema for the config file.\n\n\nload_kimmdy_schema\nReturn the schema for the config file\n\n\nload_plugin_schemas\nReturn the schemas for the reaction plugins known to kimmdy\n\n\nprune\nRemove empty dicts from a nested dict\n\n\n\n\n\nschema.convert_schema_to_dict(dictionary)\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndictionary\ndict\ndictionary from a raw json schema\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnested dictionary where each leaf entry is a dictionary with the\n“pytype”, “default” and “description” keys.\n\n\n\n\n\n\n\nschema.flatten_scheme(scheme, section='')\nRecursively get properties and their desicripions from the scheme\n\n\n\nschema.generate_markdown_table(scheme, append=False)\nGenerate markdown table from scheme\nUsed in documentation generation.\n\n\n\nschema.get_combined_scheme()\nReturn the schema for the config file.\nNested scheme where each leaf entry is a dictionary with the “pytype”, “default” and “description”. Contains the schema for the main kimmdy config file and all the plugins known at runtime.\n\n\n\nschema.load_kimmdy_schema()\nReturn the schema for the config file\n\n\n\nschema.load_plugin_schemas()\nReturn the schemas for the reaction plugins known to kimmdy\n\n\n\nschema.prune(d)\nRemove empty dicts from a nested dict" + "text": "Arguments of all KIMMDY parts." }, { - "objectID": "_reference/homolysis.reaction.Homolysis.html", - "href": "_reference/homolysis.reaction.Homolysis.html", - "title": "homolysis.reaction.Homolysis", + "objectID": "_reference/index.html#python-api", + "href": "_reference/index.html#python-api", + "title": "References", "section": "", - "text": "homolysis.reaction.Homolysis\nreaction.Homolysis(self, name, runmng)\nHomolytic bond breaking leading to 2 radicals. Implementation for time-varying rates\n\n\n\n\n Back to top" + "text": "Start KIMMDY from a python script or the command line\n\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line." }, { - "objectID": "_reference/topology.topology.html", - "href": "_reference/topology.topology.html", - "title": "topology.topology", + "objectID": "_reference/index.html#topology", + "href": "_reference/index.html#topology", + "title": "References", "section": "", - "text": "topology.topology\n\n\n\n\n\nName\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -> new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored.\n\n\n\ntopology.topology.Topology.validate_bond(atm1, atm2)\nValidates bond consistency between both atoms and top Returns True if bond exists, False if not. Raises RuntimeError if bond is not consistent." + "text": "Topology modules\n\n\n\ntopology.topology\n\n\n\ntopology.ff\n\n\n\ntopology.utils\n\n\n\ntopology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc.\n\n\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top." }, { - "objectID": "_reference/topology.topology.html#classes", - "href": "_reference/topology.topology.html#classes", - "title": "topology.topology", + "objectID": "_reference/index.html#modules", + "href": "_reference/index.html#modules", + "title": "References", "section": "", - "text": "Name\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -> new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored.\n\n\n\ntopology.topology.Topology.validate_bond(atm1, atm2)\nValidates bond consistency between both atoms and top Returns True if bond exists, False if not. Raises RuntimeError if bond is not consistent." + "text": "Modules\n\n\n\nanalysis\nAnalysis tools for KIMMDY runs.\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\nconfig\nRead and validate kimmdy.yml configuration files\n\n\nconstants\nComstants used throughout KIMMDY\n\n\ncoordinates\ncoordinate, topology and plumed modification functions\n\n\nkmc\nKinetic Monte Carlo (KMC) classes and functions.\n\n\nparsing\nAll read_<…> and write_<…> functions.\n\n\nplugins\nPlugin base classes and basic instances thereof.\n\n\nrecipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\nrunmanager\nThe Runmanager is the main entry point of the program.\n\n\nschema\nHandle the schema for the config file.\n\n\ntasks\nThe tasks module holds the TaskFiles class which organizes input and\n\n\ntools\nStandalone tools that are complementary to KIMMDY.\n\n\nutils\nUtilities for building plugins, shell convenience functions and GROMACS related functions" }, { - "objectID": "_reference/hat_naive.reaction.NaiveHAT.html", - "href": "_reference/hat_naive.reaction.NaiveHAT.html", - "title": "hat_naive.reaction.NaiveHAT", + "objectID": "_reference/index.html#reaction-plugins", + "href": "_reference/index.html#reaction-plugins", + "title": "References", "section": "", - "text": "hat_naive.reaction.NaiveHAT\nreaction.NaiveHAT(self, name, runmng)\nNaive HAT reaction, selects hydrogens at random\n\n\n\n\n Back to top" + "text": "Reaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY\n\n\n\nhomolysis.reaction.Homolysis\nHomolytic bond breaking leading to 2 radicals.\n\n\nhat_naive.reaction.NaiveHAT\nNaive HAT reaction, selects hydrogens at random\n\n\ndummyreaction.reaction.DummyReaction\nDummy reaction, returns empty RecipeCollection" }, { "objectID": "_reference/topology.ff.html", @@ -216,26 +237,82 @@ "section": "", "text": "Name\nDescription\n\n\n\n\nFF\nContainer for parsed forcefield data.\n\n\n\n\n\ntopology.ff.FF(self, top, residuetypes_path=None)\nContainer for parsed forcefield data." }, + { + "objectID": "_reference/parsing.html", + "href": "_reference/parsing.html", + "title": "parsing", + "section": "", + "text": "parsing\nAll read_<…> and write_<…> functions.\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nJSONEncoder\nEncoder that enables writing JSONs with numpy types.\n\n\nPlumed_dict\nDict representation of a plumed.dat file.\n\n\n\n\n\nparsing.JSONEncoder()\nEncoder that enables writing JSONs with numpy types.\n\n\n\nparsing.Plumed_dict()\nDict representation of a plumed.dat file.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n 'C',\n '1',\n 'URE',\n 'C',\n '1',\n '0.880229',\n '12.01000'],\n ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'bonds': {'content': [['1', '2'],\n ['1', '3'],\n ['1', '6'],\n ['3', '4'],\n ['3', '5'],\n ['6', '7'],\n ['6', '8']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n ['2', '1', '3', '5', '9'],\n ['2', '1', '6', '7', '9'],\n ['2', '1', '6', '8', '9'],\n ['3', '1', '6', '7', '9'],\n ['3', '1', '6', '8', '9'],\n ['6', '1', '3', '4', '9'],\n ['6', '1', '3', '5', '9'],\n ['3', '6', '1', '2', '4'],\n ['1', '4', '3', '5', '4'],\n ['1', '7', '6', '8', '4']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n ['2', '1', '1000', '0', '1000'],\n ['3', '1', '1000', '0', '0']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedral_restraints': {'content': [['3',\n '6',\n '1',\n '2',\n '1',\n '180',\n '0',\n '10'],\n ['1', '4', '3', '5', '1', '180', '0', '10']],\n 'else_content': [],\n 'extra': [],\n 'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\nparsing.write_top(top, outfile)\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nRaw dictionary represenation of the topology.\nrequired\n\n\noutfile\nPath\nPath to the topology file to write to.\nrequired" + }, + { + "objectID": "_reference/parsing.html#attributes", + "href": "_reference/parsing.html#attributes", + "title": "parsing", + "section": "", + "text": "Name\nDescription\n\n\n\n\nTopologyDict\nA raw representation of a topology file returned by read_top." + }, + { + "objectID": "_reference/parsing.html#classes", + "href": "_reference/parsing.html#classes", + "title": "parsing", + "section": "", + "text": "Name\nDescription\n\n\n\n\nJSONEncoder\nEncoder that enables writing JSONs with numpy types.\n\n\nPlumed_dict\nDict representation of a plumed.dat file.\n\n\n\n\n\nparsing.JSONEncoder()\nEncoder that enables writing JSONs with numpy types.\n\n\n\nparsing.Plumed_dict()\nDict representation of a plumed.dat file." + }, + { + "objectID": "_reference/parsing.html#functions", + "href": "_reference/parsing.html#functions", + "title": "parsing", + "section": "", + "text": "Name\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n 'C',\n '1',\n 'URE',\n 'C',\n '1',\n '0.880229',\n '12.01000'],\n ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'bonds': {'content': [['1', '2'],\n ['1', '3'],\n ['1', '6'],\n ['3', '4'],\n ['3', '5'],\n ['6', '7'],\n ['6', '8']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n ['2', '1', '3', '5', '9'],\n ['2', '1', '6', '7', '9'],\n ['2', '1', '6', '8', '9'],\n ['3', '1', '6', '7', '9'],\n ['3', '1', '6', '8', '9'],\n ['6', '1', '3', '4', '9'],\n ['6', '1', '3', '5', '9'],\n ['3', '6', '1', '2', '4'],\n ['1', '4', '3', '5', '4'],\n ['1', '7', '6', '8', '4']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n ['2', '1', '1000', '0', '1000'],\n ['3', '1', '1000', '0', '0']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedral_restraints': {'content': [['3',\n '6',\n '1',\n '2',\n '1',\n '180',\n '0',\n '10'],\n ['1', '4', '3', '5', '1', '180', '0', '10']],\n 'else_content': [],\n 'extra': [],\n 'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\nparsing.write_top(top, outfile)\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nRaw dictionary represenation of the topology.\nrequired\n\n\noutfile\nPath\nPath to the topology file to write to.\nrequired" + }, + { + "objectID": "_reference/topology.topology.html", + "href": "_reference/topology.topology.html", + "title": "topology.topology", + "section": "", + "text": "topology.topology\n\n\n\n\n\nName\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -> new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored.\n\n\n\ntopology.topology.Topology.validate_bond(atm1, atm2)\nValidates bond consistency between both atoms and top Returns True if bond exists, False if not. Raises RuntimeError if bond is not consistent." + }, + { + "objectID": "_reference/topology.topology.html#classes", + "href": "_reference/topology.topology.html#classes", + "title": "topology.topology", + "section": "", + "text": "Name\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -> new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored.\n\n\n\ntopology.topology.Topology.validate_bond(atm1, atm2)\nValidates bond consistency between both atoms and top Returns True if bond exists, False if not. Raises RuntimeError if bond is not consistent." + }, + { + "objectID": "_reference/homolysis.reaction.Homolysis.html", + "href": "_reference/homolysis.reaction.Homolysis.html", + "title": "homolysis.reaction.Homolysis", + "section": "", + "text": "homolysis.reaction.Homolysis\nreaction.Homolysis(self, name, runmng)\nHomolytic bond breaking leading to 2 radicals. Implementation for time-varying rates\n\n\n\n\n Back to top" + }, + { + "objectID": "_reference/dummyreaction.reaction.DummyReaction.html", + "href": "_reference/dummyreaction.reaction.DummyReaction.html", + "title": "dummyreaction.reaction.DummyReaction", + "section": "", + "text": "dummyreaction.reaction.DummyReaction\nreaction.DummyReaction(self, name, runmng)\nDummy reaction, returns empty RecipeCollection\n\n\n\n\n Back to top" + }, { "objectID": "_reference/coordinates.html", "href": "_reference/coordinates.html", "title": "coordinates", "section": "", - "text": "coordinates\ncoordinate, topology and plumed modification functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff, focus_nr=None)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB, focus_nr=None)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory" + "text": "coordinates\ncoordinate, topology and plumed modification functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory" }, { "objectID": "_reference/coordinates.html#functions", "href": "_reference/coordinates.html#functions", "title": "coordinates", "section": "", - "text": "Name\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff, focus_nr=None)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB, focus_nr=None)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory" + "text": "Name\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory" }, { "objectID": "_reference/runmanager.html", "href": "_reference/runmanager.html", "title": "runmanager", "section": "", - "text": "runmanager\nThe Runmanager is the main entry point of the program.\nIt manages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nDescription\n\n\n\n\nRunManager\nThe Runmanager is the main entry point of the program.\n\n\nState\nState of the system.\n\n\n\n\n\nrunmanager.RunManager(self, config)\nThe Runmanager is the main entry point of the program.\nManages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nconfig\nConfig\nThe configuration object.\n\n\nfrom_checkpoint\nbool\nWhether the runmanager was initialized from a checkpoint.\n\n\ntasks\nqueue.Queue[Task]\nTasks from config.\n\n\ncrr_tasks\nqueue.Queue[Task]\nCurrent tasks.\n\n\niteration\nint\nCurrent iteration.\n\n\nstate\nState\nCurrent state of the system.\n\n\nrecipe_collection\nRecipeCollection\nCollection of recipes.\n\n\nlatest_files\ndict[str, Path]\nDictionary of latest files.\n\n\nhistfile\nPath\nPath to history file.\n\n\ncptfile\nPath\nPath to checkpoint file.\n\n\ntop\n\nTopology object.\n\n\nfilehist\nlist[dict[str, TaskFiles]]\nList of dictionaries of TaskFiles.\n\n\ntask_mapping\n\nMapping of task names to runmanager methods.\n\n\nreaction_plugins\nlist[ReactionPlugin]\nList of initialized reaction plugins used in the sequence.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_latest\nReturns path to latest file of given type.\n\n\nwrite_one_checkpoint\nJust write the first checkpoint and then exit\n\n\n\n\n\nrunmanager.RunManager.get_latest(suffix)\nReturns path to latest file of given type.\nFor .dat files (in general ambiguous extensions) use full file name. Errors if file is not found.\n\n\n\nrunmanager.RunManager.write_one_checkpoint()\nJust write the first checkpoint and then exit\nUsed to generate a starting point for jobscripts on hpc clusters that can easily self-submit after a timelimit was exceeded.\n\n\n\n\n\nrunmanager.State()\nState of the system. one of IDLE, MD, REACTION, SETUP, DONE.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_existing_files\nInitialize latest_files with every existing file defined in config\n\n\n\n\n\nrunmanager.get_existing_files(config, section='root')\nInitialize latest_files with every existing file defined in config" + "text": "runmanager\nThe Runmanager is the main entry point of the program.\nIt manages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nDescription\n\n\n\n\nRunManager\nThe Runmanager is the main entry point of the program.\n\n\nState\nState of the system.\n\n\n\n\n\nrunmanager.RunManager(self, config)\nThe Runmanager is the main entry point of the program.\nManages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nconfig\nConfig\nThe configuration object.\n\n\nfrom_checkpoint\nbool\nWhether the runmanager was initialized from a checkpoint.\n\n\ntasks\nqueue.Queue[Task]\nTasks from config.\n\n\ncrr_tasks\nqueue.Queue[Task]\nCurrent tasks.\n\n\niteration\nint\nCurrent iteration.\n\n\nstate\nState\nCurrent state of the system.\n\n\nrecipe_collection\nRecipeCollection\nCollection of recipes.\n\n\nlatest_files\ndict[str, Path]\nDictionary of latest files.\n\n\nhistfile\nPath\nPath to history file.\n\n\ncptfile\nPath\nPath to checkpoint file.\n\n\ntop\n\nTopology object.\n\n\nfilehist\nlist[dict[str, TaskFiles]]\nList of dictionaries of TaskFiles.\n\n\ntask_mapping\n\nMapping of task names to runmanager methods.\n\n\nreaction_plugins\nlist[ReactionPlugin]\nList of initialized reaction plugins used in the sequence.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_latest\nReturns path to latest file of given type.\n\n\nwrite_one_checkpoint\nJust write the first checkpoint and then exit\n\n\n\n\n\nrunmanager.RunManager.get_latest(suffix)\nReturns path to latest file of given type.\nFor .dat files (in general ambiguous extensions) use full file name. Errors if file is not found.\n\n\n\nrunmanager.RunManager.write_one_checkpoint()\nJust write the first checkpoint and then exit\nUsed to generate a starting point for jobscripts on hpc clusters that can easily self-submit after a timelimit was exceeded.\n\n\n\n\n\nrunmanager.State()\nState of the system. one of IDLE, MD, REACTION, SETUP, DONE.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_existing_files\nInitialize latest_files with every existing file defined in config\n\n\n\n\n\nrunmanager.get_existing_files(config)\nInitialize latest_files with every existing file defined in config" }, { "objectID": "_reference/runmanager.html#classes", @@ -249,91 +326,56 @@ "href": "_reference/runmanager.html#functions", "title": "runmanager", "section": "", - "text": "Name\nDescription\n\n\n\n\nget_existing_files\nInitialize latest_files with every existing file defined in config\n\n\n\n\n\nrunmanager.get_existing_files(config, section='root')\nInitialize latest_files with every existing file defined in config" - }, - { - "objectID": "_reference/kmc.html", - "href": "_reference/kmc.html", - "title": "kmc", - "section": "", - "text": "kmc\nKinetic Monte Carlo (KMC) classes and functions.\nIn our system, the reaction rate r = (deterministic) reaction constant k = stochastic reaction constant c (from gillespie 1977) = propensity a (from Anderson 2007) because of the fundamental premise of chemical kinetics and because we have one reactant molecule\n\n\n\n\n\nName\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()" - }, - { - "objectID": "_reference/kmc.html#classes", - "href": "_reference/kmc.html#classes", - "title": "kmc", - "section": "", - "text": "Name\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]" - }, - { - "objectID": "_reference/kmc.html#functions", - "href": "_reference/kmc.html#functions", - "title": "kmc", - "section": "", - "text": "Name\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()" - }, - { - "objectID": "_reference/analysis.html", - "href": "_reference/analysis.html", - "title": "analysis", - "section": "", - "text": "analysis\nAnalysis tools for KIMMDY runs. For command line usage, run kimmdy-analysis -h.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nget_step_directories\ncreate list of subdirectories that match the steps.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nplot_runtime\nPlot runtime of all tasks.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot runtime of all tasks.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.get_step_directories(dir, steps='all')\ncreate list of subdirectories that match the steps. If steps is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nmd_tasks\nlist\nNames of MD tasks to color\nrequired\n\n\ndatefmt\nstr\nDate format in the KIMMDY logfile\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse" - }, - { - "objectID": "_reference/analysis.html#functions", - "href": "_reference/analysis.html#functions", - "title": "analysis", - "section": "", - "text": "Name\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nget_step_directories\ncreate list of subdirectories that match the steps.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nplot_runtime\nPlot runtime of all tasks.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot runtime of all tasks.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.get_step_directories(dir, steps='all')\ncreate list of subdirectories that match the steps. If steps is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nmd_tasks\nlist\nNames of MD tasks to color\nrequired\n\n\ndatefmt\nstr\nDate format in the KIMMDY logfile\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse" + "text": "Name\nDescription\n\n\n\n\nget_existing_files\nInitialize latest_files with every existing file defined in config\n\n\n\n\n\nrunmanager.get_existing_files(config)\nInitialize latest_files with every existing file defined in config" }, { - "objectID": "_reference/tasks.html", - "href": "_reference/tasks.html", - "title": "tasks", + "objectID": "_reference/plugins.html", + "href": "_reference/plugins.html", + "title": "plugins", "section": "", - "text": "tasks\nThe tasks module holds the TaskFiles class which organizes input and output paths and the Task class for steps in the runmanager.\n\n\n\n\n\nName\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n>>> class run():\n>>> def get_latest(self, s):\n>>> return f\"latest {s}\"\n>>> runmng = run()\n>>> files = TaskFiles(runmng)\n>>> files.input\n>>> files.input[\"top\"]\n{'top': 'latest top'}\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue)." + "text": "plugins\nPlugin base classes and basic instances thereof.\nAlso discovers and loads KIMMDY plugins.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired" }, { - "objectID": "_reference/tasks.html#classes", - "href": "_reference/tasks.html#classes", - "title": "tasks", + "objectID": "_reference/plugins.html#classes", + "href": "_reference/plugins.html#classes", + "title": "plugins", "section": "", - "text": "Name\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n>>> class run():\n>>> def get_latest(self, s):\n>>> return f\"latest {s}\"\n>>> runmng = run()\n>>> files = TaskFiles(runmng)\n>>> files.input\n>>> files.input[\"top\"]\n{'top': 'latest top'}" + "text": "Name\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired" }, { - "objectID": "_reference/tasks.html#functions", - "href": "_reference/tasks.html#functions", - "title": "tasks", + "objectID": "_reference/tools.html", + "href": "_reference/tools.html", + "title": "tools", "section": "", - "text": "Name\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue)." + "text": "tools\nStandalone tools that are complementary to KIMMDY.\n\n\n\n\n\nName\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto." }, { - "objectID": "_reference/utils.html", - "href": "_reference/utils.html", - "title": "utils", + "objectID": "_reference/tools.html#functions", + "href": "_reference/tools.html#functions", + "title": "tools", "section": "", - "text": "utils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nk_0\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\nkT\nfloat\nConstant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.\n2.479\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" + "text": "Name\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto." }, { - "objectID": "_reference/utils.html#attributes", - "href": "_reference/utils.html#attributes", - "title": "utils", + "objectID": "_reference/schema.html", + "href": "_reference/schema.html", + "title": "schema", "section": "", - "text": "Name\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology." + "text": "schema\nHandle the schema for the config file. To be used by the config module to validate the config file and set defaults for the Config object.\nReserved keywords: - pytype - default - description - type - required\n\n\n\n\n\nName\nDescription\n\n\n\n\nSequence\nA sequence of tasks.\n\n\n\n\n\nschema.Sequence(self, tasks)\nA sequence of tasks.\nTasks can be grouped together by using a dictionary with the following keys: - mult: number of times to repeat the tasks - tasks: list of tasks to repeat\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\ntasks\n\nlist of tasks\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nconvert_schema_to_dict\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\nflatten_scheme\nRecursively get properties and their desicripions from the scheme\n\n\ngenerate_markdown_table\nGenerate markdown table from scheme\n\n\nget_combined_scheme\nReturn the schema for the config file.\n\n\nload_kimmdy_schema\nReturn the schema for the config file\n\n\nload_plugin_schemas\nReturn the schemas for the reaction plugins known to kimmdy\n\n\nprune\nRemove empty dicts from a nested dict\n\n\n\n\n\nschema.convert_schema_to_dict(dictionary)\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndictionary\ndict\ndictionary from a raw json schema\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnested dictionary where each leaf entry is a dictionary with the\n“pytype”, “default” and “description” keys.\n\n\n\n\n\n\n\nschema.flatten_scheme(scheme, section='')\nRecursively get properties and their desicripions from the scheme\n\n\n\nschema.generate_markdown_table(scheme, append=False)\nGenerate markdown table from scheme\nUsed in documentation generation.\n\n\n\nschema.get_combined_scheme()\nReturn the schema for the config file.\nNested scheme where each leaf entry is a dictionary with the “pytype”, “default” and “description”. Contains the schema for the main kimmdy config file and all the plugins known at runtime.\n\n\n\nschema.load_kimmdy_schema()\nReturn the schema for the config file\n\n\n\nschema.load_plugin_schemas()\nReturn the schemas for the reaction plugins known to kimmdy\n\n\n\nschema.prune(d)\nRemove empty dicts from a nested dict" }, { - "objectID": "_reference/utils.html#functions", - "href": "_reference/utils.html#functions", - "title": "utils", + "objectID": "_reference/schema.html#classes", + "href": "_reference/schema.html#classes", + "title": "schema", "section": "", - "text": "Name\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nk_0\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\nkT\nfloat\nConstant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.\n2.479\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired" + "text": "Name\nDescription\n\n\n\n\nSequence\nA sequence of tasks.\n\n\n\n\n\nschema.Sequence(self, tasks)\nA sequence of tasks.\nTasks can be grouped together by using a dictionary with the following keys: - mult: number of times to repeat the tasks - tasks: list of tasks to repeat\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\ntasks\n\nlist of tasks" }, { - "objectID": "_reference/parsing.TopologyDict.html", - "href": "_reference/parsing.TopologyDict.html", - "title": "parsing.TopologyDict", + "objectID": "_reference/schema.html#functions", + "href": "_reference/schema.html#functions", + "title": "schema", "section": "", - "text": "parsing.TopologyDict\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n Back to top" + "text": "Name\nDescription\n\n\n\n\nconvert_schema_to_dict\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\nflatten_scheme\nRecursively get properties and their desicripions from the scheme\n\n\ngenerate_markdown_table\nGenerate markdown table from scheme\n\n\nget_combined_scheme\nReturn the schema for the config file.\n\n\nload_kimmdy_schema\nReturn the schema for the config file\n\n\nload_plugin_schemas\nReturn the schemas for the reaction plugins known to kimmdy\n\n\nprune\nRemove empty dicts from a nested dict\n\n\n\n\n\nschema.convert_schema_to_dict(dictionary)\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndictionary\ndict\ndictionary from a raw json schema\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnested dictionary where each leaf entry is a dictionary with the\n“pytype”, “default” and “description” keys.\n\n\n\n\n\n\n\nschema.flatten_scheme(scheme, section='')\nRecursively get properties and their desicripions from the scheme\n\n\n\nschema.generate_markdown_table(scheme, append=False)\nGenerate markdown table from scheme\nUsed in documentation generation.\n\n\n\nschema.get_combined_scheme()\nReturn the schema for the config file.\nNested scheme where each leaf entry is a dictionary with the “pytype”, “default” and “description”. Contains the schema for the main kimmdy config file and all the plugins known at runtime.\n\n\n\nschema.load_kimmdy_schema()\nReturn the schema for the config file\n\n\n\nschema.load_plugin_schemas()\nReturn the schemas for the reaction plugins known to kimmdy\n\n\n\nschema.prune(d)\nRemove empty dicts from a nested dict" }, { "objectID": "index.html", @@ -371,109 +413,53 @@ "text": "Clone kimmdy and the default reaction and parameterization plugins and install requirements and kimmdy as editable via\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ncd kimmdy\npython -m venv .venv\nsource ./venv/bin/activate\npip install -r requirements.txt\nConventions:\n\ncode style: black\ndocstrings: numpy\nConventional commit messages when possible for pretty release notes.\n\n\n\n\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, the easiest option is with github cli via gh extension install https://github.com/nektos/gh-act\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\nhtml coverage report is exported into artifacts" }, { - "objectID": "_reference/cmd.html", - "href": "_reference/cmd.html", - "title": "cmd", - "section": "", - "text": "cmd\nFunctions for starting KIMMDY either from python or the command line. Other entry points such as kimmdy-analysis also live here.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, checkpoint='', show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\ncheckpoint\nstr\nFile path of a kimmdy.cpt file to restart KIMMDY from a checkpoint. If a directory is given, the file kimmdy.cpt in that directory is used.\n''\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse" - }, - { - "objectID": "_reference/cmd.html#functions", - "href": "_reference/cmd.html#functions", - "title": "cmd", - "section": "", - "text": "Name\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, checkpoint='', show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\ncheckpoint\nstr\nFile path of a kimmdy.cpt file to restart KIMMDY from a checkpoint. If a directory is given, the file kimmdy.cpt in that directory is used.\n''\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse" - }, - { - "objectID": "_reference/constants.html", - "href": "_reference/constants.html", - "title": "constants", - "section": "", - "text": "constants\nComstants used throughout KIMMDY\n\n\n\n\n\nName\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical." - }, - { - "objectID": "_reference/constants.html#attributes", - "href": "_reference/constants.html#attributes", - "title": "constants", - "section": "", - "text": "Name\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical." - }, - { - "objectID": "_reference/index.html", - "href": "_reference/index.html", - "title": "References", - "section": "", - "text": "Options of the main KIMMDY input file\n\n\n\nArguments of all KIMMDY parts.\n\n\n\nStart KIMMDY from a python script or the command line\n\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\n\n\n\n\nTopology modules\n\n\n\ntopology.topology\n\n\n\ntopology.ff\n\n\n\ntopology.utils\n\n\n\ntopology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc.\n\n\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n\n\nModules\n\n\n\nanalysis\nAnalysis tools for KIMMDY runs.\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\nconfig\nRead and validate kimmdy.yml configuration files\n\n\nconstants\nComstants used throughout KIMMDY\n\n\ncoordinates\ncoordinate, topology and plumed modification functions\n\n\nkmc\nKinetic Monte Carlo (KMC) classes and functions.\n\n\nparsing\nAll read_<…> and write_<…> functions.\n\n\nplugins\nPlugin base classes and basic instances thereof.\n\n\nrecipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\nrunmanager\nThe Runmanager is the main entry point of the program.\n\n\nschema\nHandle the schema for the config file.\n\n\ntasks\nThe tasks module holds the TaskFiles class which organizes input and\n\n\ntools\nStandalone tools that are complementary to KIMMDY.\n\n\nutils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\n\nReaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY\n\n\n\nhomolysis.reaction.Homolysis\nHomolytic bond breaking leading to 2 radicals.\n\n\nhat_naive.reaction.NaiveHAT\nNaive HAT reaction, selects hydrogens at random\n\n\ndummyreaction.reaction.DummyReaction\nDummy reaction, returns empty RecipeCollection" - }, - { - "objectID": "_reference/index.html#input-file", - "href": "_reference/index.html#input-file", - "title": "References", - "section": "", - "text": "Options of the main KIMMDY input file" - }, - { - "objectID": "_reference/index.html#command-line-interface", - "href": "_reference/index.html#command-line-interface", - "title": "References", - "section": "", - "text": "Arguments of all KIMMDY parts." - }, - { - "objectID": "_reference/index.html#python-api", - "href": "_reference/index.html#python-api", - "title": "References", + "objectID": "_reference/analysis.html", + "href": "_reference/analysis.html", + "title": "analysis", "section": "", - "text": "Start KIMMDY from a python script or the command line\n\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line." + "text": "analysis\nAnalysis tools for KIMMDY runs. For command line usage, run kimmdy-analysis -h.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nget_step_directories\ncreate list of subdirectories that match the steps.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nplot_runtime\nPlot runtime of all tasks.\n\n\nradical_migration\nPlot population of radicals for a KIMMDY run.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot runtime of all tasks.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\noutput_group\nOptional[str]\nindex group for output. Default is “Protein” for xtc and “System” for trr.\nNone\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.get_step_directories(dir, steps='all')\ncreate list of subdirectories that match the steps. If steps is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nmd_tasks\nlist\nNames of MD tasks to color\nrequired\n\n\ndatefmt\nstr\nDate format in the KIMMDY logfile\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.radical_migration(dirs, type='qualitative', cutoff=1)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndirs\nlist[str]\nKIMMDY run directories to be analysed.\nrequired\n\n\ntype\nstr\nHow to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,\n'qualitative'\n\n\ncutoff\nint\nIgnore migration between two atoms if it happened less often than the specified value.\n1\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse" }, { - "objectID": "_reference/index.html#topology", - "href": "_reference/index.html#topology", - "title": "References", + "objectID": "_reference/analysis.html#functions", + "href": "_reference/analysis.html#functions", + "title": "analysis", "section": "", - "text": "Topology modules\n\n\n\ntopology.topology\n\n\n\ntopology.ff\n\n\n\ntopology.utils\n\n\n\ntopology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc.\n\n\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top." + "text": "Name\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nget_step_directories\ncreate list of subdirectories that match the steps.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nplot_runtime\nPlot runtime of all tasks.\n\n\nradical_migration\nPlot population of radicals for a KIMMDY run.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot runtime of all tasks.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\noutput_group\nOptional[str]\nindex group for output. Default is “Protein” for xtc and “System” for trr.\nNone\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.get_step_directories(dir, steps='all')\ncreate list of subdirectories that match the steps. If steps is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nmd_tasks\nlist\nNames of MD tasks to color\nrequired\n\n\ndatefmt\nstr\nDate format in the KIMMDY logfile\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.radical_migration(dirs, type='qualitative', cutoff=1)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndirs\nlist[str]\nKIMMDY run directories to be analysed.\nrequired\n\n\ntype\nstr\nHow to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,\n'qualitative'\n\n\ncutoff\nint\nIgnore migration between two atoms if it happened less often than the specified value.\n1\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse" }, { - "objectID": "_reference/index.html#modules", - "href": "_reference/index.html#modules", - "title": "References", - "section": "", - "text": "Modules\n\n\n\nanalysis\nAnalysis tools for KIMMDY runs.\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\nconfig\nRead and validate kimmdy.yml configuration files\n\n\nconstants\nComstants used throughout KIMMDY\n\n\ncoordinates\ncoordinate, topology and plumed modification functions\n\n\nkmc\nKinetic Monte Carlo (KMC) classes and functions.\n\n\nparsing\nAll read_<…> and write_<…> functions.\n\n\nplugins\nPlugin base classes and basic instances thereof.\n\n\nrecipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\nrunmanager\nThe Runmanager is the main entry point of the program.\n\n\nschema\nHandle the schema for the config file.\n\n\ntasks\nThe tasks module holds the TaskFiles class which organizes input and\n\n\ntools\nStandalone tools that are complementary to KIMMDY.\n\n\nutils\nUtilities for building plugins, shell convenience functions and GROMACS related functions" - }, - { - "objectID": "_reference/index.html#reaction-plugins", - "href": "_reference/index.html#reaction-plugins", - "title": "References", + "objectID": "_reference/config.html", + "href": "_reference/config.html", + "title": "config", "section": "", - "text": "Reaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY\n\n\n\nhomolysis.reaction.Homolysis\nHomolytic bond breaking leading to 2 radicals.\n\n\nhat_naive.reaction.NaiveHAT\nNaive HAT reaction, selects hydrogens at random\n\n\ndummyreaction.reaction.DummyReaction\nDummy reaction, returns empty RecipeCollection" + "text": "config\nRead and validate kimmdy.yml configuration files and package into a parsed format for internal use.\n\n\n\n\n\nName\nDescription\n\n\n\n\nConfig\nInternal representation of the configuration generated\n\n\n\n\n\nconfig.Config(self, input_file=None, recursive_dict=None, scheme=None, section='config', logfile=None, loglevel=None)\nInternal representation of the configuration generated from the input file, which enables validation before running and computationally expensive operations.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput_file\nPath | None\nPath to the config yaml file.\nNone\n\n\nrecursive_dict\ndict | None\nFor internal use only, used in reading settings in recursively.\nNone\n\n\nscheme\ndict | None\ndict containing types and defaults for casting and validating settings.\nNone\n\n\nsection\nstr\ncurrent section e.g. to determine the level of recursion in nested configs e.g. “config”, “config.mds” or “config.reactions.homolysis”\n'config'\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nattr\nGet the value of a specific attribute.\n\n\nget_attributes\nGet a list of all attributes without hidden ones (_<…>).\n\n\n\n\n\nconfig.Config.attr(attribute)\nGet the value of a specific attribute. Alias for self.__getattribute__\n\n\n\nconfig.Config.get_attributes()\nGet a list of all attributes without hidden ones (_<…>)." }, { - "objectID": "_reference/parsing.html", - "href": "_reference/parsing.html", - "title": "parsing", + "objectID": "_reference/config.html#classes", + "href": "_reference/config.html#classes", + "title": "config", "section": "", - "text": "parsing\nAll read_<…> and write_<…> functions.\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nJSONEncoder\nEncoder that enables writing JSONs with numpy types.\n\n\nPlumed_dict\nDict representation of a plumed.dat file.\n\n\n\n\n\nparsing.JSONEncoder()\nEncoder that enables writing JSONs with numpy types.\n\n\n\nparsing.Plumed_dict()\nDict representation of a plumed.dat file.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n 'C',\n '1',\n 'URE',\n 'C',\n '1',\n '0.880229',\n '12.01000'],\n ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'bonds': {'content': [['1', '2'],\n ['1', '3'],\n ['1', '6'],\n ['3', '4'],\n ['3', '5'],\n ['6', '7'],\n ['6', '8']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n ['2', '1', '3', '5', '9'],\n ['2', '1', '6', '7', '9'],\n ['2', '1', '6', '8', '9'],\n ['3', '1', '6', '7', '9'],\n ['3', '1', '6', '8', '9'],\n ['6', '1', '3', '4', '9'],\n ['6', '1', '3', '5', '9'],\n ['3', '6', '1', '2', '4'],\n ['1', '4', '3', '5', '4'],\n ['1', '7', '6', '8', '4']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n ['2', '1', '1000', '0', '1000'],\n ['3', '1', '1000', '0', '0']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedral_restraints': {'content': [['3',\n '6',\n '1',\n '2',\n '1',\n '180',\n '0',\n '10'],\n ['1', '4', '3', '5', '1', '180', '0', '10']],\n 'else_content': [],\n 'extra': [],\n 'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\nparsing.write_top(top, outfile)\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nRaw dictionary represenation of the topology.\nrequired\n\n\noutfile\nPath\nPath to the topology file to write to.\nrequired" + "text": "Name\nDescription\n\n\n\n\nConfig\nInternal representation of the configuration generated\n\n\n\n\n\nconfig.Config(self, input_file=None, recursive_dict=None, scheme=None, section='config', logfile=None, loglevel=None)\nInternal representation of the configuration generated from the input file, which enables validation before running and computationally expensive operations.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput_file\nPath | None\nPath to the config yaml file.\nNone\n\n\nrecursive_dict\ndict | None\nFor internal use only, used in reading settings in recursively.\nNone\n\n\nscheme\ndict | None\ndict containing types and defaults for casting and validating settings.\nNone\n\n\nsection\nstr\ncurrent section e.g. to determine the level of recursion in nested configs e.g. “config”, “config.mds” or “config.reactions.homolysis”\n'config'\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nattr\nGet the value of a specific attribute.\n\n\nget_attributes\nGet a list of all attributes without hidden ones (_<…>).\n\n\n\n\n\nconfig.Config.attr(attribute)\nGet the value of a specific attribute. Alias for self.__getattribute__\n\n\n\nconfig.Config.get_attributes()\nGet a list of all attributes without hidden ones (_<…>)." }, { - "objectID": "_reference/parsing.html#attributes", - "href": "_reference/parsing.html#attributes", - "title": "parsing", + "objectID": "_reference/parsing.TopologyDict.html", + "href": "_reference/parsing.TopologyDict.html", + "title": "parsing.TopologyDict", "section": "", - "text": "Name\nDescription\n\n\n\n\nTopologyDict\nA raw representation of a topology file returned by read_top." + "text": "parsing.TopologyDict\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n Back to top" }, { - "objectID": "_reference/parsing.html#classes", - "href": "_reference/parsing.html#classes", - "title": "parsing", + "objectID": "_reference/constants.html", + "href": "_reference/constants.html", + "title": "constants", "section": "", - "text": "Name\nDescription\n\n\n\n\nJSONEncoder\nEncoder that enables writing JSONs with numpy types.\n\n\nPlumed_dict\nDict representation of a plumed.dat file.\n\n\n\n\n\nparsing.JSONEncoder()\nEncoder that enables writing JSONs with numpy types.\n\n\n\nparsing.Plumed_dict()\nDict representation of a plumed.dat file." + "text": "constants\nComstants used throughout KIMMDY\n\n\n\n\n\nName\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical." }, { - "objectID": "_reference/parsing.html#functions", - "href": "_reference/parsing.html#functions", - "title": "parsing", + "objectID": "_reference/constants.html#attributes", + "href": "_reference/constants.html#attributes", + "title": "constants", "section": "", - "text": "Name\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n 'C',\n '1',\n 'URE',\n 'C',\n '1',\n '0.880229',\n '12.01000'],\n ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'bonds': {'content': [['1', '2'],\n ['1', '3'],\n ['1', '6'],\n ['3', '4'],\n ['3', '5'],\n ['6', '7'],\n ['6', '8']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n ['2', '1', '3', '5', '9'],\n ['2', '1', '6', '7', '9'],\n ['2', '1', '6', '8', '9'],\n ['3', '1', '6', '7', '9'],\n ['3', '1', '6', '8', '9'],\n ['6', '1', '3', '4', '9'],\n ['6', '1', '3', '5', '9'],\n ['3', '6', '1', '2', '4'],\n ['1', '4', '3', '5', '4'],\n ['1', '7', '6', '8', '4']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n ['2', '1', '1000', '0', '1000'],\n ['3', '1', '1000', '0', '0']],\n 'else_content': [],\n 'extra': [],\n 'condition': None},\n'dihedral_restraints': {'content': [['3',\n '6',\n '1',\n '2',\n '1',\n '180',\n '0',\n '10'],\n ['1', '4', '3', '5', '1', '180', '0', '10']],\n 'else_content': [],\n 'extra': [],\n 'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\nparsing.write_top(top, outfile)\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nRaw dictionary represenation of the topology.\nrequired\n\n\noutfile\nPath\nPath to the topology file to write to.\nrequired" + "text": "Name\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical." }, { "objectID": "_reference/topology.atomic.html", @@ -490,18 +476,18 @@ "text": "Name\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one improper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one proper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj < ai < ak\n\n\n\ntopology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai < aj\n\n\n\ntopology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj < ak\n\n\n\ntopology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one improper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)\n\n\n\ntopology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one proper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2\n\n\n\ntopology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh" }, { - "objectID": "_reference/plugins.html", - "href": "_reference/plugins.html", - "title": "plugins", + "objectID": "_reference/recipe.html", + "href": "_reference/recipe.html", + "title": "recipe", "section": "", - "text": "plugins\nPlugin base classes and basic instances thereof.\nAlso discovers and loads KIMMDY plugins.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired" + "text": "recipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.CustomTopMod(f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)\nChange topology and/or coordinates to place an atom.\nEither provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nNone\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nNone\n\n\n\n\n\n\n\nrecipe.Recipe(recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str\n\n\n\nrecipe.Relax()\nStart a relaxation MD.\nThe molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium." }, { - "objectID": "_reference/plugins.html#classes", - "href": "_reference/plugins.html#classes", - "title": "plugins", + "objectID": "_reference/recipe.html#classes", + "href": "_reference/recipe.html#classes", + "title": "recipe", "section": "", - "text": "Name\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired" + "text": "Name\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.CustomTopMod(f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)\nChange topology and/or coordinates to place an atom.\nEither provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nNone\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nNone\n\n\n\n\n\n\n\nrecipe.Recipe(recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str\n\n\n\nrecipe.Relax()\nStart a relaxation MD.\nThe molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium." }, { "objectID": "_reference/topology.utils.html", @@ -518,88 +504,144 @@ "text": "Name\nDescription\n\n\n\n\nget_is_reactive_predicate_f\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\nget_moleculetype_atomics\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nget_moleculetype_header\nGet content of the header of a moleculetype from a topology dict.\n\n\nget_protein_section\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nget_reactive_section\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\nget_residue_fragments\nSplits a residue into fragments after a bond has been broken.\n\n\nget_top_section\nGet content of a section from a topology dict.\n\n\nis_not_solvent_or_ion\nReturns whether a moleculetype name is not solvent or ion.\n\n\nset_moleculetype_atomics\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nset_protein_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_reactive_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_top_section\nSet content of a section from a topology dict.\n\n\n\n\n\ntopology.utils.get_is_reactive_predicate_f(cfg)\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\n\ntopology.utils.get_moleculetype_atomics(top, moleculetype)\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_moleculetype_header(top, moleculetype)\nGet content of the header of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_protein_section(top, name)\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.get_reactive_section(top, name)\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\n\ntopology.utils.get_residue_fragments(top, residue, start1, start2, iterations=20)\nSplits a residue into fragments after a bond has been broken.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopology\nTopology\nrequired\n\n\nresidue\nlist[Atom]\nAll atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond.\nrequired\n\n\nstart1\nAtom\nFirst atom with broken bond\nrequired\n\n\nstart2\nAtom\nSecond atom with broken bond\nrequired\n\n\niterations\nint\nMax number of bonds from start atoms to be included when building fragmets, by default 20\n20\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nTwo fragments, or one fragment and empty set in case the\nresidue did not change its size.\n\n\n\n\n\n\n\ntopology.utils.get_top_section(top, name, moleculetype=None)\nGet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.is_not_solvent_or_ion(name)\nReturns whether a moleculetype name is not solvent or ion.\n\n\n\ntopology.utils.set_moleculetype_atomics(top, name, atomics, create=False)\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\nIf create is True, a new section is created if it does not exist.\n\n\n\ntopology.utils.set_protein_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_reactive_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_top_section(top, name, value, moleculetype=None)\nSet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result." }, { - "objectID": "_reference/tools.html", - "href": "_reference/tools.html", - "title": "tools", + "objectID": "_reference/hat_naive.reaction.NaiveHAT.html", + "href": "_reference/hat_naive.reaction.NaiveHAT.html", + "title": "hat_naive.reaction.NaiveHAT", "section": "", - "text": "tools\nStandalone tools that are complementary to KIMMDY.\n\n\n\n\n\nName\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto." + "text": "hat_naive.reaction.NaiveHAT\nreaction.NaiveHAT(self, name, runmng)\nNaive HAT reaction, selects hydrogens at random\n\n\n\n\n Back to top" }, { - "objectID": "_reference/tools.html#functions", - "href": "_reference/tools.html#functions", - "title": "tools", + "objectID": "_reference/kmc.html", + "href": "_reference/kmc.html", + "title": "kmc", "section": "", - "text": "Name\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto." + "text": "kmc\nKinetic Monte Carlo (KMC) classes and functions.\nIn our system, the reaction rate r = (deterministic) reaction constant k = stochastic reaction constant c (from gillespie 1977) = propensity a (from Anderson 2007) because of the fundamental premise of chemical kinetics and because we have one reactant molecule\n\n\n\n\n\nName\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()" }, { - "objectID": "_reference/dummyreaction.reaction.DummyReaction.html", - "href": "_reference/dummyreaction.reaction.DummyReaction.html", - "title": "dummyreaction.reaction.DummyReaction", + "objectID": "_reference/kmc.html#classes", + "href": "_reference/kmc.html#classes", + "title": "kmc", "section": "", - "text": "dummyreaction.reaction.DummyReaction\nreaction.DummyReaction(self, name, runmng)\nDummy reaction, returns empty RecipeCollection\n\n\n\n\n Back to top" + "text": "Name\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]" }, { - "objectID": "_reference/config.html", - "href": "_reference/config.html", - "title": "config", + "objectID": "_reference/kmc.html#functions", + "href": "_reference/kmc.html#functions", + "title": "kmc", "section": "", - "text": "config\nRead and validate kimmdy.yml configuration files and package into a parsed format for internal use.\n\n\n\n\n\nName\nDescription\n\n\n\n\nConfig\nInternal representation of the configuration generated\n\n\n\n\n\nconfig.Config(self, input_file=None, recursive_dict=None, scheme=None, section='config', logfile=None, loglevel=None)\nInternal representation of the configuration generated from the input file, which enables validation before running and computationally expensive operations.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput_file\nPath | None\nPath to the config yaml file.\nNone\n\n\nrecursive_dict\ndict | None\nFor internal use only, used in reading settings in recursively.\nNone\n\n\nscheme\ndict | None\ndict containing types and defaults for casting and validating settings.\nNone\n\n\nsection\nstr\ncurrent section e.g. to determine the level of recursion in nested configs e.g. “config”, “config.mds” or “config.reactions.homolysis”\n'config'\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nattr\nGet the value of a specific attribute.\n\n\nget_attributes\nGet a list of all attributes without hidden ones (_<…>).\n\n\n\n\n\nconfig.Config.attr(attribute)\nGet the value of a specific attribute. Alias for self.__getattribute__\n\n\n\nconfig.Config.get_attributes()\nGet a list of all attributes without hidden ones (_<…>)." + "text": "Name\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()" }, { - "objectID": "_reference/config.html#classes", - "href": "_reference/config.html#classes", - "title": "config", + "objectID": "_reference/cmd.html", + "href": "_reference/cmd.html", + "title": "cmd", "section": "", - "text": "Name\nDescription\n\n\n\n\nConfig\nInternal representation of the configuration generated\n\n\n\n\n\nconfig.Config(self, input_file=None, recursive_dict=None, scheme=None, section='config', logfile=None, loglevel=None)\nInternal representation of the configuration generated from the input file, which enables validation before running and computationally expensive operations.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput_file\nPath | None\nPath to the config yaml file.\nNone\n\n\nrecursive_dict\ndict | None\nFor internal use only, used in reading settings in recursively.\nNone\n\n\nscheme\ndict | None\ndict containing types and defaults for casting and validating settings.\nNone\n\n\nsection\nstr\ncurrent section e.g. to determine the level of recursion in nested configs e.g. “config”, “config.mds” or “config.reactions.homolysis”\n'config'\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nattr\nGet the value of a specific attribute.\n\n\nget_attributes\nGet a list of all attributes without hidden ones (_<…>).\n\n\n\n\n\nconfig.Config.attr(attribute)\nGet the value of a specific attribute. Alias for self.__getattribute__\n\n\n\nconfig.Config.get_attributes()\nGet a list of all attributes without hidden ones (_<…>)." + "text": "cmd\nFunctions for starting KIMMDY either from python or the command line. Other entry points such as kimmdy-analysis also live here.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, checkpoint='', show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\ncheckpoint\nstr\nFile path of a kimmdy.cpt file to restart KIMMDY from a checkpoint. If a directory is given, the file kimmdy.cpt in that directory is used.\n''\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse" }, { - "objectID": "_reference/recipe.html", - "href": "_reference/recipe.html", - "title": "recipe", + "objectID": "_reference/cmd.html#functions", + "href": "_reference/cmd.html#functions", + "title": "cmd", "section": "", - "text": "recipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind()\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nrequired\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nrequired\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nrequired\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nrequired\n\n\n\n\n\n\n\nrecipe.BondOperation(_atom_ix_1=field(init=False, repr=False, default=None), _atom_ix_2=field(init=False, repr=False, default=None))\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nrequired\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nrequired\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nrequired\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break()\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nrequired\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nrequired\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nrequired\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nrequired\n\n\n\n\n\n\n\nrecipe.CustomTopMod(f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(new_coords, _ix_to_place=field(init=False, repr=False, default=None))\nChange topology and/or coordinates to place an atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nrequired\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nrequired\n\n\n\n\n\n\n\nrecipe.Recipe(recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncalc_averages\nCalulate average rates over some window size\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.calc_averages(window_size)\nCalulate average rates over some window size\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nwindow_size\nint\nSize of the window to average over, -1 to average over whole available range.\nrequired\n\n\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str\n\n\n\nrecipe.Relax()\nStart a relaxation MD.\nThe molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium." + "text": "Name\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, checkpoint='', show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\ncheckpoint\nstr\nFile path of a kimmdy.cpt file to restart KIMMDY from a checkpoint. If a directory is given, the file kimmdy.cpt in that directory is used.\n''\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse" }, { - "objectID": "_reference/recipe.html#classes", - "href": "_reference/recipe.html#classes", - "title": "recipe", + "objectID": "_reference/tasks.html", + "href": "_reference/tasks.html", + "title": "tasks", "section": "", - "text": "Name\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind()\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nrequired\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nrequired\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nrequired\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nrequired\n\n\n\n\n\n\n\nrecipe.BondOperation(_atom_ix_1=field(init=False, repr=False, default=None), _atom_ix_2=field(init=False, repr=False, default=None))\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nrequired\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nrequired\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nrequired\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break()\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nrequired\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nrequired\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nrequired\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nrequired\n\n\n\n\n\n\n\nrecipe.CustomTopMod(f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(new_coords, _ix_to_place=field(init=False, repr=False, default=None))\nChange topology and/or coordinates to place an atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nrequired\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nrequired\n\n\n\n\n\n\n\nrecipe.Recipe(recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncalc_averages\nCalulate average rates over some window size\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.calc_averages(window_size)\nCalulate average rates over some window size\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nwindow_size\nint\nSize of the window to average over, -1 to average over whole available range.\nrequired\n\n\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str\n\n\n\nrecipe.Relax()\nStart a relaxation MD.\nThe molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium." + "text": "tasks\nThe tasks module holds the TaskFiles class which organizes input and output paths and the Task class for steps in the runmanager.\n\n\n\n\n\nName\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n>>> class run():\n>>> def get_latest(self, s):\n>>> return f\"latest {s}\"\n>>> runmng = run()\n>>> files = TaskFiles(runmng)\n>>> files.input\n>>> files.input[\"top\"]\n{'top': 'latest top'}\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue)." }, { - "objectID": "guide/tutorials/write-plugin.html", - "href": "guide/tutorials/write-plugin.html", - "title": "Write a Reaction Plugin", + "objectID": "_reference/tasks.html#classes", + "href": "_reference/tasks.html#classes", + "title": "tasks", "section": "", - "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions." + "text": "Name\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n>>> class run():\n>>> def get_latest(self, s):\n>>> return f\"latest {s}\"\n>>> runmng = run()\n>>> files = TaskFiles(runmng)\n>>> files.input\n>>> files.input[\"top\"]\n{'top': 'latest top'}" }, { - "objectID": "guide/tutorials/write-plugin.html#creating-a-github-repository", - "href": "guide/tutorials/write-plugin.html#creating-a-github-repository", - "title": "Write a Reaction Plugin", + "objectID": "_reference/tasks.html#functions", + "href": "_reference/tasks.html#functions", + "title": "tasks", "section": "", - "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions." + "text": "Name\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue)." }, { - "objectID": "guide/tutorials/write-plugin.html#adding-the-functionality-of-the-plugin", - "href": "guide/tutorials/write-plugin.html#adding-the-functionality-of-the-plugin", - "title": "Write a Reaction Plugin", - "section": "Adding the functionality of the plugin", - "text": "Adding the functionality of the plugin\n\nMain code\nA reaction plugin has to be a derived class from the ReactionPlugin base class. Such a class has the attributes name, runmng and config and the method get_recipe_collection, which takes a TaskFiles object as argument and returns a RecipeCollection.\nThe name is a simple string and may be useful for logging. runmng is the central RunManager of a kimmdy run and has plenty of useful attributes for your plugin, especially the system Topology, which can be accessed via self.runmg.top. config contains the reaction plugin configuration as specified in the kimmdy configuration file (typically named kimmdy.yml). A RecipeCollection contains Recipes with predefined RecipeSteps that can be used to define the modification to the system for the reaction. A Recipe also contains the rates of the specified reaction and the timespans during which the corresponding rates are valid. An example plugin can be seen below.\n\n\nPlugin main code (reaction.py)\nfrom kimmdy.recipe import (\n Bind,\n Recipe,\n RecipeCollection,\n)\nfrom kimmdy.plugins import ReactionPlugin\nfrom kimmdy.tasks import TaskFiles\nfrom kimmdy.utils import (\n get_atomnrs_from_plumedid,\n)\nfrom kimmdy.parsing import (\n read_plumed,\n read_distances_dat,\n)\n\n\nclass BindReaction(ReactionPlugin):\n \"\"\"Reaction to bind two particles if they are in proximity\n \"\"\"\n\n def get_recipe_collection(self, files: TaskFiles):\n logger = files.logger\n logger.debug(\"Getting recipe for reaction: Bind\")\n\n # get cutoff distance from config, unit is [nm]\n cutoff = self.config.distance\n\n # Initialization of objects from files\n distances = read_distances_dat(files.input[\"plumed_out\"])\n plumed = read_plumed(files.input[\"plumed\"])\n\n recipes = []\n # check distances file for values lower than the cutoff\n for plumedid, dists in distances.items():\n if plumedid == \"time\":\n continue\n # checks only last frame\n if dists[-1] < cutoff:\n # get atomnrs from plumedid \n atomnrs = get_atomnrs_from_plumedid(plumedid, plumed)\n recipes.append(\n Recipe(\n recipe_steps=[\n Bind(atom_id_1=atomnrs[0], atom_id_2=atomnrs[1]),\n ],\n rates=[1],\n timespans=[(distances[\"time\"][0], distances[\"time\"][-1])],\n )\n )\n\n return RecipeCollection(recipes)\n\n\n\n\nConfiguration file schema\nA plugin defines which variables it needs in a schema. The schema can contain default values and types of these variables. For a Kimmdy run, reaction plugin variables are defined in the configuration file (kimmdy.yml). An example schema can be seen below.\n\n\nPlugin schema (kimmdy-yaml-schema.json)\n\n\n\nkimmdy-yaml-schema.json\n\n{\n \"$schema\": \"https://json-schema.org/draft/2020-12/schema\",\n \"type\": \"object\",\n \"$id\": \"bind-config\",\n \"description\": \"Settings for bind reactions\",\n \"additionalProperties\": false,\n \"properties\": {\n \"distance\": {\n \"description\": \"Cutoff distance for two particles to bind [nm]\",\n \"type\": \"float\",\n \"pytype\": \"float\"\n },\n \"kmc\": {\n \"description\": \"KMC algorithm for this reaction.\",\n \"type\": \"string\",\n \"pytype\": \"str\",\n \"enum\": [\"rfkmc\", \"frm\", \"extrande\"],\n \"default\": \"rfkmc\"\n }\n },\n \"required\": [\"distance\"]\n}" + "objectID": "guide/how-to/reaction_only.html", + "href": "guide/how-to/reaction_only.html", + "title": "Reaction only", + "section": "", + "text": "You might want to apply a KIMMDY reaction to an already existing simulation. Here are some important points for doing so." }, { - "objectID": "guide/tutorials/write-plugin.html#making-a-python-package", - "href": "guide/tutorials/write-plugin.html#making-a-python-package", - "title": "Write a Reaction Plugin", - "section": "Making a python package", - "text": "Making a python package\nIt is necessary to make the plugin a python package to interface with Kimmdy. For this, package setup configuration files are necessary, for example setup.py and setup.cfg. In setup.cfg dependencies can be specified, which will be installed alongside the plugin. The interface with kimmdy is specified in the [options.entry_points] section. This section needs to refer to the class we created in the plugin main code and assign it to kimmdy.reaction_plugins, i.e. kimmdy.reaction_plugins = bind = <path>.<to>.<main file>:<ClassName>. Also, the directory containing the source code (typically src) is defined in [options.packages.find]. An example for setup.py and setup.cfg can be found below.\n\n\nsetup.py\nfrom setuptools import setup\n\nsetup()\n\n\n\n\nsetup.cfg\n\n\n\nsetup.cfg\n\n[metadata]\nname = kimmdy-reactions\nversion = 0.1\nlicense = GPL-3.0 \ndescription = Reaction template for KIMMDY\nlong_description = file: README.md\nauthor = Eric Hartmann\nauthor_email = eric.Hartmann@h-its.org\nclassifiers=\n Programming Language :: Python :: 3\n License :: OSI Approved :: MIT License\n Operating System :: OS Independent\n\n[options]\npackages = find:\npackage_dir =\n =src\ninclude_package_data = True\ninstall_requires =\n MDAnalysis\n\npython_requires = >= 3.9\n\n[options.packages.find]\nwhere=src\n\n[options.entry_points]\nkimmdy.reaction_plugins =\n bind = bind.reaction:BindReaction\n\n\nThe main code and configuration schema file should then be moved to the specified source directory in a directory that has the name of the reaction plugin, i.e. src/<plugin name>/.\n\n\n\n\n\n\nTip\n\n\n\nBy adding the kimmdy tag on GitHub you can make your plugin discoverable by other users. It will show up in this list" + "objectID": "guide/how-to/reaction_only.html#kimmdy-yaml", + "href": "guide/how-to/reaction_only.html#kimmdy-yaml", + "title": "Reaction only", + "section": "KIMMDY yaml", + "text": "KIMMDY yaml\nIf you want to start your sequence of tasks with a reaction, you have to give KIMMDY a trajectory. This, you do with the trr key in the kimmdy.yml file." }, { - "objectID": "guide/tutorials/write-plugin.html#improving-code-quality-and-reproducibility", - "href": "guide/tutorials/write-plugin.html#improving-code-quality-and-reproducibility", - "title": "Write a Reaction Plugin", - "section": "Improving code quality and reproducibility", - "text": "Improving code quality and reproducibility\nAdding tests will help in ensuring the plugin is working as expected. An example would help users to understand what your plugin does." + "objectID": "guide/how-to/reaction_only.html#pre-averaged-plumed-input", + "href": "guide/how-to/reaction_only.html#pre-averaged-plumed-input", + "title": "Reaction only", + "section": "Pre-averaged plumed input", + "text": "Pre-averaged plumed input\nSometimes it is handy to pre-compute the averages of the distances plumed recordes. Usually, the plumed output (distances.dat) contains one line per timestep, each line starting with the time.\nIf you calculate the averages yourself, you end up having only one line, but need to tell KIMMDY how long the timeframe was, which was averaged. To do this, make sure to write the duration of your averaged simulation in the time field like this for a 10ps simulation:\n#! FIELDS time d0 d1 d2 d3 d4\n10.000000 0.142401 0.151588 0.143725 0.156734 0.152581\nYou still need the plumed config file, even if KIMMDY does not execute plumed in the current example, as KIMMDY reads the filename of the plumed output from the plumed config." + }, + { + "objectID": "guide/how-to/examples.html", + "href": "guide/how-to/examples.html", + "title": "Examples", + "section": "", + "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax'\n slow_growth: True\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - pull \n - reactions\n - equilibrium\n - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'basic'\nreactions:\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'pullf1500_equil.mdp'\n prod:\n mdp: 'pullf1500.mdp'\n use_plumed: true\n relax:\n mdp: 'pullf1500.mdp'\nchanger:\n coordinates:\n md: 'relax' \n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - mult: 1\n tasks:\n - prod\n - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n coordinates: {}\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n dummyreaction: {}\nsequence:\n - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'grappa' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n - equilibrium\n - pull\n - homolysis\n -\n mult: 2\n tasks:\n - equilibrium\n - pull\n - reactions" + }, + { + "objectID": "guide/how-to/examples.html#further-examples", + "href": "guide/how-to/examples.html#further-examples", + "title": "Examples", + "section": "", + "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax'\n slow_growth: True\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - pull \n - reactions\n - equilibrium\n - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'basic'\nreactions:\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'pullf1500_equil.mdp'\n prod:\n mdp: 'pullf1500.mdp'\n use_plumed: true\n relax:\n mdp: 'pullf1500.mdp'\nchanger:\n coordinates:\n md: 'relax' \n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - mult: 1\n tasks:\n - prod\n - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n coordinates: {}\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n dummyreaction: {}\nsequence:\n - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'grappa' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n - equilibrium\n - pull\n - homolysis\n -\n mult: 2\n tasks:\n - equilibrium\n - pull\n - reactions" + }, + { + "objectID": "guide/how-to/index.html", + "href": "guide/how-to/index.html", + "title": "How-To", + "section": "", + "text": "How-To Guides\n\n\n\n\n\n\n \n \n \n Order By\n Default\n \n Title\n \n \n Author\n \n \n \n \n \n \n \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nContribute\n\n\n \n\n\n\n\nExamples\n\n\n \n\n\n\n\nHigh Performance Computing\n\n\n \n\n\n\n\nInstall Machine Learning Plugins\n\n\n \n\n\n\n\nReaction only\n\n\nKai Riedmiller\n\n\n\n\n\nNo matching items\n\n Back to top" + }, + { + "objectID": "guide/references/cmd_ref.html", + "href": "guide/references/cmd_ref.html", + "title": "CLI Arguments", + "section": "", + "text": "The prefered method of starting a KIMMDY run is via the command line, though Python entry points are supported as well." + }, + { + "objectID": "guide/references/cmd_ref.html#kimmdy", + "href": "guide/references/cmd_ref.html#kimmdy", + "title": "CLI Arguments", + "section": "KIMMDY", + "text": "KIMMDY\n\n!kimmdy --help\n\nusage: kimmdy [-h] [--input INPUT] [--checkpoint CHECKPOINT]\n [--loglevel LOGLEVEL] [--logfile LOGFILE] [--show-plugins]\n [--generate-jobscript] [--version] [--debug] [--callgraph]\n\nWelcome to KIMMDY. `kimmdy` runs KIMMDY, further tools are available as\n`kimmdy-...` commands. These are `-analysis`, `-modify-top` and `-build-\nexamples`. Access their help with `kimmdy-... -h.`\n\noptions:\n -h, --help show this help message and exit\n --input INPUT, -i INPUT\n Kimmdy input file. Default `kimmdy.yml`\n --checkpoint CHECKPOINT, -c CHECKPOINT\n File path of a kimmdy.cpt file to restart KIMMDY from\n a checkpoint. If a directory is given, the file\n kimmdy.cpt in that directory is used.\n --loglevel LOGLEVEL, -l LOGLEVEL\n logging level (CRITICAL, ERROR, WARNING, INFO, DEBUG)\n --logfile LOGFILE, -f LOGFILE\n logfile\n --show-plugins List available plugins\n --generate-jobscript Instead of running KIMMDY directly, generate at\n jobscript.sh for slurm HPC clusters.You can then run\n this jobscript with sbatch jobscript.sh\n --version show program's version number and exit\n --debug on error, drop into debugger\n --callgraph Generate visualization of function calls. Mostly\n useful for debugging and documentation." + }, + { + "objectID": "guide/references/cmd_ref.html#analysis", + "href": "guide/references/cmd_ref.html#analysis", + "title": "CLI Arguments", + "section": "Analysis", + "text": "Analysis\n\n!kimmdy-analysis --help\n\nusage: kimmdy-analysis [-h] module ...\n\nWelcome to the KIMMDY analysis module. Use this module to analyse existing\nKIMMDY runs.\n\npositional arguments:\n module\n trjcat Concatenate trajectories of a KIMMDY run\n energy Plot GROMACS energy for a KIMMDY run\n radical_population\n Plot population of radicals for one or multiple KIMMDY\n run(s)\n rates Plot rates of all possible reactions after a MD run.\n Rates must have been saved!\n runtime Plot runtime of the tasks of a kimmdy run.\n\noptions:\n -h, --help show this help message and exit" + }, + { + "objectID": "guide/references/cmd_ref.html#remove-hydrogen", + "href": "guide/references/cmd_ref.html#remove-hydrogen", + "title": "CLI Arguments", + "section": "Remove Hydrogen", + "text": "Remove Hydrogen\nThis module builds or restores the example directory in the package.\n\n!kimmdy-modify-top --help\n\nusage: kimmdy-modify-top [-h] [-p] [-r REMOVEH [REMOVEH ...]] [-c GROFILE]\n [-t RESIDUETYPES] [-x RADICALS]\n top out\n\nWelcome to the KIMMDY modify top module\n\npositional arguments:\n top GROMACS top file\n out Output top file name\n\noptions:\n -h, --help show this help message and exit\n -p, --parameterize Parameterize topology with grappa. (default: False)\n -r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]\n Remove one or more hydrogens by atom nrs in the top\n file. (default: None)\n -c GROFILE, --grofile GROFILE\n If necessary, also apply actions on gro file to create\n a compatible gro/top file pair. (default: None)\n -t RESIDUETYPES, --residuetypes RESIDUETYPES\n GROMACS style residuetypes file. Necessary for\n parameterization with non-amber atom types. (default:\n None)\n -x RADICALS, --radicals RADICALS\n Radicals in the system PRIOR to removing hydrogens\n with the removeH option. (default: )" + }, + { + "objectID": "guide/references/cmd_ref.html#examples", + "href": "guide/references/cmd_ref.html#examples", + "title": "CLI Arguments", + "section": "Examples", + "text": "Examples\nThis module builds or restores the example directory in the package.\n\n!kimmdy-build-examples --help\n\nusage: kimmdy-build-examples [-h] [-r [RESTORE]]\n\nBuild examples for KIMMDY.\n\noptions:\n -h, --help show this help message and exit\n -r [RESTORE], --restore [RESTORE]\n Overwrite input files in existing example directories,\n use keyword 'hard' to also delete output files." }, { "objectID": "guide/tutorials/colbuilder.html", @@ -637,73 +679,31 @@ "text": "Analysis\nTry the options in kimmdy-analysis to visualize your kimmdy run." }, { - "objectID": "guide/how-to/hcp.html", - "href": "guide/how-to/hcp.html", - "title": "High Performance Computing", - "section": "", - "text": "You need an installation of python (>= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same as --from-latest-checkpoint\nkimmdy -c" - }, - { - "objectID": "guide/how-to/hcp.html#setup", - "href": "guide/how-to/hcp.html#setup", - "title": "High Performance Computing", - "section": "", - "text": "You need an installation of python (>= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same as --from-latest-checkpoint\nkimmdy -c" - }, - { - "objectID": "guide/how-to/index.html", - "href": "guide/how-to/index.html", - "title": "How-To", - "section": "", - "text": "How-To Guides\n\n\n\n\n\n\n \n \n \n Order By\n Default\n \n Title\n \n \n Author\n \n \n \n \n \n \n \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nContribute\n\n\n \n\n\n\n\nExamples\n\n\n \n\n\n\n\nHigh Performance Computing\n\n\n \n\n\n\n\nInstall Machine Learning Plugins\n\n\n \n\n\n\n\nReaction only\n\n\nKai Riedmiller\n\n\n\n\n\nNo matching items\n\n Back to top" - }, - { - "objectID": "guide/how-to/examples.html", - "href": "guide/how-to/examples.html", - "title": "Examples", - "section": "", - "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax'\n slow_growth: True\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - pull \n - reactions\n - equilibrium\n - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'basic'\nreactions:\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'pullf1500_equil.mdp'\n prod:\n mdp: 'pullf1500.mdp'\n use_plumed: true\n relax:\n mdp: 'pullf1500.mdp'\nchanger:\n coordinates:\n md: 'relax' \n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - mult: 1\n tasks:\n - prod\n - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n coordinates: {}\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n dummyreaction: {}\nsequence:\n - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'grappa' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n - equilibrium\n - pull\n - homolysis\n -\n mult: 2\n tasks:\n - equilibrium\n - pull\n - reactions" - }, - { - "objectID": "guide/how-to/examples.html#further-examples", - "href": "guide/how-to/examples.html#further-examples", - "title": "Examples", + "objectID": "guide/tutorials/index.html", + "href": "guide/tutorials/index.html", + "title": "Tutorials", "section": "", - "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax'\n slow_growth: True\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - pull \n - reactions\n - equilibrium\n - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'basic'\nreactions:\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'pullf1500_equil.mdp'\n prod:\n mdp: 'pullf1500.mdp'\n use_plumed: true\n relax:\n mdp: 'pullf1500.mdp'\nchanger:\n coordinates:\n md: 'relax' \n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\nsequence:\n - equilibrium\n - mult: 1\n tasks:\n - prod\n - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n coordinates: {}\n topology:\n parameterization: 'basic' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n dummyreaction: {}\nsequence:\n - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n pull:\n mdp: 'md.mdp'\n use_plumed: true\n relax:\n mdp: 'md_slow_growth.mdp'\nchanger:\n coordinates:\n md: 'relax' \n slow_growth: True\n topology:\n parameterization: 'grappa' \nreactions:\n homolysis:\n edis: 'edissoc.dat'\n itp: 'ffbonded.itp'\n hat_naive:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n - equilibrium\n - pull\n - homolysis\n -\n mult: 2\n tasks:\n - equilibrium\n - pull\n - reactions" + "text": "Tutorials to help you get familiar with KIMMDY.\n\n\n\n\n\n\n\n\n \n\n\n\n\nGet Started\n\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\n\n\nJannik Buhr\n\n\n\n\n\n\n \n\n\n\n\nRun KIMMDY from Colbuilder fibril\n\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\n \n\n\n\n\nWrite a Reaction Plugin\n\n\n\n\n\n\n\ndeveloper\n\n\n\n\nIn this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.\n\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\nNo matching items\n\n Back to top" }, { - "objectID": "guide/references/input.html", - "href": "guide/references/input.html", - "title": "Input File", + "objectID": "guide/explanation/topology.html", + "href": "guide/explanation/topology.html", + "title": "Visualize Topologies", "section": "", - "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml > Schema Store: Enable." + "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n \n\n1 CT\n\n 1 CT \n\n2 HC\n\n 2 HC \n\n1 CT–2 HC\n\n \n\n3 HC\n\n 3 HC \n\n1 CT–3 HC\n\n \n\n4 HC\n\n 4 HC \n\n1 CT–4 HC\n\n \n\n5 C\n\n 5 C \n\n1 CT–5 C\n\n \n\n6 O\n\n 6 O \n\n5 C–6 O\n\n \n\n7 N\n\n 7 N \n\n5 C–7 N\n\n \n\n8 H\n\n 8 H \n\n7 N–8 H\n\n \n\n9 CT\n\n 9 CT \n\n7 N–9 CT\n\n \n\n10 CT\n\n 10 CT \n\n9 CT–10 CT\n\n \n\n14 C\n\n 14 C \n\n9 CT–14 C\n\n \n\n11 HC\n\n 11 HC \n\n10 CT–11 HC\n\n \n\n12 HC\n\n 12 HC \n\n10 CT–12 HC\n\n \n\n13 HC\n\n 13 HC \n\n10 CT–13 HC\n\n \n\n15 O\n\n 15 O \n\n14 C–15 O\n\n \n\n16 N\n\n 16 N \n\n14 C–16 N\n\n \n\n17 H\n\n 17 H \n\n16 N–17 H\n\n \n\n18 CT\n\n 18 CT \n\n16 N–18 CT\n\n \n\n19 H1\n\n 19 H1 \n\n18 CT–19 H1\n\n \n\n20 H1\n\n 20 H1 \n\n18 CT–20 H1\n\n \n\n21 H1\n\n 21 H1 \n\n18 CT–21 H1\n\n \n\n\nFigure 1: A diagram of the Ala topology" }, { - "objectID": "guide/references/input.html#autocompletion", - "href": "guide/references/input.html#autocompletion", - "title": "Input File", + "objectID": "guide/explanation/topology.html#capped-alanine-with-a-radical", + "href": "guide/explanation/topology.html#capped-alanine-with-a-radical", + "title": "Visualize Topologies", "section": "", - "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml > Schema Store: Enable." - }, - { - "objectID": "guide/references/input.html#all-options", - "href": "guide/references/input.html#all-options", - "title": "Input File", - "section": "All Options", - "text": "All Options\nThe following is a list of the options that can be set in the kimmdy.yml file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a .. * denotes an arbitrary name for a section. The key for a section is bold.\n\n\nTable 1: KIMMDY options\n\n\n\n\n\n\n\n\n\nOption\nDescription\nType\nDefault\n\n\n\n\n\ndryrun\nDon’t run the actual simulations, just print the tasks\nbool\nFalse\n\n\n\nwrite_checkpoint\nWrite checkpoints to continue a KIMMDY run from. Default True\nbool\nTrue\n\n\n\ncwd\nWorking directory. Default is current working directory\nPath\n\n\n\n\nname\nUsed for output folder if out is not specified\nstr\nkimmdy\n\n\n\nout\nOutput folder\nPath\n\n\n\n\nlog\nSettings for logging\n\n\n\n\n\nmax_tasks\nMaximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit.\nint\n0\n\n\n\nmax_hours\nStop KIMMDY after max_hours hours. Set this lower than the limit of your HPC cluster for use with a re-submit jobscript. 0 Means no limit.\nint\n0\n\n\n\nkmc\nKMC algorithm overwrite. Should be set by the reactions, but can be changed here.\nstr\n\n\n\n\ntau_scale\nScaling parameter for tau in the extrande kmc algorithm.\nfloat\n1.0\n\n\n\ntop\nTopology file\nPath\ntopol.top\n\n\n\ntopology\nSettings for handling the topology file.\n\n\n\n\n\ntopology.reactive.include\nExplicitly include a moleculetype or list of moleculetypes as a space-separated string.\nstr\n\n\n\n\ntopology.reactive.exclude\nExplicitly exclude a moleculetype or a list as a space-separated string. For example the lipid moleculetype in a bilayer simulation e.g. DPPC POPC'\nstr\n\n\n\n\ngro\nCoordinate file\nPath\nconf.gro\n\n\n\nndx\nGromaxs index file\nPath\nindex.ndx\n\n\n\ngromacs_alias\nGromacs alias. e.g. gmx or mpirun gmx_mpi\nstr\ngmx\n\n\n\ngmx_mdrun_flags\nFlags passed to gmx mdrun. Default -maxh 24 -dlb yes\nstr\n-maxh 24 -dlb yes\n\n\n\nff\nForce field directory (looks for .ff in cwd if not set)\nPath\n*.ff\n\n\n\nplumed\n.dat file containing plumed config\nPath\n\n\n\n\ntpr\n.tpr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\ntrr\n.trr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\nmds\nSettings for MD steps, e.g. mdp files, plumed files, etc.\n\n\n\n\n\nmds.*.mdp\nMDP file for the MD step\nPath\n\n\n\n\nmds.*.use_plumed\nWhether plumed should be used for this run or not\nbool\nFalse\n\n\n\nchanger\nSettings for applying a reaction recipe\n\n\n\n\n\nchanger.coordinates.md\nMD step from the ‘mds’ section that is used for relaxation MDs\nstr\n\n\n\n\nchanger.coordinates.slow_growth\nWhether the chosen MD step is a slow growth/free-energy simulation\nbool\nFalse\n\n\n\nchanger.topology.parameterization\nParameterization scheme that is used on the topology file after changes to it\nstr\nbasic\n\n\n\nsequence\nList of tasks. Each task can be a string (the name of the task) or an object with the task name and a multiplicity mult: <int>\nSequence\n\n\n\n\nreactions\nSettings for reactions\n\n\n\n\n\nplot_rates\nPlot the reaction rates during the reactions step\nbool\nTrue\n\n\n\nsave_recipes\nSave recipes as csv during the reactions step\nbool\nTrue" - }, - { - "objectID": "guide/references/input.html#example-kimmdy.yml-files", - "href": "guide/references/input.html#example-kimmdy.yml-files", - "title": "Input File", - "section": "Example kimmdy.yml Files", - "text": "Example kimmdy.yml Files\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n equilibrium:\n mdp: 'md.mdp'\n relax:\n mdp: 'md_slow.mdp'\nchanger:\n coordinates:\n md: 'relax' \nreactions:\n hat_reaction:\n frequency_factor: 100000000\n h_cutoff: 3\n polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n tasks:\n - equilibrium\n - reactions" + "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n \n\n1 CT\n\n 1 CT \n\n2 HC\n\n 2 HC \n\n1 CT–2 HC\n\n \n\n3 HC\n\n 3 HC \n\n1 CT–3 HC\n\n \n\n4 HC\n\n 4 HC \n\n1 CT–4 HC\n\n \n\n5 C\n\n 5 C \n\n1 CT–5 C\n\n \n\n6 O\n\n 6 O \n\n5 C–6 O\n\n \n\n7 N\n\n 7 N \n\n5 C–7 N\n\n \n\n8 H\n\n 8 H \n\n7 N–8 H\n\n \n\n9 CT\n\n 9 CT \n\n7 N–9 CT\n\n \n\n10 CT\n\n 10 CT \n\n9 CT–10 CT\n\n \n\n14 C\n\n 14 C \n\n9 CT–14 C\n\n \n\n11 HC\n\n 11 HC \n\n10 CT–11 HC\n\n \n\n12 HC\n\n 12 HC \n\n10 CT–12 HC\n\n \n\n13 HC\n\n 13 HC \n\n10 CT–13 HC\n\n \n\n15 O\n\n 15 O \n\n14 C–15 O\n\n \n\n16 N\n\n 16 N \n\n14 C–16 N\n\n \n\n17 H\n\n 17 H \n\n16 N–17 H\n\n \n\n18 CT\n\n 18 CT \n\n16 N–18 CT\n\n \n\n19 H1\n\n 19 H1 \n\n18 CT–19 H1\n\n \n\n20 H1\n\n 20 H1 \n\n18 CT–20 H1\n\n \n\n21 H1\n\n 21 H1 \n\n18 CT–21 H1\n\n \n\n\nFigure 1: A diagram of the Ala topology" }, { - "objectID": "guide/explanation/index.html", - "href": "guide/explanation/index.html", - "title": "Explanations", - "section": "", - "text": "Pages that help you understand the inner workings of KIMMDY\n\n\n\n\n\n\n \n \n \n Order By\n Default\n \n Title\n \n \n Author\n \n \n \n \n \n \n \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nVisualize Topologies\n\n\n \n\n\n\n\n\nNo matching items\n\n Back to top" + "objectID": "guide/explanation/topology.html#multiple-molecules", + "href": "guide/explanation/topology.html#multiple-molecules", + "title": "Visualize Topologies", + "section": "Multiple molecules", + "text": "Multiple molecules\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n \n\n1 C\n\n 1 C \n\n2 O\n\n 2 O \n\n1 C–2 O\n\n \n\n3 N\n\n 3 N \n\n1 C–3 N\n\n \n\n6 N\n\n 6 N \n\n1 C–6 N\n\n \n\n4 H\n\n 4 H \n\n3 N–4 H\n\n \n\n5 H\n\n 5 H \n\n3 N–5 H\n\n \n\n7 H\n\n 7 H \n\n6 N–7 H\n\n \n\n8 H\n\n 8 H \n\n6 N–8 H\n\n \n\n\nFigure 2: Topology of one molecule of urea\n\n\n\n\nWhen we want to run reactions within molecules that are either separate moleculetypes or multiples of the same moleculetype, KIMMDY can combine those into a single moleculetype and make multiples explicit.\ni.e. if we have a topology with two molecules of urea defined as:\n[ system ]\nUrea in Water\n\n[ molecules ]\n;molecule name nr.\nUrea 2\nSOL 1000\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea-times-2.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-2-top.dot\")\n\nWe end up with\n\n\n\n\n\n\n\n\nG\n\n \n\n1 C\n\n 1 C \n\n2 O\n\n 2 O \n\n1 C–2 O\n\n \n\n3 N\n\n 3 N \n\n1 C–3 N\n\n \n\n6 N\n\n 6 N \n\n1 C–6 N\n\n \n\n4 H\n\n 4 H \n\n3 N–4 H\n\n \n\n5 H\n\n 5 H \n\n3 N–5 H\n\n \n\n7 H\n\n 7 H \n\n6 N–7 H\n\n \n\n8 H\n\n 8 H \n\n6 N–8 H\n\n \n\n9 C\n\n 9 C \n\n10 O\n\n 10 O \n\n9 C–10 O\n\n \n\n11 N\n\n 11 N \n\n9 C–11 N\n\n \n\n14 N\n\n 14 N \n\n9 C–14 N\n\n \n\n12 H\n\n 12 H \n\n11 N–12 H\n\n \n\n13 H\n\n 13 H \n\n11 N–13 H\n\n \n\n15 H\n\n 15 H \n\n14 N–15 H\n\n \n\n16 H\n\n 16 H \n\n14 N–16 H\n\n \n\n\nFigure 3: A diagram of the two urea molecules topology\n\n\n\n\nThis way, explicit atom numbers match up with the atom numbers in the coordinate file (or rather, line numbers - 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