squiggly lines begone

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"}

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
 

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)

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
 

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:

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)
 

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"