diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 0eb3b77b..3e37ddc6 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -27,12 +27,15 @@ jobs:
strategy:
fail-fast: false
matrix:
- os: [ubuntu-latest, macOS-latest]
+ os: [ubuntu-latest, macos-latest]
python-version: ["3.8", "3.9", "3.10"]
latest-openff-toolkit: [true, false]
+ exclude:
+ - python-version: "3.10"
+ os: macos-latest
steps:
- - uses: actions/checkout@v3.0.2
+ - uses: actions/checkout@v3
- name: Setup Conda Environment
uses: mamba-org/provision-with-micromamba@main
@@ -52,25 +55,29 @@ jobs:
- name: "Install latest openff-toolkit"
if: ${{ matrix.latest-openff-toolkit == true }}
run: |
- # Until #225 is complete, we should not assume compatibility with new API
- micromamba install "openff-toolkit =0.10.6" -c conda-forge -y
+ micromamba update -y -c conda-forge "openff-toolkit >=0.11.0"
- name: Install Package
run: |
- # Can't use 'develop' mode because we remove symlinks after install is complete
- python setup.py install
+ pip list
+ micromamba list
+ micromamba remove --force openmmforcefields
+ python -m pip install .
- name: Conda Environment Information
run: |
- conda info
- conda list
+ micromamba info
+ micromamba list
+ python -c "from openmmforcefields import __version__, __file__; print(__version__, __file__)"
- name: Test Installed Package
run: |
- pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_amber_import.py
- pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_template_generators.py
- pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_system_generator.py
+ pytest -v -x --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
+ openmmforcefields/tests/test_amber_import.py \
+ openmmforcefields/tests/test_template_generators.py \
+ openmmforcefields/tests/test_system_generator.py
env:
+ COV_ARGS: --cov=openmmforcefields --cov-config=setup.cfg --cov-append --cov-report=xml
LOGLEVEL: "INFO"
KMP_DUPLICATE_LIB_OK: "True"
@@ -93,11 +100,11 @@ jobs:
working-directory: ./charmm
- - name: CodeCov
+ - name: Upload coverage report to CodeCov
+ uses: codecov/codecov-action@v3.1.0
if: ${{ github.repository == 'openmm/openmmforcefields'
&& github.event != 'schedule' }}
- uses: codecov/codecov-action@v3.1.0
with:
+ token: ${{ secrets.CODECOV_TOKEN }}
file: ./coverage.xml
- flags: unittests
- name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+ fail_ci_if_error: true
diff --git a/.gitignore b/.gitignore
index 655d7cf7..893538fe 100644
--- a/.gitignore
+++ b/.gitignore
@@ -53,7 +53,10 @@ coverage.xml
# Django stuff:
*.log
-local_settings.py
+
+# Sphinx documentation
+docs/_build/
+docs/api/generated
# Flask stuff:
instance/
@@ -62,12 +65,13 @@ instance/
# Scrapy stuff:
.scrapy
-# Sphinx documentation
-docs/_build/
-
# PyBuilder
target/
+# PyCharm
+*.idea/vcs.xml
+
+# Jupyter
# Jupyter Notebook
.ipynb_checkpoints
@@ -108,5 +112,11 @@ ENV/
# In-tree generated files
*/_version.py
-# OS X extra files
+# macOS
*.DS_Store
+
+# Caches
+openmmforcefields/data/perses_jacs_systems/*/cache.json
+
+# Test molecules
+testsystem-bace*
diff --git a/amber/convert_amber.py b/amber/convert_amber.py
index 7097930f..68a9bf23 100644
--- a/amber/convert_amber.py
+++ b/amber/convert_amber.py
@@ -1,42 +1,43 @@
# AMBER --> OpenMM force-field conversion script
# Author: Rafal P. Wiewiora, ChoderaLab
-from __future__ import print_function, division
-from io import StringIO
-import parmed
-import openmm
-import openmm.app as app
-import openmm.unit as u
+import argparse
+import csv
+import glob
+import hashlib
import os
-import sys
import re
+import sys
import tempfile
-import yaml
-from distutils.spawn import find_executable
-import hashlib
-from collections import OrderedDict
-import glob
-import argparse
-from lxml import etree as et
-import csv
-import logging
import warnings
import xml.etree.ElementTree as etree
+from collections import OrderedDict
from copy import deepcopy
+from distutils.spawn import find_executable
+from io import StringIO
+
+import openmm
+import openmm.app as app
+import openmm.unit as u
+import parmed
+import yaml
+from lxml import etree as et
from parmed.exceptions import ParameterWarning
-warnings.filterwarnings('error', category=ParameterWarning)
+from pkg_resources import resource_filename
+
+warnings.filterwarnings("error", category=ParameterWarning)
-_loadoffre = re.compile(r'loadoff (\S*)', re.I)
-_sourcere = re.compile(r'source (\S*)', re.I)
+_loadoffre = re.compile(r"loadoff (\S*)", re.I)
+_sourcere = re.compile(r"source (\S*)", re.I)
# check for AMBERHOME, find from tleap location if not set, exception if can't
-if os.getenv('AMBERHOME'):
- AMBERHOME = os.getenv('AMBERHOME')
+if os.getenv("AMBERHOME"):
+ AMBERHOME = os.getenv("AMBERHOME")
else:
- if not find_executable('tleap'):
- raise Exception('AMBERHOME not set and tleap not available from PATH')
- tleap_path = find_executable('tleap')
+ if not find_executable("tleap"):
+ raise Exception("AMBERHOME not set and tleap not available from PATH")
+ tleap_path = find_executable("tleap")
AMBERHOME = os.path.split(tleap_path)[0]
- AMBERHOME = os.path.join(AMBERHOME, '../')
+ AMBERHOME = os.path.join(AMBERHOME, "../")
parmed.amber.AMBERHOME = AMBERHOME
# set global defaults for verbose and log
@@ -46,8 +47,13 @@
# set files that are ignored in leaprc's
# solvents and ions converted separately; leaprc.ff10 calls phosphoaa10.lib
# which does not exist anymore, LeAP skips it on error so we do too
-ignore = {'solvents.lib', 'atomic_ions.lib', 'ions94.lib', 'ions91.lib',
- 'phosphoaa10.lib'}
+ignore = {
+ "solvents.lib",
+ "atomic_ions.lib",
+ "ions94.lib",
+ "ions91.lib",
+ "phosphoaa10.lib",
+}
# define NEARLYZERO to replace numerical comparisons to zero
NEARLYZERO = 1e-10
@@ -56,66 +62,105 @@
temperature = 300.0 * u.kelvin
kB = u.BOLTZMANN_CONSTANT_kB * u.AVOGADRO_CONSTANT_NA
kT = kB * temperature
-beta = 1.0/kT
+beta = 1.0 / kT
+
class LeapException(Exception):
def __init__(self, leaprc_filename):
- msg = 'Something went wrong in processing this LEaP input file:\n'
- msg += '\n'
- infile = open(leaprc_filename, 'rt')
+ msg = "Something went wrong in processing this LEaP input file:\n"
+ msg += "\n"
+ infile = open(leaprc_filename)
contents = infile.read()
msg += contents
- msg += '\n'
- super(LeapException, self).__init__(msg)
+ msg += "\n"
+ super().__init__(msg)
+
def main():
global verbose
global no_log
global logger
# argparse
- parser = argparse.ArgumentParser(description='AMBER --> OpenMM forcefield '
- 'conversion script')
- parser.add_argument('--input', '-i', default='master.yaml',
- help='path of the input file. Default: "master.yaml"')
- parser.add_argument('--input-format', '-if', default='yaml',
- help='format of the input file: "yaml" or "leaprc". Default: "yaml"')
- parser.add_argument('--output-dir', '-od', help='path of the output directory. '
- 'Default: "ffxml/" for yaml, "./" for leaprc')
- parser.add_argument('--verbose', '-v', action='store_true',
- help='turns verbosity on')
- parser.add_argument('--log', action='store', dest='log_filename', default=None,
- help='log energies for tests to specified CSV file')
- parser.add_argument('--protein-test', action='store_true',
- help='validate resulting XML through protein tests')
- parser.add_argument('--nucleic-test', action='store_true',
- help='validate resulting XML through nucleic acid tests')
- parser.add_argument('--protein-ua-test', action='store_true',
- help='validate resulting XML through united-atom protein tests')
- parser.add_argument('--phospho-protein-test', action='store_true',
- help='validate resulting XML through phosphorylated protein tests')
- parser.add_argument('--gaff-test', action='store_true',
- help='validate resulting XML through small-molecule (GAFF) test')
- parser.add_argument('--lipids-test', action='store_true',
- help='validate resulting XML through lipids tests')
+ parser = argparse.ArgumentParser(
+ description="AMBER --> OpenMM forcefield " "conversion script"
+ )
+ parser.add_argument(
+ "--input",
+ "-i",
+ default="master.yaml",
+ help='path of the input file. Default: "master.yaml"',
+ )
+ parser.add_argument(
+ "--input-format",
+ "-if",
+ default="yaml",
+ help='format of the input file: "yaml" or "leaprc". Default: "yaml"',
+ )
+ parser.add_argument(
+ "--output-dir",
+ "-od",
+ help="path of the output directory. "
+ 'Default: "ffxml/" for yaml, "./" for leaprc',
+ )
+ parser.add_argument(
+ "--verbose", "-v", action="store_true", help="turns verbosity on"
+ )
+ parser.add_argument(
+ "--log",
+ action="store",
+ dest="log_filename",
+ default=None,
+ help="log energies for tests to specified CSV file",
+ )
+ parser.add_argument(
+ "--protein-test",
+ action="store_true",
+ help="validate resulting XML through protein tests",
+ )
+ parser.add_argument(
+ "--nucleic-test",
+ action="store_true",
+ help="validate resulting XML through nucleic acid tests",
+ )
+ parser.add_argument(
+ "--protein-ua-test",
+ action="store_true",
+ help="validate resulting XML through united-atom protein tests",
+ )
+ parser.add_argument(
+ "--phospho-protein-test",
+ action="store_true",
+ help="validate resulting XML through phosphorylated protein tests",
+ )
+ parser.add_argument(
+ "--gaff-test",
+ action="store_true",
+ help="validate resulting XML through small-molecule (GAFF) test",
+ )
+ parser.add_argument(
+ "--lipids-test",
+ action="store_true",
+ help="validate resulting XML through lipids tests",
+ )
args = parser.parse_args()
verbose = args.verbose
if args.log_filename:
- logger = Logger(args.log_filename) # log to file
+ logger = Logger(args.log_filename) # log to file
else:
- logger = Logger() # be silent
+ logger = Logger() # be silent
# input is either a YAML or a leaprc - default is leaprc
# output directory hardcoded here for ffxml/
- if args.input_format == 'yaml':
+ if args.input_format == "yaml":
if args.output_dir is None:
- convert_yaml(args.input, ffxml_dir='ffxml/')
+ convert_yaml(args.input, ffxml_dir="../openmmforcefields/ffxml/amber")
else:
convert_yaml(args.input, ffxml_dir=args.output_dir)
# if leaprc converted - output to the same dir
- elif args.input_format == 'leaprc':
+ elif args.input_format == "leaprc":
if args.output_dir is None:
- ffxml_name = convert_leaprc(args.input, ffxml_dir='./')
+ ffxml_name = convert_leaprc(args.input, ffxml_dir="./")
else:
ffxml_name = convert_leaprc(args.input, ffxml_dir=args.output_dir)
if args.protein_test:
@@ -131,19 +176,24 @@ def main():
if args.lipids_test:
validate_lipids(ffxml_name, args.input)
else:
- sys.exit('Wrong input_format chosen.')
+ sys.exit("Wrong input_format chosen.")
logger.close()
+
def read_lines(filename):
"""
Read lines from file, stripping comments and newlines.
"""
- with open(filename, 'rt') as f:
- lines = [ line if '#' not in line else line[:line.index('#')] for line in f.readlines() ]
+ with open(filename) as f:
+ lines = [
+ line if "#" not in line else line[: line.index("#")]
+ for line in f.readlines()
+ ]
return lines
+
def write_file(file, contents):
"""
Write text to file.
@@ -157,33 +207,45 @@ def write_file(file, contents):
"""
if type(file) == str:
- outfile = open(file, 'w')
+ outfile = open(file, "w")
else:
- outfile = os.fdopen(file, 'w')
+ outfile = os.fdopen(file, "w")
outfile.write(contents)
outfile.close()
-def convert_leaprc(files, split_filename=False, ffxml_dir='./', ignore=ignore,
- provenance=None, write_unused=False, override_level=None, filter_warnings='error', is_glycam=False):
- if verbose: print('\nConverting %s to ffxml...' % files)
+
+def convert_leaprc(
+ files,
+ split_filename=False,
+ ffxml_dir="./",
+ ignore=ignore,
+ provenance=None,
+ write_unused=False,
+ override_level=None,
+ filter_warnings="error",
+ is_glycam=False,
+):
+ if verbose:
+ print("\nConverting %s to ffxml..." % files)
# allow for multiple source files - further code assuming list is passed
if not isinstance(files, list):
files = [files]
- basename = ''
+ basename = ""
for f in files:
f_basename = os.path.basename(f)
if split_filename:
- f_basename = f_basename.split('.')[1:]
- f_basename = '.'.join(f_basename)
+ f_basename = f_basename.split(".")[1:]
+ f_basename = ".".join(f_basename)
if not basename:
basename = f_basename
else:
- basename += '_'
+ basename += "_"
basename += f_basename
- ffxml_name = os.path.join(ffxml_dir, (basename + '.xml'))
+ ffxml_name = os.path.join(ffxml_dir, (basename + ".xml"))
if not os.path.exists(ffxml_dir):
os.mkdir(ffxml_dir)
- if verbose: print('Preprocessing the leaprc for %s...' % basename)
+ if verbose:
+ print("Preprocessing the leaprc for %s..." % basename)
# do source processing
new_files = []
for fil in files:
@@ -191,8 +253,9 @@ def convert_leaprc(files, split_filename=False, ffxml_dir='./', ignore=ignore,
for line in lines:
if _sourcere.findall(line):
replace_leaprc = _sourcere.findall(line)[0]
- replace_leaprc_path = os.path.join(os.path.join(AMBERHOME,
- 'dat/leap/cmd', replace_leaprc))
+ replace_leaprc_path = os.path.join(
+ os.path.join(AMBERHOME, "dat/leap/cmd", replace_leaprc)
+ )
new_files.append(replace_leaprc_path)
new_files.append(fil)
# now do ignore processing and join multiple leaprc's
@@ -202,15 +265,21 @@ def convert_leaprc(files, split_filename=False, ffxml_dir='./', ignore=ignore,
lines = read_lines(fil)
fil_new_lines = []
for line in lines:
- if (ignore is not None and _loadoffre.findall(line) and
- _loadoffre.findall(line)[0] in ignore):
+ if (
+ ignore is not None
+ and _loadoffre.findall(line)
+ and _loadoffre.findall(line)[0] in ignore
+ ):
continue
fil_new_lines += line
new_lines += fil_new_lines
- leaprc = StringIO(''.join(new_lines))
- if verbose: print('Converting to ffxml %s...' % ffxml_name)
+ leaprc = StringIO("".join(new_lines))
+ if verbose:
+ print("Converting to ffxml %s..." % ffxml_name)
params = parmed.amber.AmberParameterSet.from_leaprc(leaprc)
- params = parmed.openmm.OpenMMParameterSet.from_parameterset(params, remediate_residues=(not write_unused))
+ params = parmed.openmm.OpenMMParameterSet.from_parameterset(
+ params, remediate_residues=(not write_unused)
+ )
if override_level:
for name, residue in params.residues.items():
residue.override_level = override_level
@@ -218,41 +287,87 @@ def convert_leaprc(files, split_filename=False, ffxml_dir='./', ignore=ignore,
skip_duplicates = False
else:
skip_duplicates = True
- if filter_warnings != 'error':
+ if filter_warnings != "error":
with warnings.catch_warnings():
warnings.filterwarnings(filter_warnings, category=ParameterWarning)
- params.write(ffxml_name, provenance=provenance, write_unused=write_unused, improper_dihedrals_ordering='amber', skip_duplicates=skip_duplicates, is_glycam=is_glycam)
+ params.write(
+ ffxml_name,
+ provenance=provenance,
+ write_unused=write_unused,
+ improper_dihedrals_ordering="amber",
+ skip_duplicates=skip_duplicates,
+ is_glycam=is_glycam,
+ )
else:
- params.write(ffxml_name, provenance=provenance, write_unused=write_unused, improper_dihedrals_ordering='amber', skip_duplicates=skip_duplicates, is_glycam=is_glycam)
- if verbose: print('%s successfully written!' % ffxml_name)
+ params.write(
+ ffxml_name,
+ provenance=provenance,
+ write_unused=write_unused,
+ improper_dihedrals_ordering="amber",
+ skip_duplicates=skip_duplicates,
+ is_glycam=is_glycam,
+ )
+ if verbose:
+ print("%s successfully written!" % ffxml_name)
return ffxml_name
-def convert_gaff(files, ffxml_basename='', split_filename=False, ffxml_dir='./', ignore=ignore,
- provenance=None, write_unused=False, filter_warnings='error'):
- if verbose: print('\nConverting %s to ffxml...' % files)
+
+def convert_gaff(
+ files,
+ ffxml_basename="",
+ split_filename=False,
+ ffxml_dir="../openmmforcefields/ffxml",
+ ignore=ignore,
+ provenance=None,
+ write_unused=False,
+ filter_warnings="error",
+):
+ if verbose:
+ print("\nConverting %s to ffxml..." % files)
# allow for multiple source files - further code assuming list is passed
if not isinstance(files, list):
files = [files]
# Create ffxml
- ffxml_name = os.path.join(ffxml_dir, (ffxml_basename + '.xml'))
+ ffxml_name = os.path.join(ffxml_dir, (ffxml_basename + ".xml"))
if not os.path.exists(ffxml_dir):
os.mkdir(ffxml_dir)
# Process parameter file
params = parmed.amber.AmberParameterSet(files)
- params = parmed.openmm.OpenMMParameterSet.from_parameterset(params, remediate_residues=(not write_unused))
- if filter_warnings != 'error':
+ params = parmed.openmm.OpenMMParameterSet.from_parameterset(
+ params, remediate_residues=(not write_unused)
+ )
+ if filter_warnings != "error":
with warnings.catch_warnings():
warnings.filterwarnings(filter_warnings, category=ParameterWarning)
- params.write(ffxml_name, provenance=provenance, write_unused=write_unused, improper_dihedrals_ordering='amber')
+ params.write(
+ ffxml_name,
+ provenance=provenance,
+ write_unused=write_unused,
+ improper_dihedrals_ordering="amber",
+ )
else:
- params.write(ffxml_name, provenance=provenance, write_unused=write_unused, improper_dihedrals_ordering='amber')
- if verbose: print('%s successfully written!' % ffxml_name)
+ params.write(
+ ffxml_name,
+ provenance=provenance,
+ write_unused=write_unused,
+ improper_dihedrals_ordering="amber",
+ )
+ if verbose:
+ print("%s successfully written!" % ffxml_name)
return ffxml_name
-def convert_recipe(files, solvent_file=None, ffxml_dir='./', provenance=None, ffxml_basename=None,
- filter_warnings='always'):
- if verbose: print('\nConverting %s to ffxml...' % files)
- ffxml_name = os.path.join(ffxml_dir, (ffxml_basename + '.xml'))
+
+def convert_recipe(
+ files,
+ solvent_file=None,
+ ffxml_dir="./",
+ provenance=None,
+ ffxml_basename=None,
+ filter_warnings="always",
+):
+ if verbose:
+ print("\nConverting %s to ffxml..." % files)
+ ffxml_name = os.path.join(ffxml_dir, (ffxml_basename + ".xml"))
ffxml_temp_stringio = StringIO()
params = parmed.amber.AmberParameterSet(files)
print(params.atom_types.keys())
@@ -261,244 +376,294 @@ def convert_recipe(files, solvent_file=None, ffxml_dir='./', provenance=None, ff
# atom_types
new_atom_types = OrderedDict()
for name, atom_type in params.atom_types.items():
- new_name = ffxml_basename + '-' + name
+ new_name = ffxml_basename + "-" + name
new_atom_types[new_name] = atom_type
params.atom_types = new_atom_types
# atoms in residues
for name, residue in params.residues.items():
for atom in residue:
- new_type = ffxml_basename + '-' + atom.type
+ new_type = ffxml_basename + "-" + atom.type
atom.type = new_type
if solvent_file is None:
- # this means this file does not include a water model - hard-coded assumption it is
- # then a 'multivalent' file - set overrideLevel to 1 for all residue templates
+ # this means this file does not include a water model - hard-coded assumption it is
+ # then a 'multivalent' file - set overrideLevel to 1 for all residue templates
for name, residue in params.residues.items():
residue.override_level = 1
with warnings.catch_warnings():
warnings.filterwarnings(filter_warnings, category=ParameterWarning)
- params.write(ffxml_name, provenance=provenance, write_unused=False, improper_dihedrals_ordering='amber')
+ params.write(
+ ffxml_name,
+ provenance=provenance,
+ write_unused=False,
+ improper_dihedrals_ordering="amber",
+ )
else:
with warnings.catch_warnings():
warnings.filterwarnings(filter_warnings, category=ParameterWarning)
- params.write(ffxml_temp_stringio, provenance=provenance, write_unused=False, improper_dihedrals_ordering='amber')
+ params.write(
+ ffxml_temp_stringio,
+ provenance=provenance,
+ write_unused=False,
+ improper_dihedrals_ordering="amber",
+ )
ffxml_temp_stringio.seek(0)
- if verbose: print('Modifying converted ffxml to append solvent parameters')
+ if verbose:
+ print("Modifying converted ffxml to append solvent parameters")
tree_main = et.parse(ffxml_temp_stringio)
tree_water = et.parse(solvent_file)
root_main = tree_main.getroot()
root_water = tree_water.getroot()
- with open(ffxml_name, 'wb') as f:
- f.write(b'\n ')
- f.write(et.tostring(root_main.findall('Info')[0]))
- f.write(b'\n ')
- for subelement in root_main.findall('AtomTypes')[0]:
+ with open(ffxml_name, "wb") as f:
+ f.write(b"\n ")
+ f.write(et.tostring(root_main.findall("Info")[0]))
+ f.write(b"\n ")
+ for subelement in root_main.findall("AtomTypes")[0]:
f.write(et.tostring(subelement))
- f.write(b' ')
- for subelement in root_water.findall('AtomTypes')[0]:
+ f.write(b" ")
+ for subelement in root_water.findall("AtomTypes")[0]:
f.write(et.tostring(subelement))
- f.write(b'\n \n ')
- for subelement in root_main.findall('Residues')[0]:
+ f.write(b"\n \n ")
+ for subelement in root_main.findall("Residues")[0]:
f.write(et.tostring(subelement))
- f.write(b' ')
- for subelement in root_water.findall('Residues')[0]:
+ f.write(b" ")
+ for subelement in root_water.findall("Residues")[0]:
f.write(et.tostring(subelement))
- f.write(b'\n \n ')
- for subelement in root_water.findall('HarmonicBondForce')[0]:
+ f.write(b"\n \n ")
+ for subelement in root_water.findall("HarmonicBondForce")[0]:
f.write(et.tostring(subelement))
- f.write(b'\n \n ')
- for subelement in root_water.findall('HarmonicAngleForce')[0]:
+ f.write(b"\n \n ")
+ for subelement in root_water.findall("HarmonicAngleForce")[0]:
f.write(et.tostring(subelement))
- f.write(b'\n ')
- f.write(('\n ' %
- (root_main.findall('NonbondedForce')[0].attrib['coulomb14scale'],
- root_main.findall('NonbondedForce')[0].attrib['lj14scale'])
- ).encode('utf-8'))
- for subelement in root_main.findall('NonbondedForce')[0]:
+ f.write(b"\n ")
+ f.write(
+ (
+ '\n '
+ % (
+ root_main.findall("NonbondedForce")[0].attrib["coulomb14scale"],
+ root_main.findall("NonbondedForce")[0].attrib["lj14scale"],
+ )
+ ).encode("utf-8")
+ )
+ for subelement in root_main.findall("NonbondedForce")[0]:
f.write(et.tostring(subelement))
- f.write(b' ')
- for subelement in root_water.findall('NonbondedForce')[0]:
- if subelement.tag == 'UseAttributeFromResidue': continue
+ f.write(b" ")
+ for subelement in root_water.findall("NonbondedForce")[0]:
+ if subelement.tag == "UseAttributeFromResidue":
+ continue
f.write(et.tostring(subelement))
- f.write(b'\n')
- if verbose: print('%s successfully written!' % ffxml_name)
+ f.write(b"\n")
+ if verbose:
+ print("%s successfully written!" % ffxml_name)
return ffxml_name
+
def convert_yaml(yaml_name, ffxml_dir, ignore=ignore):
data = yaml.load(open(yaml_name), Loader=yaml.FullLoader)
# TODO: Verify that the version that is installed via conda matches sourcePackageVersion
# Default yaml reading mode is leaprc
- ALLOWED_MODES = ('LEAPRC', 'RECIPE', 'GAFF')
+ ALLOWED_MODES = ("LEAPRC", "RECIPE", "GAFF")
for entry in data:
# Handle MODE switching
- if 'MODE' in entry:
- MODE = entry['MODE']
+ if "MODE" in entry:
+ MODE = entry["MODE"]
if not MODE in ALLOWED_MODES:
- raise Exception(f'MODE definition must be one of {ALLOWED_MODES}')
+ raise Exception(f"MODE definition must be one of {ALLOWED_MODES}")
continue
# Handle definition of source packages
- if 'sourcePackage' in entry:
- source_pack = entry['sourcePackage']
- source_pack_ver = entry['sourcePackageVersion']
+ if "sourcePackage" in entry:
+ source_pack = entry["sourcePackage"]
+ source_pack_ver = entry["sourcePackageVersion"]
continue
- if 'sourcePackage2' in entry:
+ if "sourcePackage2" in entry:
# Switch mode to RECIPE processing
- source_pack2 = entry['sourcePackage2']
- source_pack_ver2 = entry['sourcePackageVersion2']
+ source_pack2 = entry["sourcePackage2"]
+ source_pack_ver2 = entry["sourcePackageVersion2"]
continue
# Extract source files, reference, and test files
- source_files = entry['Source']
- reference = entry['Reference']
- test_filename = entry['Test']
+ source_files = entry["Source"]
+ reference = entry["Reference"]
+ test_filename = entry["Test"]
# Make sure source_files is a list
if isinstance(source_files, str):
source_files = [source_files]
# Recipes require extra definitions
- if MODE == 'RECIPE':
- recipe_name = entry['Name']
- solvent_name = entry['Solvent']
- if 'Solvent_source' in entry:
- recipe_source2 = entry['Solvent_source']
+ if MODE == "RECIPE":
+ recipe_name = entry["Name"]
+ solvent_name = entry["Solvent"]
+ if "Solvent_source" in entry:
+ recipe_source2 = entry["Solvent_source"]
else:
recipe_source2 = None
- if 'Standard' in entry:
- standard_ffxml = os.path.join(ffxml_dir, (entry['Standard'] + '.xml'))
+ if "Standard" in entry:
+ standard_ffxml = os.path.join(ffxml_dir, (entry["Standard"] + ".xml"))
else:
standard_ffxml = None
- elif MODE == 'GAFF':
- recipe_name = entry['Name']
+ elif MODE == "GAFF":
+ recipe_name = entry["Name"]
# Create provenance object
provenance = OrderedDict()
files = []
- source = provenance['Source'] = []
+ source = provenance["Source"] = []
for source_file in source_files:
- if MODE == 'LEAPRC':
- if os.path.exists(source_file):
- _filename = os.path.join('./', source_file)
- else:
- _filename = os.path.join(AMBERHOME, 'dat/leap/cmd', source_file)
- elif MODE == 'RECIPE':
- _filename = os.path.join(AMBERHOME, 'dat/leap/', source_file)
- elif MODE == 'GAFF':
- _filename = os.path.join('gaff', 'dat', source_file)
+ if MODE == "LEAPRC":
+ if os.path.exists(source_file):
+ _filename = os.path.join("./", source_file)
+ else:
+ _filename = os.path.join(AMBERHOME, "dat/leap/cmd", source_file)
+ elif MODE == "RECIPE":
+ _filename = os.path.join(AMBERHOME, "dat/leap/", source_file)
+ elif MODE == "GAFF":
+ _filename = os.path.join(
+ resource_filename("openmmforcefields", "ffxml/amber/gaff/dat"),
+ source_file,
+ )
files.append(_filename)
source.append(OrderedDict())
- source[-1]['Source'] = source_file
+ source[-1]["Source"] = source_file
md5 = hashlib.md5()
- with open(_filename, 'rb') as f:
+ with open(_filename, "rb") as f:
md5.update(f.read())
md5 = md5.hexdigest()
- source[-1]['md5hash'] = md5
- source[-1]['sourcePackage'] = source_pack
- source[-1]['sourcePackageVersion'] = source_pack_ver
+ source[-1]["md5hash"] = md5
+ source[-1]["sourcePackage"] = source_pack
+ source[-1]["sourcePackageVersion"] = source_pack_ver
# For recipes, add water file and source info for it
- if MODE == 'RECIPE' and recipe_source2 is not None:
- _filename = os.path.join('files', recipe_source2)
+ if MODE == "RECIPE" and recipe_source2 is not None:
+ _filename = os.path.join("files", recipe_source2)
solvent_file = _filename
source.append(OrderedDict())
- source[-1]['Source'] = recipe_source2
+ source[-1]["Source"] = recipe_source2
md5 = hashlib.md5()
- with open(_filename, 'rb') as f:
+ with open(_filename, "rb") as f:
md5.update(f.read())
md5 = md5.hexdigest()
- source[-1]['md5hash'] = md5
- source[-1]['sourcePackage'] = source_pack2
- source[-1]['sourcePackageVersion'] = source_pack_ver2
- elif MODE == 'RECIPE' and recipe_source2 is None:
+ source[-1]["md5hash"] = md5
+ source[-1]["sourcePackage"] = source_pack2
+ source[-1]["sourcePackageVersion"] = source_pack_ver2
+ elif MODE == "RECIPE" and recipe_source2 is None:
solvent_file = None
- provenance['Reference'] = reference
+ provenance["Reference"] = reference
# set default conversion options
write_unused = False
- filter_warnings = 'error'
+ filter_warnings = "error"
override_level = None
# set conversion options if present
- if 'Options' in entry:
- for option in entry['Options']:
- if option == 'write_unused':
- write_unused = entry['Options'][option]
- elif option == 'filter_warnings':
- filter_warnings = entry['Options'][option]
- elif option == 'ffxml_dir':
- ffxml_dir = entry['Options'][option]
- elif option == 'override_level':
- override_level = entry['Options'][option]
+ if "Options" in entry:
+ for option in entry["Options"]:
+ if option == "write_unused":
+ write_unused = entry["Options"][option]
+ elif option == "filter_warnings":
+ filter_warnings = entry["Options"][option]
+ elif option == "ffxml_dir":
+ ffxml_dir = entry["Options"][option]
+ elif option == "override_level":
+ override_level = entry["Options"][option]
else:
- raise Exception("Wrong option used in Options for %s"
- % source_files)
+ raise Exception(
+ "Wrong option used in Options for %s" % source_files
+ )
# Convert files
- if MODE == 'LEAPRC':
+ if MODE == "LEAPRC":
is_glycam = False
for source_file in source_files:
- if 'GLYCAM' in source_file:
+ if "GLYCAM" in source_file:
is_glycam = True
- ffxml_name = convert_leaprc(files, ffxml_dir=ffxml_dir, ignore=ignore,
- provenance=provenance, write_unused=write_unused, override_level=override_level,
- filter_warnings=filter_warnings, split_filename=True, is_glycam=is_glycam)
- elif MODE == 'RECIPE':
- ffxml_name = convert_recipe(files, solvent_file=solvent_file,
- ffxml_dir=ffxml_dir, provenance=provenance,
- ffxml_basename=recipe_name)
- elif MODE == 'GAFF':
- ffxml_name = convert_gaff(files, ffxml_basename=recipe_name, ffxml_dir=ffxml_dir, ignore=ignore,
- provenance=provenance, write_unused=write_unused,
- filter_warnings=filter_warnings, split_filename=True)
-
- if 'CharmmFFXMLFilename' in entry:
- charmm_ffxml_filename = entry['CharmmFFXMLFilename']
- charmm_lipid2amber_filename = entry['CharmmLipid2AmberFilename']
- if verbose: print('Merging lipid entries...')
+ ffxml_name = convert_leaprc(
+ files,
+ ffxml_dir=ffxml_dir,
+ ignore=ignore,
+ provenance=provenance,
+ write_unused=write_unused,
+ override_level=override_level,
+ filter_warnings=filter_warnings,
+ split_filename=True,
+ is_glycam=is_glycam,
+ )
+ elif MODE == "RECIPE":
+ ffxml_name = convert_recipe(
+ files,
+ solvent_file=solvent_file,
+ ffxml_dir=ffxml_dir,
+ provenance=provenance,
+ ffxml_basename=recipe_name,
+ )
+ elif MODE == "GAFF":
+ ffxml_name = convert_gaff(
+ files,
+ ffxml_basename=recipe_name,
+ ffxml_dir=ffxml_dir,
+ ignore=ignore,
+ provenance=provenance,
+ write_unused=write_unused,
+ filter_warnings=filter_warnings,
+ split_filename=True,
+ )
+
+ if "CharmmFFXMLFilename" in entry:
+ charmm_ffxml_filename = entry["CharmmFFXMLFilename"]
+ charmm_lipid2amber_filename = entry["CharmmLipid2AmberFilename"]
+ if verbose:
+ print("Merging lipid entries...")
merge_lipids(ffxml_name, charmm_ffxml_filename, charmm_lipid2amber_filename)
- if 'Prefix' in entry:
- prefix = entry['Prefix']
- if verbose: print('Rewriting %s to append prefix "%s"...' % (ffxml_name, prefix))
+ if "Prefix" in entry:
+ prefix = entry["Prefix"]
+ if verbose:
+ print(f'Rewriting {ffxml_name} to append prefix "{prefix}"...')
add_prefix_to_ffxml(ffxml_name, prefix)
- if verbose: print('Validating the conversion...')
+ if verbose:
+ print("Validating the conversion...")
tested = False
for test in test_filename:
- if test == 'protein':
- validate_protein(ffxml_name, entry['Source'])
+ if test == "protein":
+ validate_protein(ffxml_name, entry["Source"])
tested = True
- elif test == 'nucleic':
- validate_dna(ffxml_name, entry['Source'])
- validate_rna(ffxml_name, entry['Source'])
+ elif test == "nucleic":
+ validate_dna(ffxml_name, entry["Source"])
+ validate_rna(ffxml_name, entry["Source"])
tested = True
- elif test == 'protein_ua':
- validate_protein(ffxml_name, entry['Source'], united_atom=True)
+ elif test == "protein_ua":
+ validate_protein(ffxml_name, entry["Source"], united_atom=True)
tested = True
- elif test == 'protein_phospho':
- validate_phospho_protein(ffxml_name, entry['Source'])
+ elif test == "protein_phospho":
+ validate_phospho_protein(ffxml_name, entry["Source"])
tested = True
- elif test == 'gaff':
- validate_gaff(ffxml_name, entry['leaprc'], entry['Source'])
+ elif test == "gaff":
+ validate_gaff(ffxml_name, entry["leaprc"], entry["Source"])
tested = True
- elif test == 'water_ion':
- validate_water_ion(ffxml_name, files, solvent_name, recipe_name,
- standard_ffxml=standard_ffxml)
+ elif test == "water_ion":
+ validate_water_ion(
+ ffxml_name,
+ files,
+ solvent_name,
+ recipe_name,
+ standard_ffxml=standard_ffxml,
+ )
tested = True
- elif test == 'dna':
- validate_dna(ffxml_name, entry['Source'])
+ elif test == "dna":
+ validate_dna(ffxml_name, entry["Source"])
tested = True
- elif test == 'rna':
- validate_rna(ffxml_name, entry['Source'])
+ elif test == "rna":
+ validate_rna(ffxml_name, entry["Source"])
tested = True
- elif test == 'lipids':
- #validate_lipids(ffxml_name, source_files)
- validate_merged_lipids(ffxml_name, entry['Source'])
+ elif test == "lipids":
+ # validate_lipids(ffxml_name, source_files)
+ validate_merged_lipids(ffxml_name, entry["Source"])
tested = True
- elif test == 'protein_glycan':
- validate_glyco_protein(ffxml_name, entry['Source'])
+ elif test == "protein_glycan":
+ validate_glyco_protein(ffxml_name, entry["Source"])
tested = True
if not tested:
- raise Exception('No validation tests have been run for %s' %
- source_files)
+ raise Exception("No validation tests have been run for %s" % source_files)
+
def merge_lipids(ffxml_filename, charmm_ffxml_filename, charmm_lipid2amber_filename):
"""
@@ -517,26 +682,26 @@ def merge_lipids(ffxml_filename, charmm_ffxml_filename, charmm_lipid2amber_filen
# Read the input files.
charmmff = etree.parse(charmm_ffxml_filename)
amberff = etree.parse(ffxml_filename)
- charmmResidues = charmmff.getroot().find('Residues').findall('Residue')
- amberResidues = amberff.getroot().find('Residues').findall('Residue')
+ charmmResidues = charmmff.getroot().find("Residues").findall("Residue")
+ amberResidues = amberff.getroot().find("Residues").findall("Residue")
amberResMap = {}
for res in amberResidues:
- atoms = dict((atom.attrib['name'], atom) for atom in res.findall('Atom'))
- amberResMap[res.attrib['name']] = atoms
+ atoms = {atom.attrib["name"]: atom for atom in res.findall("Atom")}
+ amberResMap[res.attrib["name"]] = atoms
translations = {}
with open(charmm_lipid2amber_filename) as input:
# Skip the first two lines.
input.readline()
input.readline()
for line in input:
- fields = line.split(',')
+ fields = line.split(",")
mergedRes = fields[0]
mergedAtom = fields[2].split()[0]
originalAtom, originalRes = fields[3].split()
translations[(mergedRes, mergedAtom)] = (originalRes, originalAtom)
# Remove all residues from the Amber file.
- parentNode = amberff.getroot().find('Residues')
+ parentNode = amberff.getroot().find("Residues")
for res in amberResidues:
parentNode.remove(res)
@@ -544,19 +709,22 @@ def merge_lipids(ffxml_filename, charmm_ffxml_filename, charmm_lipid2amber_filen
def translateResidue(residue):
newres = deepcopy(residue)
# Translate atom properties
- for atom in newres.findall('Atom'):
- key = (residue.attrib['name'], atom.attrib['name'])
+ for atom in newres.findall("Atom"):
+ key = (residue.attrib["name"], atom.attrib["name"])
if key not in translations:
- return None # We don't have a translation.
+ return None # We don't have a translation.
amberResName, amberAtomName = translations[key]
- if amberResName not in amberResMap or amberAtomName not in amberResMap[amberResName]:
- return None # We don't have a translation.
+ if (
+ amberResName not in amberResMap
+ or amberAtomName not in amberResMap[amberResName]
+ ):
+ return None # We don't have a translation.
amberAtom = amberResMap[amberResName][amberAtomName]
for attrib in amberAtom.attrib:
- if attrib != 'name':
+ if attrib != "name":
atom.attrib[attrib] = amberAtom.attrib[attrib]
# Remove Patches from CHARMM residues
- for patch in newres.findall('AllowPatch'):
+ for patch in newres.findall("AllowPatch"):
newres.remove(patch)
return newres
@@ -570,6 +738,7 @@ def translateResidue(residue):
# Write merged lipid ffxml file (overwriting original file)
amberff.write(ffxml_filename)
+
def add_prefix_to_ffxml(ffxml_filename, prefix):
"""
Replace the contents of an ffxml file with a modified version in which every atom type is prefixed with `prefix`.
@@ -589,18 +758,18 @@ def add_prefix_to_ffxml(ffxml_filename, prefix):
inTypes = False
replacements = {}
- modified_contents = ''
- with open(ffxml_filename, 'r') as infile:
+ modified_contents = ""
+ with open(ffxml_filename) as infile:
for line in infile:
- if '' in line:
+ if "" in line:
inTypes = True
- if '' in line:
+ if "" in line:
inTypes = False
if inTypes:
match = re.search('name="(.*?)"', line)
if match is not None:
name = match.group(1)
- newName = prefix + '-' + name
+ newName = prefix + "-" + name
line = line.replace('name="%s"' % name, 'name="%s"' % newName)
replacements['type="%s"' % name] = 'type="%s"' % newName
replacements['type1="%s"' % name] = 'type1="%s"' % newName
@@ -611,13 +780,14 @@ def add_prefix_to_ffxml(ffxml_filename, prefix):
for key in replacements:
if key in line:
line = line.replace(key, replacements[key])
- if line.endswith('\n'):
+ if line.endswith("\n"):
line = line[:-1]
- modified_contents += line + '\n'
+ modified_contents += line + "\n"
- with open(ffxml_filename, 'w') as outfile:
+ with open(ffxml_filename, "w") as outfile:
outfile.write(modified_contents)
+
def assert_energies_glyco_protein(prmtop, inpcrd, ffxml, tolerance=1e-1):
import math
@@ -635,16 +805,22 @@ def assert_energies_glyco_protein(prmtop, inpcrd, ffxml, tolerance=1e-1):
for residue in chain.residues():
new_name = residue.name
if residue.index in [0, 5, 13, 21, 29]:
- new_name = 'N' + residue.name
+ new_name = "N" + residue.name
elif residue.index in [4, 9, 17, 25, 33]:
- new_name = 'C' + residue.name
- new_residue = destination_topology.addResidue(new_name, new_chain, residue.id)
+ new_name = "C" + residue.name
+ new_residue = destination_topology.addResidue(
+ new_name, new_chain, residue.id
+ )
for atom in residue.atoms():
- new_atom = destination_topology.addAtom(atom.name, atom.element, new_residue, atom.id)
+ new_atom = destination_topology.addAtom(
+ atom.name, atom.element, new_residue, atom.id
+ )
new_atoms[atom] = new_atom
for bond in source_topology.bonds():
order = bond.order
- destination_topology.addBond(new_atoms[bond[0]], new_atoms[bond[1]], order=order)
+ destination_topology.addBond(
+ new_atoms[bond[0]], new_atoms[bond[1]], order=order
+ )
# Get OpenMM system
if isinstance(ffxml, str):
@@ -660,16 +836,19 @@ def compute_potential_components(system, positions, beta=beta):
for index in range(system.getNumForces()):
force = system.getForce(index)
force.setForceGroup(index)
- integrator = openmm.VerletIntegrator(1.0*u.femtosecond)
- platform = openmm.Platform.getPlatformByName('Reference')
+ integrator = openmm.VerletIntegrator(1.0 * u.femtosecond)
+ platform = openmm.Platform.getPlatformByName("Reference")
context = openmm.Context(system, integrator, platform)
context.setPositions(positions)
energy_components = list()
for index in range(system.getNumForces()):
force = system.getForce(index)
forcename = force.__class__.__name__
- groups = 1< NEARLYZERO:
- rel_energies.append((i[0], abs((i[1]-j[1])/i[1])))
+ rel_energies.append((i[0], abs((i[1] - j[1]) / i[1])))
else:
if abs(j[1]) > NEARLYZERO:
- raise AssertionError('One of AMBER %s energies (%s) for %s is zero, '
- 'while the corresponding OpenMM energy is non-zero' %
- (system_name, i[0], ffxml))
+ raise AssertionError(
+ "One of AMBER %s energies (%s) for %s is zero, "
+ "while the corresponding OpenMM energy is non-zero"
+ % (system_name, i[0], ffxml)
+ )
rel_energies.append((i[0], 0))
dihedrals_done = False
- for (i, amber_energy, openmm_energy) in zip(rel_energies, amber_energies, omm_energies):
- if i[0] != 'PeriodicTorsionForce':
+ for (i, amber_energy, openmm_energy) in zip(
+ rel_energies, amber_energies, omm_energies
+ ):
+ if i[0] != "PeriodicTorsionForce":
if i[1] > tolerance:
- raise AssertionError('%s relative energy error (%s, %f) outside of allowed tolerance (%f) for %s: AMBER %s OpenMM %s' %
- (system_name, i[0], i[1], tolerance, ffxml, amber_energy, openmm_energy))
+ raise AssertionError(
+ "%s relative energy error (%s, %f) outside of allowed tolerance (%f) for %s: AMBER %s OpenMM %s"
+ % (
+ system_name,
+ i[0],
+ i[1],
+ tolerance,
+ ffxml,
+ amber_energy,
+ openmm_energy,
+ )
+ )
else:
if not dihedrals_done:
if i[1] > tolerance:
- raise AssertionError('%s relative energy error (%s, %f) outside of allowed tolerance (%f) for %s: AMBER %s OpenMM %s' %
- (system_name, i[0], i[1], tolerance, ffxml, amber_energy, openmm_energy))
+ raise AssertionError(
+ "%s relative energy error (%s, %f) outside of allowed tolerance (%f) for %s: AMBER %s OpenMM %s"
+ % (
+ system_name,
+ i[0],
+ i[1],
+ tolerance,
+ ffxml,
+ amber_energy,
+ openmm_energy,
+ )
+ )
dihedrals_done = True
- else: #impropers
+ else: # impropers
if i[1] > improper_tolerance:
- raise AssertionError('%s relative energy error (%s-impropers, %f) outside of allowed tolerance (%f) for %s: AMBER %s OpenMM %s' %
- (system_name, i[0], i[1], improper_tolerance, ffxml, amber_energy, openmm_energy))
+ raise AssertionError(
+ "%s relative energy error (%s-impropers, %f) outside of allowed tolerance (%f) for %s: AMBER %s OpenMM %s"
+ % (
+ system_name,
+ i[0],
+ i[1],
+ improper_tolerance,
+ ffxml,
+ amber_energy,
+ openmm_energy,
+ )
+ )
# logging
if not no_log:
amber_energies_log = dict()
omm_energies_log = dict()
rel_energies_log = dict()
- amber_energies_log['ffxml_name'] = ffxml
- amber_energies_log['test_system'] = system_name
- amber_energies_log['data_type'] = 'AMBER'
- amber_energies_log['units'] = units
- omm_energies_log['ffxml_name'] = ffxml
- omm_energies_log['test_system'] = system_name
- omm_energies_log['data_type'] = 'OpenMM'
- omm_energies_log['units'] = units
- rel_energies_log['ffxml_name'] = ffxml
- rel_energies_log['test_system'] = system_name
- rel_energies_log['data_type'] = 'abs((AMBER-OpenMM)/AMBER)'
+ amber_energies_log["ffxml_name"] = ffxml
+ amber_energies_log["test_system"] = system_name
+ amber_energies_log["data_type"] = "AMBER"
+ amber_energies_log["units"] = units
+ omm_energies_log["ffxml_name"] = ffxml
+ omm_energies_log["test_system"] = system_name
+ omm_energies_log["data_type"] = "OpenMM"
+ omm_energies_log["units"] = units
+ rel_energies_log["ffxml_name"] = ffxml
+ rel_energies_log["test_system"] = system_name
+ rel_energies_log["data_type"] = "abs((AMBER-OpenMM)/AMBER)"
dihedrals_done = False
for item in amber_energies:
- if item[0] == 'PeriodicTorsionForce' and not dihedrals_done:
- amber_energies_log['PeriodicTorsionForce_dihedrals'] = item[1]
+ if item[0] == "PeriodicTorsionForce" and not dihedrals_done:
+ amber_energies_log["PeriodicTorsionForce_dihedrals"] = item[1]
dihedrals_done = True
- elif item[0] == 'PeriodicTorsionForce' and dihedrals_done:
- amber_energies_log['PeriodicTorsionForce_impropers'] = item[1]
- elif item[0] == 'CMMotionRemover':
+ elif item[0] == "PeriodicTorsionForce" and dihedrals_done:
+ amber_energies_log["PeriodicTorsionForce_impropers"] = item[1]
+ elif item[0] == "CMMotionRemover":
continue
else:
amber_energies_log[item[0]] = item[1]
dihedrals_done = False
for item in omm_energies:
- if item[0] == 'PeriodicTorsionForce' and not dihedrals_done:
- omm_energies_log['PeriodicTorsionForce_dihedrals'] = item[1]
+ if item[0] == "PeriodicTorsionForce" and not dihedrals_done:
+ omm_energies_log["PeriodicTorsionForce_dihedrals"] = item[1]
dihedrals_done = True
- elif item[0] == 'PeriodicTorsionForce' and dihedrals_done:
- omm_energies_log['PeriodicTorsionForce_impropers'] = item[1]
- elif item[0] == 'CMMotionRemover':
+ elif item[0] == "PeriodicTorsionForce" and dihedrals_done:
+ omm_energies_log["PeriodicTorsionForce_impropers"] = item[1]
+ elif item[0] == "CMMotionRemover":
continue
else:
omm_energies_log[item[0]] = item[1]
dihedrals_done = False
for item in rel_energies:
- if item[0] == 'PeriodicTorsionForce' and not dihedrals_done:
- rel_energies_log['PeriodicTorsionForce_dihedrals'] = item[1]
+ if item[0] == "PeriodicTorsionForce" and not dihedrals_done:
+ rel_energies_log["PeriodicTorsionForce_dihedrals"] = item[1]
dihedrals_done = True
- elif item[0] == 'PeriodicTorsionForce' and dihedrals_done:
- rel_energies_log['PeriodicTorsionForce_impropers'] = item[1]
- elif item[0] == 'CMMotionRemover':
+ elif item[0] == "PeriodicTorsionForce" and dihedrals_done:
+ rel_energies_log["PeriodicTorsionForce_impropers"] = item[1]
+ elif item[0] == "CMMotionRemover":
continue
else:
rel_energies_log[item[0]] = item[1]
@@ -796,9 +1023,12 @@ def assert_energies(prmtop, inpcrd, ffxml, system_name='unknown', tolerance=2.5e
logger.log(omm_energies_log)
logger.log(rel_energies_log)
+
def validate_protein(ffxml_name, leaprc_name, united_atom=False):
- if verbose: print('Protein energy validation for %s' % ffxml_name)
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("Protein energy validation for %s" % ffxml_name)
+ if verbose:
+ print("Preparing temporary files for validation...")
ala3_top = tempfile.mkstemp()
ala3_crd = tempfile.mkstemp()
villin_top = tempfile.mkstemp()
@@ -806,326 +1036,418 @@ def validate_protein(ffxml_name, leaprc_name, united_atom=False):
leap_script_ala3_file = tempfile.mkstemp()
leap_script_villin_file = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
+ if verbose:
+ print("Preparing LeaP scripts...")
if not united_atom:
- leap_script_ala3_string = """source %s
+ leap_script_ala3_string = """source {}
x = loadPdb files/ala3.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, ala3_top[1], ala3_crd[1])
- leap_script_villin_string = """source %s
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, ala3_top[1], ala3_crd[1]
+ )
+ leap_script_villin_string = """source {}
x = loadPdb files/villin.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, villin_top[1], villin_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, villin_top[1], villin_crd[1]
+ )
else:
- leap_script_ala3_string = """source %s
+ leap_script_ala3_string = """source {}
x = loadPdb files/ala3_ua.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, ala3_top[1], ala3_crd[1])
- leap_script_villin_string = """source %s
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, ala3_top[1], ala3_crd[1]
+ )
+ leap_script_villin_string = """source {}
x = loadPdb files/villin_ua.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, villin_top[1], villin_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, villin_top[1], villin_crd[1]
+ )
write_file(leap_script_ala3_file[0], leap_script_ala3_string)
write_file(leap_script_villin_file[0], leap_script_villin_string)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_ala3_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_ala3_file[1]} > {os.devnull}")
if os.path.getsize(ala3_top[1]) == 0 or os.path.getsize(ala3_crd[1]) == 0:
raise LeapException(leap_script_ala3_file[1])
- os.system('tleap -f %s > %s' % (leap_script_villin_file[1], os.devnull))
+ os.system(f"tleap -f {leap_script_villin_file[1]} > {os.devnull}")
if os.path.getsize(villin_top[1]) == 0 or os.path.getsize(villin_crd[1]) == 0:
raise LeapException(leap_script_villin_file[1])
try:
- if verbose: print('Calculating and validating ala_ala_ala energies...')
- assert_energies(ala3_top[1], ala3_crd[1], ffxml_name,
- system_name='protein-ala_ala_ala')
- if verbose: print('Ala_ala_ala energy validation successful!')
-
- if verbose: print('Calculating and validating villin headpiece energies...')
- assert_energies(villin_top[1], villin_crd[1], ffxml_name,
- system_name='protein-villin headpiece')
- if verbose: print('Villin headpiece energy validation successful!')
+ if verbose:
+ print("Calculating and validating ala_ala_ala energies...")
+ assert_energies(
+ ala3_top[1], ala3_crd[1], ffxml_name, system_name="protein-ala_ala_ala"
+ )
+ if verbose:
+ print("Ala_ala_ala energy validation successful!")
+
+ if verbose:
+ print("Calculating and validating villin headpiece energies...")
+ assert_energies(
+ villin_top[1],
+ villin_crd[1],
+ ffxml_name,
+ system_name="protein-villin headpiece",
+ )
+ if verbose:
+ print("Villin headpiece energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
- for f in (ala3_top, ala3_crd, villin_top, villin_crd, leap_script_ala3_file,
- leap_script_villin_file):
+ if verbose:
+ print("Deleting temp files...")
+ for f in (
+ ala3_top,
+ ala3_crd,
+ villin_top,
+ villin_crd,
+ leap_script_ala3_file,
+ leap_script_villin_file,
+ ):
os.unlink(f[1])
- if verbose: print('Protein energy validation for %s done!' % ffxml_name)
+ if verbose:
+ print("Protein energy validation for %s done!" % ffxml_name)
+
def validate_dna(ffxml_name, leaprc_name):
- if verbose: print('DNA energy validation for %s' % ffxml_name)
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("DNA energy validation for %s" % ffxml_name)
+ if verbose:
+ print("Preparing temporary files for validation...")
dna_top = tempfile.mkstemp()
dna_crd = tempfile.mkstemp()
leap_script_dna_file = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
- leap_script_dna_string = """addPdbAtomMap {
-{ "H1'" "H1*" }
-{ "H2'" "H2'1" }
-{ "H2''" "H2'2" }
-{ "H3'" "H3*" }
-{ "H4'" "H4*" }
-{ "H5'" "H5'1" }
-{ "H5''" "H5'2" }
-{ "HO2'" "HO'2" }
-{ "HO5'" "H5T" }
-{ "HO3'" "H3T" }
-{ "OP1" "O1P" }
-{ "OP2" "O2P" }
-}
-source %s
-addPdbResMap {
-{ 0 "DG" "DG5" } { 1 "DG" "DG3" }
-{ 0 "DA" "DA5" } { 1 "DA" "DA3" }
-{ 0 "DC" "DC5" } { 1 "DC" "DC3" }
-{ 0 "DT" "DT5" } { 1 "DT" "DT3" }
-}
+ if verbose:
+ print("Preparing LeaP scripts...")
+ leap_script_dna_string = """addPdbAtomMap {{
+{{ "H1'" "H1*" }}
+{{ "H2'" "H2'1" }}
+{{ "H2''" "H2'2" }}
+{{ "H3'" "H3*" }}
+{{ "H4'" "H4*" }}
+{{ "H5'" "H5'1" }}
+{{ "H5''" "H5'2" }}
+{{ "HO2'" "HO'2" }}
+{{ "HO5'" "H5T" }}
+{{ "HO3'" "H3T" }}
+{{ "OP1" "O1P" }}
+{{ "OP2" "O2P" }}
+}}
+source {}
+addPdbResMap {{
+{{ 0 "DG" "DG5" }} {{ 1 "DG" "DG3" }}
+{{ 0 "DA" "DA5" }} {{ 1 "DA" "DA3" }}
+{{ 0 "DC" "DC5" }} {{ 1 "DC" "DC3" }}
+{{ 0 "DT" "DT5" }} {{ 1 "DT" "DT3" }}
+}}
x = loadPdb files/4rzn_dna.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, dna_top[1], dna_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, dna_top[1], dna_crd[1]
+ )
write_file(leap_script_dna_file[0], leap_script_dna_string)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_dna_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_dna_file[1]} > {os.devnull}")
if os.path.getsize(dna_top[1]) == 0 or os.path.getsize(dna_crd[1]) == 0:
raise LeapException(leap_script_dna_file[1])
try:
- if verbose: print('Calculating and validating DNA energies...')
- assert_energies(dna_top[1], dna_crd[1], ffxml_name,
- system_name='nucleic-DNA')
- if verbose: print('DNA energy validation successful!')
+ if verbose:
+ print("Calculating and validating DNA energies...")
+ assert_energies(dna_top[1], dna_crd[1], ffxml_name, system_name="nucleic-DNA")
+ if verbose:
+ print("DNA energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
+ if verbose:
+ print("Deleting temp files...")
for f in (dna_top, dna_crd, leap_script_dna_file):
os.unlink(f[1])
- if verbose: print('DNA energy validation for %s done!' % ffxml_name)
+ if verbose:
+ print("DNA energy validation for %s done!" % ffxml_name)
+
def validate_rna(ffxml_name, leaprc_name):
- if verbose: print('RNA energy validation for %s' % ffxml_name)
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("RNA energy validation for %s" % ffxml_name)
+ if verbose:
+ print("Preparing temporary files for validation...")
rna_top = tempfile.mkstemp()
rna_crd = tempfile.mkstemp()
leap_script_rna_file = tempfile.mkstemp()
leap_script_rna_file_alt = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
+ if verbose:
+ print("Preparing LeaP scripts...")
leap_script_rna_string = """
-addPdbAtomMap {
-{ "H1'" "H1*" }
-{ "H2'" "H2'1" }
-{ "H2''" "H2'2" }
-{ "H3'" "H3*" }
-{ "H4'" "H4*" }
-{ "H5'" "H5'1" }
-{ "H5''" "H5'2" }
-{ "HO2'" "HO'2" }
-{ "HO5'" "H5T" }
-{ "HO3'" "H3T" }
-{ "OP1" "O1P" }
-{ "OP2" "O2P" }
-}
-source %s
-addPdbResMap {
-{ 0 "G" "G5" } { 1 "G" "G3" } { "G" "G" }
-{ 0 "A" "A5" } { 1 "A" "A3" } { "A" "A" }
-{ 0 "C" "C5" } { 1 "C" "C3" } { "C" "C" }
-{ 0 "U" "U5" } { 1 "U" "U3" } { "U" "U" }
-}
+addPdbAtomMap {{
+{{ "H1'" "H1*" }}
+{{ "H2'" "H2'1" }}
+{{ "H2''" "H2'2" }}
+{{ "H3'" "H3*" }}
+{{ "H4'" "H4*" }}
+{{ "H5'" "H5'1" }}
+{{ "H5''" "H5'2" }}
+{{ "HO2'" "HO'2" }}
+{{ "HO5'" "H5T" }}
+{{ "HO3'" "H3T" }}
+{{ "OP1" "O1P" }}
+{{ "OP2" "O2P" }}
+}}
+source {}
+addPdbResMap {{
+{{ 0 "G" "G5" }} {{ 1 "G" "G3" }} {{ "G" "G" }}
+{{ 0 "A" "A5" }} {{ 1 "A" "A3" }} {{ "A" "A" }}
+{{ 0 "C" "C5" }} {{ 1 "C" "C3" }} {{ "C" "C" }}
+{{ 0 "U" "U5" }} {{ 1 "U" "U3" }} {{ "U" "U" }}
+}}
x = loadPdb files/5c5w_rna.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, rna_top[1], rna_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, rna_top[1], rna_crd[1]
+ )
leap_script_rna_string_alt = """
-addPdbAtomMap {
-{ "H1'" "H1*" }
-{ "H2'" "H2'1" }
-{ "H2''" "H2'2" }
-{ "H3'" "H3*" }
-{ "H4'" "H4*" }
-{ "H5'" "H5'1" }
-{ "H5''" "H5'2" }
-{ "HO2'" "HO'2" }
-{ "HO5'" "H5T" }
-{ "HO3'" "H3T" }
-{ "OP1" "O1P" }
-{ "OP2" "O2P" }
-}
-source %s
-addPdbResMap {
-{ 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" }
-{ 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" }
-{ 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" }
-{ 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" }
-}
+addPdbAtomMap {{
+{{ "H1'" "H1*" }}
+{{ "H2'" "H2'1" }}
+{{ "H2''" "H2'2" }}
+{{ "H3'" "H3*" }}
+{{ "H4'" "H4*" }}
+{{ "H5'" "H5'1" }}
+{{ "H5''" "H5'2" }}
+{{ "HO2'" "HO'2" }}
+{{ "HO5'" "H5T" }}
+{{ "HO3'" "H3T" }}
+{{ "OP1" "O1P" }}
+{{ "OP2" "O2P" }}
+}}
+source {}
+addPdbResMap {{
+{{ 0 "G" "RG5" }} {{ 1 "G" "RG3" }} {{ "G" "RG" }}
+{{ 0 "A" "RA5" }} {{ 1 "A" "RA3" }} {{ "A" "RA" }}
+{{ 0 "C" "RC5" }} {{ 1 "C" "RC3" }} {{ "C" "RC" }}
+{{ 0 "U" "RU5" }} {{ 1 "U" "RU3" }} {{ "U" "RU" }}
+}}
x = loadPdb files/5c5w_rna.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, rna_top[1], rna_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, rna_top[1], rna_crd[1]
+ )
write_file(leap_script_rna_file[0], leap_script_rna_string)
write_file(leap_script_rna_file_alt[0], leap_script_rna_string_alt)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_rna_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_rna_file[1]} > {os.devnull}")
if os.path.getsize(rna_top[1]) == 0 or os.path.getsize(rna_crd[1]) == 0:
# try alternative name mappings
- os.system('tleap -f %s > %s' % (leap_script_rna_file_alt[1], os.devnull))
+ os.system(f"tleap -f {leap_script_rna_file_alt[1]} > {os.devnull}")
if os.path.getsize(rna_top[1]) == 0 or os.path.getsize(rna_crd[1]) == 0:
raise LeapException(leap_script_rna_file_alt[1])
try:
- if verbose: print('Calculating and validating RNA energies...')
+ if verbose:
+ print("Calculating and validating RNA energies...")
# improper testing turned off pending solution to problems
- assert_energies(rna_top[1], rna_crd[1], ffxml_name,
- system_name='nucleic-RNA')
- if verbose: print('RNA energy validation successful!')
+ assert_energies(rna_top[1], rna_crd[1], ffxml_name, system_name="nucleic-RNA")
+ if verbose:
+ print("RNA energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
+ if verbose:
+ print("Deleting temp files...")
for f in (rna_top, rna_crd, leap_script_rna_file, leap_script_rna_file_alt):
os.unlink(f[1])
- if verbose: print('RNA energy validation for %s done!' % ffxml_name)
+ if verbose:
+ print("RNA energy validation for %s done!" % ffxml_name)
+
def validate_gaff(ffxml_name, leaprc_name, gaff_dat_name):
- if verbose: print('GAFF energy validation for %s' % ffxml_name)
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("GAFF energy validation for %s" % ffxml_name)
+ if verbose:
+ print("Preparing temporary files for validation...")
imatinib_top = tempfile.mkstemp()
imatinib_crd = tempfile.mkstemp()
leap_script_imatinib_file = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
+ if verbose:
+ print("Preparing LeaP scripts...")
leap_script_imatinib_string = """\
-source %s
-loadamberparams gaff/dat/%s
+source {}
+loadamberparams ../openmmforcefields/ffxml/amber/gaff/dat/{}
loadamberparams files/frcmod.imatinib
x = loadMol2 files/imatinib.mol2
-saveAmberParm x %s %s
-quit""" % (leaprc_name, gaff_dat_name, imatinib_top[1], imatinib_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, gaff_dat_name, imatinib_top[1], imatinib_crd[1]
+ )
write_file(leap_script_imatinib_file[0], leap_script_imatinib_string)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_imatinib_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_imatinib_file[1]} > {os.devnull}")
if os.path.getsize(imatinib_top[1]) == 0 or os.path.getsize(imatinib_crd[1]) == 0:
raise LeapException(leap_script_imatinib_file[1])
try:
- if verbose: print('Calculating and validating imatinib energies...')
- assert_energies(imatinib_top[1], imatinib_crd[1], (ffxml_name,
- 'files/imatinib.xml', 'files/imatinib_frcmod.xml'),
- system_name='gaff-imatinib')
- if verbose: print('Imatinib energy validation successful!')
+ if verbose:
+ print("Calculating and validating imatinib energies...")
+ assert_energies(
+ imatinib_top[1],
+ imatinib_crd[1],
+ (ffxml_name, "files/imatinib.xml", "files/imatinib_frcmod.xml"),
+ system_name="gaff-imatinib",
+ )
+ if verbose:
+ print("Imatinib energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
+ if verbose:
+ print("Deleting temp files...")
for f in (imatinib_top, imatinib_crd, leap_script_imatinib_file):
os.unlink(f[1])
- if verbose: print('GAFF energy validation for %s done!' % ffxml_name)
-
-def validate_phospho_protein(ffxml_name, leaprc_name,
- supp_leaprc_name = 'oldff/leaprc.ff99SBildn',
- supp_ffxml_name='ffxml/ff99SBildn.xml',
- phospho="phospho10"):
- if '14' in leaprc_name:
+ if verbose:
+ print("GAFF energy validation for %s done!" % ffxml_name)
+
+
+def validate_phospho_protein(
+ ffxml_name,
+ leaprc_name,
+ supp_leaprc_name="oldff/leaprc.ff99SBildn",
+ supp_ffxml_name="ffxml/ff99SBildn.xml",
+ phospho="phospho10",
+):
+ if "14" in leaprc_name:
# Use AMBER14SB
- supp_leaprc_name = 'oldff/leaprc.ff14SB'
- supp_ffxml_name='ffxml/ff14SB.xml'
- phospho = 'phospho14'
+ supp_leaprc_name = "oldff/leaprc.ff14SB"
+ supp_ffxml_name = "ffxml/ff14SB.xml"
+ phospho = "phospho14"
# this function assumes ffxml/ff14SB.xml already exists
- if verbose: print('Phosphorylated protein energy validation for %s' %
- ffxml_name)
- for pdbname in glob.iglob(f'files/{phospho}/*.pdb'):
- if verbose: print('Now testing with pdb %s' % os.path.basename(pdbname))
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("Phosphorylated protein energy validation for %s" % ffxml_name)
+ for pdbname in glob.iglob(f"files/{phospho}/*.pdb"):
+ if verbose:
+ print("Now testing with pdb %s" % os.path.basename(pdbname))
+ if verbose:
+ print("Preparing temporary files for validation...")
top = tempfile.mkstemp()
crd = tempfile.mkstemp()
leap_script_file = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
- leap_script_string = """source %s
-source %s
-x = loadPdb %s
-saveAmberParm x %s %s
-quit""" % (supp_leaprc_name, leaprc_name, pdbname, top[1], crd[1])
+ if verbose:
+ print("Preparing LeaP scripts...")
+ leap_script_string = """source {}
+source {}
+x = loadPdb {}
+saveAmberParm x {} {}
+quit""".format(
+ supp_leaprc_name, leaprc_name, pdbname, top[1], crd[1]
+ )
write_file(leap_script_file[0], leap_script_string)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_file[1]} > {os.devnull}")
if os.path.getsize(top[1]) == 0 or os.path.getsize(crd[1]) == 0:
raise LeapException(leap_script_file[1])
try:
- if verbose: print('Calculating and validating energies...')
- assert_energies(top[1], crd[1], (supp_ffxml_name, ffxml_name),
- system_name='phospho_protein: %s'
- % os.path.basename(pdbname))
- if verbose: print('Energy validation successful!')
+ if verbose:
+ print("Calculating and validating energies...")
+ assert_energies(
+ top[1],
+ crd[1],
+ (supp_ffxml_name, ffxml_name),
+ system_name="phospho_protein: %s" % os.path.basename(pdbname),
+ )
+ if verbose:
+ print("Energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
+ if verbose:
+ print("Deleting temp files...")
for f in (top, crd, leap_script_file):
os.unlink(f[1])
- if verbose: print('Phosphorylated protein energy validation for %s done!'
- % ffxml_name)
-
-def validate_water_ion(ffxml_name, source_recipe_files, solvent_name, recipe_name,
- standard_ffxml=None):
- if verbose: print('Water and ions energy validation for %s' %
- ffxml_name)
- if solvent_name == 'tip3p':
- HOH = 'TP3'
+ if verbose:
+ print("Phosphorylated protein energy validation for %s done!" % ffxml_name)
+
+
+def validate_water_ion(
+ ffxml_name, source_recipe_files, solvent_name, recipe_name, standard_ffxml=None
+):
+ if verbose:
+ print("Water and ions energy validation for %s" % ffxml_name)
+ if solvent_name == "tip3p":
+ HOH = "TP3"
solvent_frcmod = None
- elif solvent_name == 'tip4pew':
- HOH = 'T4E'
- solvent_frcmod = 'frcmod.tip4pew'
- elif solvent_name == 'spce':
- HOH = 'SPC'
- solvent_frcmod = 'frcmod.spce'
- elif solvent_name == 'tip3pfb':
- HOH = 'FB3'
- solvent_frcmod = 'frcmod.tip3pfb'
- elif solvent_name == 'tip4pfb':
- HOH = 'FB4'
- solvent_frcmod = 'frcmod.tip4pfb'
- pdb_name = 'files/water_ion/' + recipe_name + '.pdb'
- if verbose: print('Preparing temporary files for validation...')
+ elif solvent_name == "tip4pew":
+ HOH = "T4E"
+ solvent_frcmod = "frcmod.tip4pew"
+ elif solvent_name == "spce":
+ HOH = "SPC"
+ solvent_frcmod = "frcmod.spce"
+ elif solvent_name == "tip3pfb":
+ HOH = "FB3"
+ solvent_frcmod = "frcmod.tip3pfb"
+ elif solvent_name == "tip4pfb":
+ HOH = "FB4"
+ solvent_frcmod = "frcmod.tip4pfb"
+ pdb_name = "files/water_ion/" + recipe_name + ".pdb"
+ if verbose:
+ print("Preparing temporary files for validation...")
top = tempfile.mkstemp()
crd = tempfile.mkstemp()
leap_script_file = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
+ if verbose:
+ print("Preparing LeaP scripts...")
leap_script_string_part1 = """loadamberparams parm10.dat
-loadamberparams %s
-loadamberparams %s\n""" % (source_recipe_files[0], source_recipe_files[1])
+loadamberparams {}
+loadamberparams {}\n""".format(
+ source_recipe_files[0], source_recipe_files[1]
+ )
leap_script_string_part2 = """\nloadOff atomic_ions.lib
loadoff solvents.lib
-HOH = %s
+HOH = {}
# for TIP4PEW
-addPdbAtomMap {{ "M" "EPW" }}
-x = loadPdb %s
-saveAmberParm x %s %s
-quit""" % (HOH, pdb_name, top[1], crd[1])
+addPdbAtomMap {{{{ "M" "EPW" }}}}
+x = loadPdb {}
+saveAmberParm x {} {}
+quit""".format(
+ HOH, pdb_name, top[1], crd[1]
+ )
if solvent_frcmod:
- leap_script_string = (leap_script_string_part1 + ('loadamberparams %s'
- % solvent_frcmod) + leap_script_string_part2)
+ leap_script_string = (
+ leap_script_string_part1
+ + ("loadamberparams %s" % solvent_frcmod)
+ + leap_script_string_part2
+ )
else:
leap_script_string = leap_script_string_part1 + leap_script_string_part2
write_file(leap_script_file[0], leap_script_string)
# this test does it's own energy assertion because of differences
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_file[1]} > {os.devnull}")
if os.path.getsize(top[1]) == 0 or os.path.getsize(crd[1]) == 0:
raise LeapException(leap_script_file[1])
try:
- if verbose: print('Calculating and validating energies...')
- pdb = app.PDBFile(pdb_name, extraParticleIdentifier='')
+ if verbose:
+ print("Calculating and validating energies...")
+ pdb = app.PDBFile(pdb_name, extraParticleIdentifier="")
if standard_ffxml is None:
ff = app.ForceField(ffxml_name)
else:
@@ -1134,26 +1456,32 @@ def validate_water_ion(ffxml_name, source_recipe_files, solvent_name, recipe_nam
parm_omm = parmed.openmm.load_topology(pdb.topology, xyz=pdb.positions)
parm_amber = parmed.load_file(top[1], crd[1])
system_amber = parm_amber.createSystem()
- omm_energies = parmed.openmm.energy_decomposition_system(parm_omm,
- system_omm, nrg=u.kilojoules_per_mole)
+ omm_energies = parmed.openmm.energy_decomposition_system(
+ parm_omm, system_omm, nrg=u.kilojoules_per_mole
+ )
for entry in omm_energies:
- if entry[0] == 'NonbondedForce':
+ if entry[0] == "NonbondedForce":
omm_nonbonded = entry[1]
- amber_energies = parmed.openmm.energy_decomposition_system(parm_amber,
- system_amber, nrg=u.kilojoules_per_mole)
+ amber_energies = parmed.openmm.energy_decomposition_system(
+ parm_amber, system_amber, nrg=u.kilojoules_per_mole
+ )
for entry in amber_energies:
- if entry[0] == 'NonbondedForce':
+ if entry[0] == "NonbondedForce":
amber_nonbonded = entry[1]
- rel_nonbonded = abs((amber_nonbonded-omm_nonbonded) / amber_nonbonded)
+ rel_nonbonded = abs((amber_nonbonded - omm_nonbonded) / amber_nonbonded)
if rel_nonbonded > 1e-5:
- raise AssertionError('NonbondedForce Water and ions energy (%f) outside of '
- 'allowed tolerance (%f) for %s:' % (rel_nonbonded, 1e-5, ffxml_name))
- if verbose: print('Energy validation successful!')
+ raise AssertionError(
+ "NonbondedForce Water and ions energy (%f) outside of "
+ "allowed tolerance (%f) for %s:" % (rel_nonbonded, 1e-5, ffxml_name)
+ )
+ if verbose:
+ print("Energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
+ if verbose:
+ print("Deleting temp files...")
for f in (top, crd, leap_script_file):
os.unlink(f[1])
# logging
@@ -1161,29 +1489,32 @@ def validate_water_ion(ffxml_name, source_recipe_files, solvent_name, recipe_nam
amber_energies_log = dict()
omm_energies_log = dict()
rel_energies_log = dict()
- amber_energies_log['ffxml_name'] = ffxml_name
- amber_energies_log['test_system'] = 'water_ion'
- amber_energies_log['data_type'] = 'AMBER'
- amber_energies_log['NonbondedForce'] = amber_nonbonded
- amber_energies_log['units'] = u.kilojoules_per_mole
- omm_energies_log['ffxml_name'] = ffxml_name
- omm_energies_log['test_system'] = 'water_ion'
- omm_energies_log['data_type'] = 'OpenMM'
- omm_energies_log['NonbondedForce'] = omm_nonbonded
- omm_energies_log['units'] = u.kilojoules_per_mole
- rel_energies_log['ffxml_name'] = ffxml_name
- rel_energies_log['test_system'] = 'water_ion'
- rel_energies_log['data_type'] = 'abs((AMBER-OpenMM)/AMBER)'
- rel_energies_log['NonbondedForce'] = rel_nonbonded
+ amber_energies_log["ffxml_name"] = ffxml_name
+ amber_energies_log["test_system"] = "water_ion"
+ amber_energies_log["data_type"] = "AMBER"
+ amber_energies_log["NonbondedForce"] = amber_nonbonded
+ amber_energies_log["units"] = u.kilojoules_per_mole
+ omm_energies_log["ffxml_name"] = ffxml_name
+ omm_energies_log["test_system"] = "water_ion"
+ omm_energies_log["data_type"] = "OpenMM"
+ omm_energies_log["NonbondedForce"] = omm_nonbonded
+ omm_energies_log["units"] = u.kilojoules_per_mole
+ rel_energies_log["ffxml_name"] = ffxml_name
+ rel_energies_log["test_system"] = "water_ion"
+ rel_energies_log["data_type"] = "abs((AMBER-OpenMM)/AMBER)"
+ rel_energies_log["NonbondedForce"] = rel_nonbonded
logger.log(amber_energies_log)
logger.log(omm_energies_log)
logger.log(rel_energies_log)
- if verbose: print('Water and ions energy validation for %s done!'
- % ffxml_name)
+ if verbose:
+ print("Water and ions energy validation for %s done!" % ffxml_name)
+
def validate_impropers(ffxml_name, leaprc_name):
- if verbose: print('Impropers validation for %s' % ffxml_name)
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("Impropers validation for %s" % ffxml_name)
+ if verbose:
+ print("Preparing temporary files for validation...")
top_villin = tempfile.mkstemp()
crd_villin = tempfile.mkstemp()
top_dna = tempfile.mkstemp()
@@ -1192,20 +1523,29 @@ def validate_impropers(ffxml_name, leaprc_name):
crd_rna = tempfile.mkstemp()
leap_script_file = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
- leap_script_string = """source %s
+ if verbose:
+ print("Preparing LeaP scripts...")
+ leap_script_string = """source {}
x = loadPdb files/villin.pdb
y = loadPdb files/4rzn_dna.pdb
z = loadPdb files/5c5w_rna.pdb
-saveAmberParm x %s %s
-saveAmberParm y %s %s
-saveAmberParm z %s %s
-quit""" % (leaprc_name, top_villin[1], crd_villin[1], top_dna[1], crd_dna[1],
- top_rna[1], crd_rna[1])
+saveAmberParm x {} {}
+saveAmberParm y {} {}
+saveAmberParm z {} {}
+quit""".format(
+ leaprc_name,
+ top_villin[1],
+ crd_villin[1],
+ top_dna[1],
+ crd_dna[1],
+ top_rna[1],
+ crd_rna[1],
+ )
write_file(leap_script_file[0], leap_script_string)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_file[1]} > {os.devnull}")
if os.path.getsize(top_villin[1]) == 0 or os.path.getsize(crd_villin[1]) == 0:
raise LeapException(leap_script_file[1])
if os.path.getsize(top_dna[1]) == 0 or os.path.getsize(crd_dna[1]) == 0:
@@ -1223,117 +1563,178 @@ def validate_impropers(ffxml_name, leaprc_name):
sys_omm_villin = ff.createSystem(parm_amber_villin.topology)
sys_omm_dna = ff.createSystem(parm_amber_dna.topology)
sys_omm_rna = ff.createSystem(parm_amber_rna.topology)
- parm_omm_villin = parmed.openmm.load_topology(parm_amber_villin.topology,
- sys_omm_villin)
- parm_omm_dna = parmed.openmm.load_topology(parm_amber_dna.topology,
- sys_omm_dna)
- parm_omm_rna = parmed.openmm.load_topology(parm_amber_rna.topology,
- sys_omm_rna)
+ parm_omm_villin = parmed.openmm.load_topology(
+ parm_amber_villin.topology, sys_omm_villin
+ )
+ parm_omm_dna = parmed.openmm.load_topology(parm_amber_dna.topology, sys_omm_dna)
+ parm_omm_rna = parmed.openmm.load_topology(parm_amber_rna.topology, sys_omm_rna)
# prepare sets of idxs
- set_amber_villin = set([(dih.atom1.idx, dih.atom2.idx, dih.atom3.idx,
- dih.atom4.idx) for dih in parm_amber_villin.dihedrals if dih.improper])
- set_amber_dna = set([(dih.atom1.idx, dih.atom2.idx, dih.atom3.idx,
- dih.atom4.idx) for dih in parm_amber_dna.dihedrals if dih.improper])
- set_amber_rna = set([(dih.atom1.idx, dih.atom2.idx, dih.atom3.idx,
- dih.atom4.idx) for dih in parm_amber_rna.dihedrals if dih.improper])
- set_omm_villin = set([(dih.atom1.idx, dih.atom2.idx, dih.atom3.idx,
- dih.atom4.idx) for dih in parm_omm_villin.dihedrals if dih.improper])
- set_omm_dna = set([(dih.atom1.idx, dih.atom2.idx, dih.atom3.idx,
- dih.atom4.idx) for dih in parm_omm_dna.dihedrals if dih.improper])
- set_omm_rna = set([(dih.atom1.idx, dih.atom2.idx, dih.atom3.idx,
- dih.atom4.idx) for dih in parm_omm_rna.dihedrals if dih.improper])
+ set_amber_villin = {
+ (dih.atom1.idx, dih.atom2.idx, dih.atom3.idx, dih.atom4.idx)
+ for dih in parm_amber_villin.dihedrals
+ if dih.improper
+ }
+ set_amber_dna = {
+ (dih.atom1.idx, dih.atom2.idx, dih.atom3.idx, dih.atom4.idx)
+ for dih in parm_amber_dna.dihedrals
+ if dih.improper
+ }
+ set_amber_rna = {
+ (dih.atom1.idx, dih.atom2.idx, dih.atom3.idx, dih.atom4.idx)
+ for dih in parm_amber_rna.dihedrals
+ if dih.improper
+ }
+ set_omm_villin = {
+ (dih.atom1.idx, dih.atom2.idx, dih.atom3.idx, dih.atom4.idx)
+ for dih in parm_omm_villin.dihedrals
+ if dih.improper
+ }
+ set_omm_dna = {
+ (dih.atom1.idx, dih.atom2.idx, dih.atom3.idx, dih.atom4.idx)
+ for dih in parm_omm_dna.dihedrals
+ if dih.improper
+ }
+ set_omm_rna = {
+ (dih.atom1.idx, dih.atom2.idx, dih.atom3.idx, dih.atom4.idx)
+ for dih in parm_omm_rna.dihedrals
+ if dih.improper
+ }
try:
- if (set_amber_villin - set_omm_villin != set() or
- set_omm_villin - set_amber_villin != set()):
- raise AssertionError("""Impropers validation fail for %s (villin)
- set_amber - set_omm: %s
- set_omm - set_amber: %s""" % (ffxml_name,
- set_amber_villin-set_omm_villin,
- set_omm_villin-set_amber_villin))
- if (set_amber_dna - set_omm_dna != set() or
- set_omm_dna - set_amber_dna != set()):
- raise AssertionError("""Impropers validation fail for %s (DNA)
- set_amber - set_omm: %s
- set_omm - set_amber: %s""" % (ffxml_name,
- set_amber_dna-set_omm_dna,
- set_omm_dna-set_amber_dna))
- if (set_amber_rna - set_omm_rna != set() or
- set_omm_rna - set_amber_rna != set()):
- raise AssertionError("""Impropers validation fail for %s (RNA)
- set_amber - set_omm: %s
- set_omm - set_amber: %s""" % (ffxml_name,
- set_amber_rna-set_omm_rna,
- set_omm_rna-set_amber_rna))
+ if (
+ set_amber_villin - set_omm_villin != set()
+ or set_omm_villin - set_amber_villin != set()
+ ):
+ raise AssertionError(
+ """Impropers validation fail for {} (villin)
+ set_amber - set_omm: {}
+ set_omm - set_amber: {}""".format(
+ ffxml_name,
+ set_amber_villin - set_omm_villin,
+ set_omm_villin - set_amber_villin,
+ )
+ )
+ if set_amber_dna - set_omm_dna != set() or set_omm_dna - set_amber_dna != set():
+ raise AssertionError(
+ """Impropers validation fail for {} (DNA)
+ set_amber - set_omm: {}
+ set_omm - set_amber: {}""".format(
+ ffxml_name, set_amber_dna - set_omm_dna, set_omm_dna - set_amber_dna
+ )
+ )
+ if set_amber_rna - set_omm_rna != set() or set_omm_rna - set_amber_rna != set():
+ raise AssertionError(
+ """Impropers validation fail for {} (RNA)
+ set_amber - set_omm: {}
+ set_omm - set_amber: {}""".format(
+ ffxml_name, set_amber_rna - set_omm_rna, set_omm_rna - set_amber_rna
+ )
+ )
finally:
- if verbose: print('Deleting temp files...')
- for f in (top_villin, crd_villin, top_dna, crd_dna, top_rna, crd_rna,
- leap_script_file):
+ if verbose:
+ print("Deleting temp files...")
+ for f in (
+ top_villin,
+ crd_villin,
+ top_dna,
+ crd_dna,
+ top_rna,
+ crd_rna,
+ leap_script_file,
+ ):
os.unlink(f[1])
- if verbose: print('Improper validation for %s done!' % ffxml_name)
+ if verbose:
+ print("Improper validation for %s done!" % ffxml_name)
+
def validate_lipids(ffxml_name, leaprc_name):
- if verbose: print('Lipids energy validation for %s' % ffxml_name)
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("Lipids energy validation for %s" % ffxml_name)
+ if verbose:
+ print("Preparing temporary files for validation...")
lipids_top = tempfile.mkstemp()
lipids_crd = tempfile.mkstemp()
leap_script_lipids_file = tempfile.mkstemp()
- if verbose: print('Preparing LeaP scripts...')
- leap_script_lipids_string = """source %s
+ if verbose:
+ print("Preparing LeaP scripts...")
+ leap_script_lipids_string = """source {}
x = loadPdb files/POPC-nowater-amber.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, lipids_top[1], lipids_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, lipids_top[1], lipids_crd[1]
+ )
write_file(leap_script_lipids_file[0], leap_script_lipids_string)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_lipids_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_lipids_file[1]} > {os.devnull}")
if os.path.getsize(lipids_top[1]) == 0 or os.path.getsize(lipids_crd[1]) == 0:
raise LeapException(leap_script_lipids_file[1])
try:
- if verbose: print('Calculating and validating lipids energies...')
- assert_energies(lipids_top[1], lipids_crd[1], ffxml_name,
- system_name='lipids')
- if verbose: print('Lipids energy validation successful!')
+ if verbose:
+ print("Calculating and validating lipids energies...")
+ assert_energies(lipids_top[1], lipids_crd[1], ffxml_name, system_name="lipids")
+ if verbose:
+ print("Lipids energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
+ if verbose:
+ print("Deleting temp files...")
for f in (lipids_top, lipids_crd, leap_script_lipids_file):
os.unlink(f[1])
- if verbose: print('Lipids energy validation for %s done!' % ffxml_name)
+ if verbose:
+ print("Lipids energy validation for %s done!" % ffxml_name)
+
def validate_merged_lipids(ffxml_name, leaprc_name):
- if verbose: print('Lipids (merged) energy validation for %s' % ffxml_name)
- if verbose: print('Preparing temporary files for validation...')
+ if verbose:
+ print("Lipids (merged) energy validation for %s" % ffxml_name)
+ if verbose:
+ print("Preparing temporary files for validation...")
lipids_top = tempfile.mkstemp()
lipids_crd = tempfile.mkstemp()
leap_script_lipids_file = tempfile.mkstemp()
- pdbfile = app.PDBFile('files/POPC-nowater-charmm.pdb')
+ pdbfile = app.PDBFile("files/POPC-nowater-charmm.pdb")
- if verbose: print('Preparing LeaP scripts...')
- leap_script_lipids_string = """source %s
+ if verbose:
+ print("Preparing LeaP scripts...")
+ leap_script_lipids_string = """source {}
x = loadPdb files/POPC-nowater-amber.pdb
-saveAmberParm x %s %s
-quit""" % (leaprc_name, lipids_top[1], lipids_crd[1])
+saveAmberParm x {} {}
+quit""".format(
+ leaprc_name, lipids_top[1], lipids_crd[1]
+ )
write_file(leap_script_lipids_file[0], leap_script_lipids_string)
- if verbose: print('Running LEaP...')
- os.system('tleap -f %s > %s' % (leap_script_lipids_file[1], os.devnull))
+ if verbose:
+ print("Running LEaP...")
+ os.system(f"tleap -f {leap_script_lipids_file[1]} > {os.devnull}")
if os.path.getsize(lipids_top[1]) == 0 or os.path.getsize(lipids_crd[1]) == 0:
raise LeapException(leap_script_lipids_file[1])
try:
- if verbose: print('Calculating and validating lipids energies...')
- assert_energies(lipids_top[1], lipids_crd[1], ffxml_name,
- system_name='lipids',
- openmm_topology=pdbfile.topology, openmm_positions=pdbfile.positions)
- if verbose: print('Lipids energy validation successful!')
+ if verbose:
+ print("Calculating and validating lipids energies...")
+ assert_energies(
+ lipids_top[1],
+ lipids_crd[1],
+ ffxml_name,
+ system_name="lipids",
+ openmm_topology=pdbfile.topology,
+ openmm_positions=pdbfile.positions,
+ )
+ if verbose:
+ print("Lipids energy validation successful!")
finally:
- if verbose: print('Deleting temp files...')
+ if verbose:
+ print("Deleting temp files...")
for f in (lipids_top, lipids_crd, leap_script_lipids_file):
os.unlink(f[1])
- if verbose: print('Lipids energy validation for %s done!' % ffxml_name)
+ if verbose:
+ print("Lipids energy validation for %s done!" % ffxml_name)
+
def modify_glycan_ffxml(input_ffxml_path):
@@ -1357,141 +1758,201 @@ def modify_glycan_ffxml(input_ffxml_path):
"""
- import xml.etree.ElementTree as etree
import re
+ import xml.etree.ElementTree as etree
# Define atom types
- protein_types = set(["C", "CA", "CB", "CC", "CN", "CR", "CT", "CV", "CW", "C*", "CX", "H", "HC", "H1", "HA", "H4", "H5", "HO", "HS", "HP", "N", "NA", "NB", "N2", "N3", "O", "O2", "OH", "S", "SH", "CO", "2C", "3C", "C8"])
- solvent_types = set(["HW", "OW", "Li+", "Na+", "K+", "Rb+", "Cs+", "F-", "Cl-", "Br-", "I-"])
+ protein_types = {
+ "C",
+ "CA",
+ "CB",
+ "CC",
+ "CN",
+ "CR",
+ "CT",
+ "CV",
+ "CW",
+ "C*",
+ "CX",
+ "H",
+ "HC",
+ "H1",
+ "HA",
+ "H4",
+ "H5",
+ "HO",
+ "HS",
+ "HP",
+ "N",
+ "NA",
+ "NB",
+ "N2",
+ "N3",
+ "O",
+ "O2",
+ "OH",
+ "S",
+ "SH",
+ "CO",
+ "2C",
+ "3C",
+ "C8",
+ }
+ solvent_types = {
+ "HW",
+ "OW",
+ "Li+",
+ "Na+",
+ "K+",
+ "Rb+",
+ "Cs+",
+ "F-",
+ "Cl-",
+ "Br-",
+ "I-",
+ }
glycam_types = set()
replacements = {}
for type in protein_types:
- replacements[type] = 'protein-'+type
+ replacements[type] = "protein-" + type
# Process
tree = etree.parse(input_ffxml_path)
root = tree.getroot()
- types = root.find('AtomTypes')
- for type in types.findall('Type'):
- name = type.get('name')
+ types = root.find("AtomTypes")
+ for type in types.findall("Type"):
+ name = type.get("name")
if name in protein_types or name in solvent_types:
types.remove(type)
else:
glycam_types.add(name)
- replacements[name] = 'glycam-'+name
- type.set('name', replacements[name])
+ replacements[name] = "glycam-" + name
+ type.set("name", replacements[name])
# Process
- residues = root.find('Residues')
- for residue in residues.findall('Residue'):
- for atom in residue.findall('Atom'):
- atom.set('type', replacements[atom.get('type')])
+ residues = root.find("Residues")
+ for residue in residues.findall("Residue"):
+ for atom in residue.findall("Atom"):
+ atom.set("type", replacements[atom.get("type")])
# Process
- force = root.find('HarmonicBondForce')
- for bond in force.findall('Bond'):
+ force = root.find("HarmonicBondForce")
+ for bond in force.findall("Bond"):
# Change attributes from class to type
- bond.attrib['type1'] = bond.attrib['class1']
- bond.attrib['type2'] = bond.attrib['class2']
- del bond.attrib['class1']
- del bond.attrib['class2']
+ bond.attrib["type1"] = bond.attrib["class1"]
+ bond.attrib["type2"] = bond.attrib["class2"]
+ del bond.attrib["class1"]
+ del bond.attrib["class2"]
# Fix prefixes
- types = [bond.get('type1'), bond.get('type2')]
+ types = [bond.get("type1"), bond.get("type2")]
if any(t in glycam_types for t in types):
- bond.set('type1', replacements[types[0]])
- bond.set('type2', replacements[types[1]])
+ bond.set("type1", replacements[types[0]])
+ bond.set("type2", replacements[types[1]])
else:
force.remove(bond)
# Process
- force = root.find('HarmonicAngleForce')
- for angle in force.findall('Angle'):
+ force = root.find("HarmonicAngleForce")
+ for angle in force.findall("Angle"):
# Change attributes from class to type
- angle.attrib['type1'] = angle.attrib['class1']
- angle.attrib['type2'] = angle.attrib['class2']
- angle.attrib['type3'] = angle.attrib['class3']
- del angle.attrib['class1']
- del angle.attrib['class2']
- del angle.attrib['class3']
+ angle.attrib["type1"] = angle.attrib["class1"]
+ angle.attrib["type2"] = angle.attrib["class2"]
+ angle.attrib["type3"] = angle.attrib["class3"]
+ del angle.attrib["class1"]
+ del angle.attrib["class2"]
+ del angle.attrib["class3"]
# Fix prefixes
- types = [angle.get('type1'), angle.get('type2'), angle.get('type3')]
+ types = [angle.get("type1"), angle.get("type2"), angle.get("type3")]
if any(t in glycam_types for t in types):
- angle.set('type1', replacements[types[0]])
- angle.set('type2', replacements[types[1]])
- angle.set('type3', replacements[types[2]])
+ angle.set("type1", replacements[types[0]])
+ angle.set("type2", replacements[types[1]])
+ angle.set("type3", replacements[types[2]])
else:
force.remove(angle)
# Process
- force = root.find('PeriodicTorsionForce')
- for tag in ['Proper', 'Improper']:
+ force = root.find("PeriodicTorsionForce")
+ for tag in ["Proper", "Improper"]:
for torsion in force.findall(tag):
# Change attributes from class to type and remove bad torsion
- torsion.attrib['type1'] = torsion.attrib['class1']
- torsion.attrib['type2'] = torsion.attrib['class2']
- torsion.attrib['type3'] = torsion.attrib['class3']
- torsion.attrib['type4'] = torsion.attrib['class4']
- del torsion.attrib['class1']
- del torsion.attrib['class2']
- del torsion.attrib['class3']
- del torsion.attrib['class4']
- if torsion.attrib['type1'] == 'NH' and torsion.attrib['type2'] == 'Cg' and torsion.attrib['type3'] == 'Cg' and torsion.attrib['type4'] == 'Sm':
+ torsion.attrib["type1"] = torsion.attrib["class1"]
+ torsion.attrib["type2"] = torsion.attrib["class2"]
+ torsion.attrib["type3"] = torsion.attrib["class3"]
+ torsion.attrib["type4"] = torsion.attrib["class4"]
+ del torsion.attrib["class1"]
+ del torsion.attrib["class2"]
+ del torsion.attrib["class3"]
+ del torsion.attrib["class4"]
+ if (
+ torsion.attrib["type1"] == "NH"
+ and torsion.attrib["type2"] == "Cg"
+ and torsion.attrib["type3"] == "Cg"
+ and torsion.attrib["type4"] == "Sm"
+ ):
force.remove(torsion)
continue
# Fix prefixes
- types = [torsion.get('type1'), torsion.get('type2'), torsion.get('type3'), torsion.get('type4')]
+ types = [
+ torsion.get("type1"),
+ torsion.get("type2"),
+ torsion.get("type3"),
+ torsion.get("type4"),
+ ]
if any(t in glycam_types for t in types):
- torsion.set('type1', replacements[types[0]])
- torsion.set('type2', replacements[types[1]])
- torsion.set('type3', replacements[types[2]])
- torsion.set('type4', replacements[types[3]])
+ torsion.set("type1", replacements[types[0]])
+ torsion.set("type2", replacements[types[1]])
+ torsion.set("type3", replacements[types[2]])
+ torsion.set("type4", replacements[types[3]])
else:
force.remove(torsion)
# Process
- force = root.find('NonbondedForce')
- for atom in force.findall('Atom'):
+ force = root.find("NonbondedForce")
+ for atom in force.findall("Atom"):
# Change attributes from class to type
- atom.attrib['type'] = atom.attrib['class']
- del atom.attrib['class']
+ atom.attrib["type"] = atom.attrib["class"]
+ del atom.attrib["class"]
# Fix prefixes
- type = atom.get('type')
+ type = atom.get("type")
if type in glycam_types:
- atom.set('type', replacements[type])
+ atom.set("type", replacements[type])
else:
force.remove(atom)
# Remove bad NH torsion and update the unscaled types in the script
- script = root.find('Script')
+ script = root.find("Script")
text = script.text
# Bad NH torsion
- text_split = text.split('\n')
- text_NH_removed = [line for line in text_split if not 'NH' in line]
- text = '\n'.join(text_NH_removed)
+ text_split = text.split("\n")
+ text_NH_removed = [line for line in text_split if not "NH" in line]
+ text = "\n".join(text_NH_removed)
# Unscaled types
- pattern = re.compile('unscaled_types = set\((\[(.*\n)*?.*?\])\)')
+ pattern = re.compile("unscaled_types = set\\((\\[(.*\n)*?.*?\\])\\)")
match = pattern.search(text)
types = eval(match.group(1))
- types = [(replacements[t[0]], replacements[t[1]], replacements[t[2]], replacements[t[3]]) for t in types]
- types = ',\n '.join(str(t) for t in types)
- script.text = pattern.sub('unscaled_types = set([%s])' % types, text)
+ types = [
+ (replacements[t[0]], replacements[t[1]], replacements[t[2]], replacements[t[3]])
+ for t in types
+ ]
+ types = ",\n ".join(str(t) for t in types)
+ script.text = pattern.sub("unscaled_types = set([%s])" % types, text)
# Add initialization script for setting up GlycamTemplateMatcher
- initialization_script = etree.SubElement(root, 'InitializationScript')
+ initialization_script = etree.SubElement(root, "InitializationScript")
initialization_script.text = """
from openmm.app.internal import compiled
@@ -1527,20 +1988,27 @@ def __call__(self, ff, residue, bondedToAtom, ignoreExternalBonds, ignoreExtraPa
tree.write(input_ffxml_path)
-def validate_glyco_protein(ffxml_name, leaprc_name,
- supp_leaprc_name = 'oldff/leaprc.ff14SB',
- supp_ffxml_name='ffxml/protein.ff14SB.xml'):
+
+def validate_glyco_protein(
+ ffxml_name,
+ leaprc_name,
+ supp_leaprc_name="oldff/leaprc.ff14SB",
+ supp_ffxml_name="ffxml/protein.ff14SB.xml",
+):
modify_glycan_ffxml(ffxml_name)
- if verbose: print('Glycosylated protein energy validation for %s' %
- ffxml_name)
- top = 'files/glycam/Glycoprotein_shortened.parm7'
- crd = 'files/glycam/Glycoprotein_shortened.rst7'
+ if verbose:
+ print("Glycosylated protein energy validation for %s" % ffxml_name)
+ top = "files/glycam/Glycoprotein_shortened.parm7"
+ crd = "files/glycam/Glycoprotein_shortened.rst7"
assert_energies_glyco_protein(top, crd, (supp_ffxml_name, ffxml_name))
- if verbose: print('Glycosylated protein energy validation for %s was successful!'
- % ffxml_name)
+ if verbose:
+ print(
+ "Glycosylated protein energy validation for %s was successful!" % ffxml_name
+ )
+
-class Logger():
+class Logger:
"""
Log energy discrepancies to a file.
@@ -1550,13 +2018,22 @@ class Logger():
Name of CSV file to write to
"""
+
# logs testing energies into csv
def __init__(self, log_filename=None):
if log_filename:
- csvfile = open(log_filename, 'w')
- fieldnames = ['ffxml_name', 'data_type', 'test_system', 'units', 'HarmonicBondForce',
- 'HarmonicAngleForce', 'PeriodicTorsionForce_dihedrals',
- 'PeriodicTorsionForce_impropers', 'NonbondedForce']
+ csvfile = open(log_filename, "w")
+ fieldnames = [
+ "ffxml_name",
+ "data_type",
+ "test_system",
+ "units",
+ "HarmonicBondForce",
+ "HarmonicAngleForce",
+ "PeriodicTorsionForce_dihedrals",
+ "PeriodicTorsionForce_impropers",
+ "NonbondedForce",
+ ]
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
writer.writeheader()
self.csvfile = csvfile
@@ -1573,5 +2050,6 @@ def log(self, energies):
if self.writer:
self.writer.writerow(energies)
-if __name__ == '__main__':
+
+if __name__ == "__main__":
main()
diff --git a/amber/gaff-tests.csv b/amber/gaff-tests.csv
index d9b7e658..b568e2be 100644
--- a/amber/gaff-tests.csv
+++ b/amber/gaff-tests.csv
@@ -1,22 +1,22 @@
ffxml_name,data_type,test_system,units,HarmonicBondForce,HarmonicAngleForce,PeriodicTorsionForce_dihedrals,PeriodicTorsionForce_impropers,NonbondedForce
-"('gaff/ffxml/gaff-1.4.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,25.777545928955078,22.304170608520508,55.1888542175293,0.26479068398475647,-852.433349609375
-"('gaff/ffxml/gaff-1.4.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,25.77754102337972,22.304065829309252,55.188839283957066,0.26423707974575467,-852.4326586681362
-"('gaff/ffxml/gaff-1.4.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.9030420400684673e-07,4.697740754180669e-06,2.7059036544581625e-07,0.0020907240038462744,8.105516273796546e-07
-"('gaff/ffxml/gaff-1.7.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,26.143211364746094,22.300186157226562,36.337039947509766,0.26479068398475647,-852.433349609375
-"('gaff/ffxml/gaff-1.7.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,26.14322206368444,22.300082421870197,36.33698290353448,0.26423707974575467,-852.4326586681362
-"('gaff/ffxml/gaff-1.7.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,4.0924346276937394e-07,4.651770870159464e-06,1.5698575165055766e-06,0.0020907240038462744,8.105516273796546e-07
-"('gaff/ffxml/gaff-1.8.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,16.870708465576172,22.636985778808594,36.337039947509766,0.26479068398475647,-852.433349609375
-"('gaff/ffxml/gaff-1.8.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,16.870679277659608,22.63682360600831,36.33698290353448,0.26423707974575467,-852.4326586681362
-"('gaff/ffxml/gaff-1.8.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.7300943006191098e-06,7.1640633549220915e-06,1.5698575165055766e-06,0.0020907240038462744,8.105516273796546e-07
-"('gaff/ffxml/gaff-1.81.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,16.870708465576172,22.63513946533203,36.337039947509766,0.26479068398475647,-852.433349609375
-"('gaff/ffxml/gaff-1.81.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,16.870679277659608,22.634976391529953,36.33698290353448,0.26423707974575467,-852.4326586681362
-"('gaff/ffxml/gaff-1.81.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.7300943006191098e-06,7.204453161319435e-06,1.5698575165055766e-06,0.0020907240038462744,8.105516273796546e-07
-"('gaff/ffxml/gaff.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,16.870708465576172,22.63513946533203,36.337039947509766,0.26479068398475647,-852.433349609375
-"('gaff/ffxml/gaff.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,16.870679277659608,22.634976391529953,36.33698290353448,0.26423707974575467,-852.4326586681362
-"('gaff/ffxml/gaff.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.7300943006191098e-06,7.204453161319435e-06,1.5698575165055766e-06,0.0020907240038462744,8.105516273796546e-07
-"('gaff/ffxml/gaff-2.1.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,14.073978424072266,24.22649383544922,28.998537063598633,0.26479068398475647,-869.61474609375
-"('gaff/ffxml/gaff-2.1.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,14.074003032028392,24.22633229264447,28.998474252684986,0.26423707974575467,-869.6145738718743
-"('gaff/ffxml/gaff-2.1.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.7484719234784995e-06,6.668022448665338e-06,2.166002840397494e-06,0.0020907240038462744,1.9804387685510414e-07
-"('gaff/ffxml/gaff-2.11.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,14.074195861816406,24.23253631591797,28.998537063598633,0.26479068398475647,-869.61474609375
-"('gaff/ffxml/gaff-2.11.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,14.074219501502814,24.232374455829078,28.998474252684986,0.26423707974575467,-869.6145738718743
-"('gaff/ffxml/gaff-2.11.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.6796473943950934e-06,6.679453061822155e-06,2.166002840397494e-06,0.0020907240038462744,1.9804387685510414e-07
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.4.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,25.777557373046875,22.30413055419922,55.188804626464844,0.26478666067123413,-852.43310546875
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.4.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,25.777541023379726,22.304065829309273,55.18883928395708,0.2642370763604315,-852.4326586681362
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.4.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,6.34259752094455e-07,2.901923918898549e-06,6.279804839161042e-07,0.002075574008937826,5.24147420943811e-07
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.7.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,26.14322280883789,22.300148010253906,36.336997985839844,0.26478666067123413,-852.43310546875
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.7.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,26.143222063684448,22.30008242187022,36.336982903534484,0.2642370763604315,-852.4326586681362
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.7.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,2.8502738487824353e-08,2.9411636038287786e-06,4.1506745730779966e-07,0.002075574008937826,5.24147420943811e-07
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.8.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,16.870697021484375,22.636943817138672,36.336997985839844,0.26478666067123413,-852.43310546875
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.8.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,16.870679277659615,22.63682360600832,36.336982903534484,0.2642370763604315,-852.4326586681362
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.8.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.0517540998527325e-06,5.3103957549388315e-06,4.1506745730779966e-07,0.002075574008937826,5.24147420943811e-07
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.81.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,16.870697021484375,22.63509750366211,36.336997985839844,0.26478666067123413,-852.43310546875
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.81.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,16.870679277659615,22.63497639152996,36.336982903534484,0.2642370763604315,-852.4326586681362
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.81.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.0517540998527325e-06,5.350634435276571e-06,4.1506745730779966e-07,0.002075574008937826,5.24147420943811e-07
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,16.870697021484375,22.63509750366211,36.336997985839844,0.26478666067123413,-852.43310546875
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,16.870679277659615,22.63497639152996,36.336982903534484,0.2642370763604315,-852.4326586681362
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,1.0517540998527325e-06,5.350634435276571e-06,4.1506745730779966e-07,0.002075574008937826,5.24147420943811e-07
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.1.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,14.073968887329102,24.226451873779297,28.998493194580078,0.26478666067123413,-869.614990234375
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.1.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,14.074003032028394,24.226332292644475,28.99847425268499,0.2642370763604315,-869.6145738718743
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.1.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,2.4260888712573548e-06,4.935973928201381e-06,6.532027358037606e-07,0.002075574008937826,4.787894704696351e-07
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.11.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",AMBER,gaff-imatinib,kilojoule/mole,14.07418441772461,24.23249626159668,28.998493194580078,0.26478666067123413,-869.614990234375
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.11.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",OpenMM,gaff-imatinib,kilojoule/mole,14.074219501502816,24.232374455829074,28.99847425268499,0.2642370763604315,-869.6145738718743
+"('../openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.11.xml', 'files/imatinib.xml', 'files/imatinib_frcmod.xml')",abs((AMBER-OpenMM)/AMBER),gaff-imatinib,,2.492775223406482e-06,5.026546431314265e-06,6.532027358037606e-07,0.002075574008937826,4.787894704696351e-07
diff --git a/amber/gaff.yaml b/amber/gaff.yaml
index 4e786440..2a3594bf 100644
--- a/amber/gaff.yaml
+++ b/amber/gaff.yaml
@@ -6,7 +6,7 @@
leaprc: leaprc.gaff
Options:
write_unused: True
- ffxml_dir: gaff/ffxml
+ ffxml_dir: ../openmmforcefields/ffxml/amber/gaff/ffxml
Test:
- gaff
Reference:
@@ -22,7 +22,7 @@
leaprc: leaprc.gaff
Options:
write_unused: True
- ffxml_dir: gaff/ffxml
+ ffxml_dir: ../openmmforcefields/ffxml/amber/gaff/ffxml
Test:
- gaff
Reference:
@@ -38,7 +38,7 @@
leaprc: leaprc.gaff
Options:
write_unused: True
- ffxml_dir: gaff/ffxml
+ ffxml_dir: ../openmmforcefields/ffxml/amber/gaff/ffxml
Test:
- gaff
Reference:
@@ -54,7 +54,7 @@
leaprc: leaprc.gaff
Options:
write_unused: True
- ffxml_dir: gaff/ffxml
+ ffxml_dir: ../openmmforcefields/ffxml/amber/gaff/ffxml
Test:
- gaff
Reference:
@@ -70,7 +70,7 @@
leaprc: leaprc.gaff
Options:
write_unused: True
- ffxml_dir: gaff/ffxml
+ ffxml_dir: ../openmmforcefields/ffxml/amber/gaff/ffxml
Test:
- gaff
Reference:
@@ -86,7 +86,7 @@
leaprc: leaprc.gaff2
Options:
write_unused: True
- ffxml_dir: gaff/ffxml
+ ffxml_dir: ../openmmforcefields/ffxml/amber/gaff/ffxml
Test:
- gaff
Reference:
@@ -102,7 +102,7 @@
leaprc: leaprc.gaff2
Options:
write_unused: True
- ffxml_dir: gaff/ffxml
+ ffxml_dir: ../openmmforcefields/ffxml/amber/gaff/ffxml
Test:
- gaff
Reference:
diff --git a/amber/gaff/ffxml/gaff-1.4.xml b/amber/gaff/ffxml/gaff-1.4.xml
deleted file mode 100644
index f54141aa..00000000
--- a/amber/gaff/ffxml/gaff-1.4.xml
+++ /dev/null
@@ -1,5695 +0,0 @@
-
-
- 2021-01-26
- gaff-1.4.dat
- Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
- Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/amber/gaff/ffxml/gaff-1.7.xml b/amber/gaff/ffxml/gaff-1.7.xml
deleted file mode 100644
index 7b4dca2d..00000000
--- a/amber/gaff/ffxml/gaff-1.7.xml
+++ /dev/null
@@ -1,5892 +0,0 @@
-
-
- 2021-01-26
- gaff-1.7.dat
- Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
- Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/amber/gaff/ffxml/gaff-1.8.xml b/amber/gaff/ffxml/gaff-1.8.xml
deleted file mode 100644
index d5de7baa..00000000
--- a/amber/gaff/ffxml/gaff-1.8.xml
+++ /dev/null
@@ -1,6299 +0,0 @@
-
-
- 2021-01-26
- gaff-1.8.dat
- Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
- Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/amber/gaff/ffxml/gaff-1.81.xml b/amber/gaff/ffxml/gaff-1.81.xml
deleted file mode 100644
index 91580a9b..00000000
--- a/amber/gaff/ffxml/gaff-1.81.xml
+++ /dev/null
@@ -1,7116 +0,0 @@
-
-
- 2021-01-26
- gaff-1.81.dat
- Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
- Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/amber/gaff/ffxml/gaff-2.1.xml b/amber/gaff/ffxml/gaff-2.1.xml
deleted file mode 100644
index 12480da1..00000000
--- a/amber/gaff/ffxml/gaff-2.1.xml
+++ /dev/null
@@ -1,6654 +0,0 @@
-
-
- 2021-01-26
- gaff-2.1.dat
- Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
- Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/amber/gaff/ffxml/gaff-2.11.xml b/amber/gaff/ffxml/gaff-2.11.xml
deleted file mode 100644
index 23b61ad6..00000000
--- a/amber/gaff/ffxml/gaff-2.11.xml
+++ /dev/null
@@ -1,7475 +0,0 @@
-
-
- 2021-01-26
- gaff-2.11.dat
- Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
- Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/amber/gaff/ffxml/gaff.xml b/amber/gaff/ffxml/gaff.xml
deleted file mode 100644
index 91580a9b..00000000
--- a/amber/gaff/ffxml/gaff.xml
+++ /dev/null
@@ -1,7116 +0,0 @@
-
-
- 2021-01-26
- gaff-1.81.dat
- Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
- Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/amber/test/test.py b/amber/test/test.py
index 49756d97..98e1eb0f 100644
--- a/amber/test/test.py
+++ b/amber/test/test.py
@@ -1,5 +1,6 @@
-import unittest
import os
+import unittest
+
os.chdir('..')
class Testamber2ommmScript(unittest.TestCase):
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 271c5c60..70240427 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -1,4 +1,4 @@
-name: test
+name: openmmforcefields-test
channels:
- conda-forge
@@ -30,10 +30,6 @@ dependencies:
# OpenEye toolkits are only used to speed up testing; they are not required for use
- openeye-toolkits
- # OpenFF toolkit and force fields
- - openff-toolkit =0.10.6
- - openff-forcefields >=1.2.0
-
# Validating URLs
- validators
diff --git a/openmmforcefields/__init__.py b/openmmforcefields/__init__.py
index 8c66453b..7db1e859 100644
--- a/openmmforcefields/__init__.py
+++ b/openmmforcefields/__init__.py
@@ -1,8 +1,8 @@
# Add imports here
-from .utils import get_ffxml_path
-
# Handle versioneer
from ._version import get_versions
+from .utils import get_ffxml_path
+
versions = get_versions()
__version__ = versions['version']
__git_revision__ = versions['full-revisionid']
diff --git a/openmmforcefields/_version.py b/openmmforcefields/_version.py
index fc52d96c..49c6b0fb 100644
--- a/openmmforcefields/_version.py
+++ b/openmmforcefields/_version.py
@@ -1,4 +1,3 @@
-
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
@@ -81,7 +80,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
stderr=(subprocess.PIPE if hide_stderr
else None))
break
- except EnvironmentError:
+ except OSError:
e = sys.exc_info()[1]
if e.errno == errno.ENOENT:
continue
@@ -91,7 +90,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
return None, None
else:
if verbose:
- print("unable to find command, tried %s" % (commands,))
+ print("unable to find command, tried {}".format(commands))
return None, None
stdout = p.communicate()[0].strip()
if sys.version_info[0] >= 3:
@@ -138,7 +137,7 @@ def git_get_keywords(versionfile_abs):
# _version.py.
keywords = {}
try:
- f = open(versionfile_abs, "r")
+ f = open(versionfile_abs)
for line in f.readlines():
if line.strip().startswith("git_refnames ="):
mo = re.search(r'=\s*"(.*)"', line)
@@ -153,7 +152,7 @@ def git_get_keywords(versionfile_abs):
if mo:
keywords["date"] = mo.group(1)
f.close()
- except EnvironmentError:
+ except OSError:
pass
return keywords
@@ -177,11 +176,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
if verbose:
print("keywords are unexpanded, not using")
raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
- refs = set([r.strip() for r in refnames.strip("()").split(",")])
+ refs = {r.strip() for r in refnames.strip("()").split(",")}
# starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
# just "foo-1.0". If we see a "tag: " prefix, prefer those.
TAG = "tag: "
- tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+ tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
if not tags:
# Either we're using git < 1.8.3, or there really are no tags. We use
# a heuristic: assume all version tags have a digit. The old git %d
@@ -190,7 +189,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
# between branches and tags. By ignoring refnames without digits, we
# filter out many common branch names like "release" and
# "stabilization", as well as "HEAD" and "master".
- tags = set([r for r in refs if re.search(r'\d', r)])
+ tags = {r for r in refs if re.search(r'\d', r)}
if verbose:
print("discarding '%s', no digits" % ",".join(refs - tags))
if verbose:
diff --git a/openmmforcefields/data/perses_jacs_systems/tests/test_outputs.py b/openmmforcefields/data/perses_jacs_systems/tests/test_outputs.py
index 220de6d9..3edfe94e 100644
--- a/openmmforcefields/data/perses_jacs_systems/tests/test_outputs.py
+++ b/openmmforcefields/data/perses_jacs_systems/tests/test_outputs.py
@@ -1,7 +1,7 @@
import sys
from argparse import ArgumentParser
-from simtk.openmm import app
+from openmm import app
if __name__ == "__main__":
parser = ArgumentParser(epilog='''This program reads a pdb file and tests whether the file that is compatible
@@ -22,4 +22,4 @@
print(error)
sys.exit("File %s was not properly prepared and cannot be parsed by openmm" % args.protein)
- sys.exit("Test passed! Output %s was prepared properly and can be parsed by openmm" % args.protein)
\ No newline at end of file
+ sys.exit("Test passed! Output %s was prepared properly and can be parsed by openmm" % args.protein)
diff --git a/amber/ffxml/DNA.OL15.xml b/openmmforcefields/ffxml/amber/DNA.OL15.xml
similarity index 100%
rename from amber/ffxml/DNA.OL15.xml
rename to openmmforcefields/ffxml/amber/DNA.OL15.xml
diff --git a/amber/ffxml/DNA.bsc0.xml b/openmmforcefields/ffxml/amber/DNA.bsc0.xml
similarity index 100%
rename from amber/ffxml/DNA.bsc0.xml
rename to openmmforcefields/ffxml/amber/DNA.bsc0.xml
diff --git a/amber/ffxml/DNA.bsc1.xml b/openmmforcefields/ffxml/amber/DNA.bsc1.xml
similarity index 100%
rename from amber/ffxml/DNA.bsc1.xml
rename to openmmforcefields/ffxml/amber/DNA.bsc1.xml
diff --git a/amber/ffxml/GLYCAM_06j-1.xml b/openmmforcefields/ffxml/amber/GLYCAM_06j-1.xml
similarity index 100%
rename from amber/ffxml/GLYCAM_06j-1.xml
rename to openmmforcefields/ffxml/amber/GLYCAM_06j-1.xml
diff --git a/amber/ffxml/RNA.OL3.xml b/openmmforcefields/ffxml/amber/RNA.OL3.xml
similarity index 100%
rename from amber/ffxml/RNA.OL3.xml
rename to openmmforcefields/ffxml/amber/RNA.OL3.xml
diff --git a/amber/ffxml/RNA.ROC.xml b/openmmforcefields/ffxml/amber/RNA.ROC.xml
similarity index 100%
rename from amber/ffxml/RNA.ROC.xml
rename to openmmforcefields/ffxml/amber/RNA.ROC.xml
diff --git a/amber/ffxml/RNA.YIL.xml b/openmmforcefields/ffxml/amber/RNA.YIL.xml
similarity index 100%
rename from amber/ffxml/RNA.YIL.xml
rename to openmmforcefields/ffxml/amber/RNA.YIL.xml
diff --git a/amber/ffxml/ff03.xml b/openmmforcefields/ffxml/amber/ff03.xml
similarity index 100%
rename from amber/ffxml/ff03.xml
rename to openmmforcefields/ffxml/amber/ff03.xml
diff --git a/amber/ffxml/ff10.xml b/openmmforcefields/ffxml/amber/ff10.xml
similarity index 100%
rename from amber/ffxml/ff10.xml
rename to openmmforcefields/ffxml/amber/ff10.xml
diff --git a/amber/ffxml/ff14SB.redq.xml b/openmmforcefields/ffxml/amber/ff14SB.redq.xml
similarity index 100%
rename from amber/ffxml/ff14SB.redq.xml
rename to openmmforcefields/ffxml/amber/ff14SB.redq.xml
diff --git a/amber/ffxml/ff14SB.xml b/openmmforcefields/ffxml/amber/ff14SB.xml
similarity index 100%
rename from amber/ffxml/ff14SB.xml
rename to openmmforcefields/ffxml/amber/ff14SB.xml
diff --git a/amber/ffxml/ff94.xml b/openmmforcefields/ffxml/amber/ff94.xml
similarity index 100%
rename from amber/ffxml/ff94.xml
rename to openmmforcefields/ffxml/amber/ff94.xml
diff --git a/amber/ffxml/ff96.xml b/openmmforcefields/ffxml/amber/ff96.xml
similarity index 100%
rename from amber/ffxml/ff96.xml
rename to openmmforcefields/ffxml/amber/ff96.xml
diff --git a/amber/ffxml/ff98.xml b/openmmforcefields/ffxml/amber/ff98.xml
similarity index 100%
rename from amber/ffxml/ff98.xml
rename to openmmforcefields/ffxml/amber/ff98.xml
diff --git a/amber/ffxml/ff99.xml b/openmmforcefields/ffxml/amber/ff99.xml
similarity index 100%
rename from amber/ffxml/ff99.xml
rename to openmmforcefields/ffxml/amber/ff99.xml
diff --git a/amber/ffxml/ff99SB.xml b/openmmforcefields/ffxml/amber/ff99SB.xml
similarity index 100%
rename from amber/ffxml/ff99SB.xml
rename to openmmforcefields/ffxml/amber/ff99SB.xml
diff --git a/amber/ffxml/ff99SBildn.xml b/openmmforcefields/ffxml/amber/ff99SBildn.xml
similarity index 100%
rename from amber/ffxml/ff99SBildn.xml
rename to openmmforcefields/ffxml/amber/ff99SBildn.xml
diff --git a/amber/ffxml/ff99SBnmr.xml b/openmmforcefields/ffxml/amber/ff99SBnmr.xml
similarity index 100%
rename from amber/ffxml/ff99SBnmr.xml
rename to openmmforcefields/ffxml/amber/ff99SBnmr.xml
diff --git a/amber/ffxml/ff99bsc0.xml b/openmmforcefields/ffxml/amber/ff99bsc0.xml
similarity index 100%
rename from amber/ffxml/ff99bsc0.xml
rename to openmmforcefields/ffxml/amber/ff99bsc0.xml
diff --git a/amber/ffxml/ffAM1.xml b/openmmforcefields/ffxml/amber/ffAM1.xml
similarity index 100%
rename from amber/ffxml/ffAM1.xml
rename to openmmforcefields/ffxml/amber/ffAM1.xml
diff --git a/amber/ffxml/ffPM3.xml b/openmmforcefields/ffxml/amber/ffPM3.xml
similarity index 100%
rename from amber/ffxml/ffPM3.xml
rename to openmmforcefields/ffxml/amber/ffPM3.xml
diff --git a/amber/gaff/dat/gaff-1.4.dat b/openmmforcefields/ffxml/amber/gaff/dat/gaff-1.4.dat
similarity index 100%
rename from amber/gaff/dat/gaff-1.4.dat
rename to openmmforcefields/ffxml/amber/gaff/dat/gaff-1.4.dat
diff --git a/amber/gaff/dat/gaff-1.7.dat b/openmmforcefields/ffxml/amber/gaff/dat/gaff-1.7.dat
similarity index 100%
rename from amber/gaff/dat/gaff-1.7.dat
rename to openmmforcefields/ffxml/amber/gaff/dat/gaff-1.7.dat
diff --git a/amber/gaff/dat/gaff-1.8.dat b/openmmforcefields/ffxml/amber/gaff/dat/gaff-1.8.dat
similarity index 100%
rename from amber/gaff/dat/gaff-1.8.dat
rename to openmmforcefields/ffxml/amber/gaff/dat/gaff-1.8.dat
diff --git a/amber/gaff/dat/gaff-1.81.dat b/openmmforcefields/ffxml/amber/gaff/dat/gaff-1.81.dat
similarity index 100%
rename from amber/gaff/dat/gaff-1.81.dat
rename to openmmforcefields/ffxml/amber/gaff/dat/gaff-1.81.dat
diff --git a/amber/gaff/dat/gaff-2.1.dat b/openmmforcefields/ffxml/amber/gaff/dat/gaff-2.1.dat
similarity index 100%
rename from amber/gaff/dat/gaff-2.1.dat
rename to openmmforcefields/ffxml/amber/gaff/dat/gaff-2.1.dat
diff --git a/amber/gaff/dat/gaff-2.11.dat b/openmmforcefields/ffxml/amber/gaff/dat/gaff-2.11.dat
similarity index 100%
rename from amber/gaff/dat/gaff-2.11.dat
rename to openmmforcefields/ffxml/amber/gaff/dat/gaff-2.11.dat
diff --git a/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.4.xml b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.4.xml
new file mode 100644
index 00000000..430d8620
--- /dev/null
+++ b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.4.xml
@@ -0,0 +1,5695 @@
+
+
+ 2022-09-09
+ gaff-1.4.dat
+ Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
+ Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.7.xml b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.7.xml
new file mode 100644
index 00000000..6b098ce0
--- /dev/null
+++ b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.7.xml
@@ -0,0 +1,5892 @@
+
+
+ 2022-09-09
+ gaff-1.7.dat
+ Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
+ Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
+
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diff --git a/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.8.xml b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.8.xml
new file mode 100644
index 00000000..2311bec7
--- /dev/null
+++ b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.8.xml
@@ -0,0 +1,6299 @@
+
+
+ 2022-09-09
+ gaff-1.8.dat
+ Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
+ Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.81.xml b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.81.xml
new file mode 100644
index 00000000..57dc2bff
--- /dev/null
+++ b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-1.81.xml
@@ -0,0 +1,7116 @@
+
+
+ 2022-09-09
+ gaff-1.81.dat
+ Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
+ Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.1.xml b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.1.xml
new file mode 100644
index 00000000..a36418fe
--- /dev/null
+++ b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.1.xml
@@ -0,0 +1,6654 @@
+
+
+ 2022-09-09
+ gaff-2.1.dat
+ Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
+ Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.11.xml b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.11.xml
new file mode 100644
index 00000000..0806c0ff
--- /dev/null
+++ b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff-2.11.xml
@@ -0,0 +1,7475 @@
+
+
+ 2022-09-09
+ gaff-2.11.dat
+ Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
+ Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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diff --git a/openmmforcefields/ffxml/amber/gaff/ffxml/gaff.xml b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff.xml
new file mode 100644
index 00000000..57dc2bff
--- /dev/null
+++ b/openmmforcefields/ffxml/amber/gaff/ffxml/gaff.xml
@@ -0,0 +1,7116 @@
+
+
+ 2022-09-09
+ gaff-1.81.dat
+ Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., and Case, D.A. (2004). Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
+ Wang, J., Wang, W., Kollman P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/amber/ffxml/lipid17.xml b/openmmforcefields/ffxml/amber/lipid17.xml
similarity index 100%
rename from amber/ffxml/lipid17.xml
rename to openmmforcefields/ffxml/amber/lipid17.xml
diff --git a/amber/ffxml/lipid17_merged.xml b/openmmforcefields/ffxml/amber/lipid17_merged.xml
similarity index 100%
rename from amber/ffxml/lipid17_merged.xml
rename to openmmforcefields/ffxml/amber/lipid17_merged.xml
diff --git a/amber/ffxml/phosaa10.xml b/openmmforcefields/ffxml/amber/phosaa10.xml
similarity index 100%
rename from amber/ffxml/phosaa10.xml
rename to openmmforcefields/ffxml/amber/phosaa10.xml
diff --git a/amber/ffxml/phosaa14SB.xml b/openmmforcefields/ffxml/amber/phosaa14SB.xml
similarity index 100%
rename from amber/ffxml/phosaa14SB.xml
rename to openmmforcefields/ffxml/amber/phosaa14SB.xml
diff --git a/amber/ffxml/protein.fb15.xml b/openmmforcefields/ffxml/amber/protein.fb15.xml
similarity index 100%
rename from amber/ffxml/protein.fb15.xml
rename to openmmforcefields/ffxml/amber/protein.fb15.xml
diff --git a/amber/ffxml/protein.ff03.r1.xml b/openmmforcefields/ffxml/amber/protein.ff03.r1.xml
similarity index 100%
rename from amber/ffxml/protein.ff03.r1.xml
rename to openmmforcefields/ffxml/amber/protein.ff03.r1.xml
diff --git a/amber/ffxml/protein.ff03ua.xml b/openmmforcefields/ffxml/amber/protein.ff03ua.xml
similarity index 100%
rename from amber/ffxml/protein.ff03ua.xml
rename to openmmforcefields/ffxml/amber/protein.ff03ua.xml
diff --git a/amber/ffxml/protein.ff14SB.xml b/openmmforcefields/ffxml/amber/protein.ff14SB.xml
similarity index 100%
rename from amber/ffxml/protein.ff14SB.xml
rename to openmmforcefields/ffxml/amber/protein.ff14SB.xml
diff --git a/amber/ffxml/protein.ff14SBonlysc.xml b/openmmforcefields/ffxml/amber/protein.ff14SBonlysc.xml
similarity index 100%
rename from amber/ffxml/protein.ff14SBonlysc.xml
rename to openmmforcefields/ffxml/amber/protein.ff14SBonlysc.xml
diff --git a/amber/ffxml/protein.ff15ipq-vac.xml b/openmmforcefields/ffxml/amber/protein.ff15ipq-vac.xml
similarity index 100%
rename from amber/ffxml/protein.ff15ipq-vac.xml
rename to openmmforcefields/ffxml/amber/protein.ff15ipq-vac.xml
diff --git a/amber/ffxml/protein.ff15ipq.xml b/openmmforcefields/ffxml/amber/protein.ff15ipq.xml
similarity index 100%
rename from amber/ffxml/protein.ff15ipq.xml
rename to openmmforcefields/ffxml/amber/protein.ff15ipq.xml
diff --git a/amber/ffxml/spce_HFE_multivalent.xml b/openmmforcefields/ffxml/amber/spce_HFE_multivalent.xml
similarity index 100%
rename from amber/ffxml/spce_HFE_multivalent.xml
rename to openmmforcefields/ffxml/amber/spce_HFE_multivalent.xml
diff --git a/amber/ffxml/spce_IOD_multivalent.xml b/openmmforcefields/ffxml/amber/spce_IOD_multivalent.xml
similarity index 100%
rename from amber/ffxml/spce_IOD_multivalent.xml
rename to openmmforcefields/ffxml/amber/spce_IOD_multivalent.xml
diff --git a/amber/ffxml/spce_standard.xml b/openmmforcefields/ffxml/amber/spce_standard.xml
similarity index 100%
rename from amber/ffxml/spce_standard.xml
rename to openmmforcefields/ffxml/amber/spce_standard.xml
diff --git a/amber/ffxml/tip3p_HFE_multivalent.xml b/openmmforcefields/ffxml/amber/tip3p_HFE_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip3p_HFE_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip3p_HFE_multivalent.xml
diff --git a/amber/ffxml/tip3p_IOD_multivalent.xml b/openmmforcefields/ffxml/amber/tip3p_IOD_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip3p_IOD_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip3p_IOD_multivalent.xml
diff --git a/amber/ffxml/tip3p_standard.xml b/openmmforcefields/ffxml/amber/tip3p_standard.xml
similarity index 100%
rename from amber/ffxml/tip3p_standard.xml
rename to openmmforcefields/ffxml/amber/tip3p_standard.xml
diff --git a/amber/ffxml/tip3pfb_HFE_multivalent.xml b/openmmforcefields/ffxml/amber/tip3pfb_HFE_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip3pfb_HFE_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip3pfb_HFE_multivalent.xml
diff --git a/amber/ffxml/tip3pfb_IOD_multivalent.xml b/openmmforcefields/ffxml/amber/tip3pfb_IOD_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip3pfb_IOD_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip3pfb_IOD_multivalent.xml
diff --git a/amber/ffxml/tip3pfb_standard.xml b/openmmforcefields/ffxml/amber/tip3pfb_standard.xml
similarity index 100%
rename from amber/ffxml/tip3pfb_standard.xml
rename to openmmforcefields/ffxml/amber/tip3pfb_standard.xml
diff --git a/amber/ffxml/tip4pew_HFE_multivalent.xml b/openmmforcefields/ffxml/amber/tip4pew_HFE_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip4pew_HFE_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip4pew_HFE_multivalent.xml
diff --git a/amber/ffxml/tip4pew_IOD_multivalent.xml b/openmmforcefields/ffxml/amber/tip4pew_IOD_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip4pew_IOD_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip4pew_IOD_multivalent.xml
diff --git a/amber/ffxml/tip4pew_standard.xml b/openmmforcefields/ffxml/amber/tip4pew_standard.xml
similarity index 100%
rename from amber/ffxml/tip4pew_standard.xml
rename to openmmforcefields/ffxml/amber/tip4pew_standard.xml
diff --git a/amber/ffxml/tip4pfb_HFE_multivalent.xml b/openmmforcefields/ffxml/amber/tip4pfb_HFE_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip4pfb_HFE_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip4pfb_HFE_multivalent.xml
diff --git a/amber/ffxml/tip4pfb_IOD_multivalent.xml b/openmmforcefields/ffxml/amber/tip4pfb_IOD_multivalent.xml
similarity index 100%
rename from amber/ffxml/tip4pfb_IOD_multivalent.xml
rename to openmmforcefields/ffxml/amber/tip4pfb_IOD_multivalent.xml
diff --git a/amber/ffxml/tip4pfb_standard.xml b/openmmforcefields/ffxml/amber/tip4pfb_standard.xml
similarity index 100%
rename from amber/ffxml/tip4pfb_standard.xml
rename to openmmforcefields/ffxml/amber/tip4pfb_standard.xml
diff --git a/charmm/ffxml/charmm36.xml b/openmmforcefields/ffxml/charmm/charmm36.xml
similarity index 100%
rename from charmm/ffxml/charmm36.xml
rename to openmmforcefields/ffxml/charmm/charmm36.xml
diff --git a/charmm/ffxml/charmm36_nowaters.xml b/openmmforcefields/ffxml/charmm/charmm36_nowaters.xml
similarity index 100%
rename from charmm/ffxml/charmm36_nowaters.xml
rename to openmmforcefields/ffxml/charmm/charmm36_nowaters.xml
diff --git a/charmm/ffxml/charmm_polar_2019.xml b/openmmforcefields/ffxml/charmm/charmm_polar_2019.xml
similarity index 100%
rename from charmm/ffxml/charmm_polar_2019.xml
rename to openmmforcefields/ffxml/charmm/charmm_polar_2019.xml
diff --git a/charmm/ffxml/toppar_all36_carb_model.xml b/openmmforcefields/ffxml/charmm/toppar_all36_carb_model.xml
similarity index 100%
rename from charmm/ffxml/toppar_all36_carb_model.xml
rename to openmmforcefields/ffxml/charmm/toppar_all36_carb_model.xml
diff --git a/charmm/ffxml/toppar_all36_lipid_model.xml b/openmmforcefields/ffxml/charmm/toppar_all36_lipid_model.xml
similarity index 100%
rename from charmm/ffxml/toppar_all36_lipid_model.xml
rename to openmmforcefields/ffxml/charmm/toppar_all36_lipid_model.xml
diff --git a/charmm/ffxml/toppar_all36_na_model.xml b/openmmforcefields/ffxml/charmm/toppar_all36_na_model.xml
similarity index 100%
rename from charmm/ffxml/toppar_all36_na_model.xml
rename to openmmforcefields/ffxml/charmm/toppar_all36_na_model.xml
diff --git a/charmm/ffxml/toppar_all36_prot_model.xml b/openmmforcefields/ffxml/charmm/toppar_all36_prot_model.xml
similarity index 100%
rename from charmm/ffxml/toppar_all36_prot_model.xml
rename to openmmforcefields/ffxml/charmm/toppar_all36_prot_model.xml
diff --git a/charmm/ffxml/waters_ions_default.xml b/openmmforcefields/ffxml/charmm/waters_ions_default.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_default.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_default.xml
diff --git a/charmm/ffxml/waters_ions_spc.xml b/openmmforcefields/ffxml/charmm/waters_ions_spc.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_spc.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_spc.xml
diff --git a/charmm/ffxml/waters_ions_spc_e.xml b/openmmforcefields/ffxml/charmm/waters_ions_spc_e.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_spc_e.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_spc_e.xml
diff --git a/charmm/ffxml/waters_ions_tip3p_pme_b.xml b/openmmforcefields/ffxml/charmm/waters_ions_tip3p_pme_b.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_tip3p_pme_b.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_tip3p_pme_b.xml
diff --git a/charmm/ffxml/waters_ions_tip3p_pme_f.xml b/openmmforcefields/ffxml/charmm/waters_ions_tip3p_pme_f.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_tip3p_pme_f.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_tip3p_pme_f.xml
diff --git a/charmm/ffxml/waters_ions_tip4p.xml b/openmmforcefields/ffxml/charmm/waters_ions_tip4p.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_tip4p.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_tip4p.xml
diff --git a/charmm/ffxml/waters_ions_tip4p_2005.xml b/openmmforcefields/ffxml/charmm/waters_ions_tip4p_2005.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_tip4p_2005.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_tip4p_2005.xml
diff --git a/charmm/ffxml/waters_ions_tip4p_ew.xml b/openmmforcefields/ffxml/charmm/waters_ions_tip4p_ew.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_tip4p_ew.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_tip4p_ew.xml
diff --git a/charmm/ffxml/waters_ions_tip5p.xml b/openmmforcefields/ffxml/charmm/waters_ions_tip5p.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_tip5p.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_tip5p.xml
diff --git a/charmm/ffxml/waters_ions_tip5p_ew.xml b/openmmforcefields/ffxml/charmm/waters_ions_tip5p_ew.xml
similarity index 100%
rename from charmm/ffxml/waters_ions_tip5p_ew.xml
rename to openmmforcefields/ffxml/charmm/waters_ions_tip5p_ew.xml
diff --git a/openmmforcefields/generators/__init__.py b/openmmforcefields/generators/__init__.py
index f4a48eff..f78e8b5d 100644
--- a/openmmforcefields/generators/__init__.py
+++ b/openmmforcefields/generators/__init__.py
@@ -1,2 +1,6 @@
-from .template_generators import GAFFTemplateGenerator, SMIRNOFFTemplateGenerator, EspalomaTemplateGenerator
from .system_generators import SystemGenerator
+from .template_generators import (
+ EspalomaTemplateGenerator,
+ GAFFTemplateGenerator,
+ SMIRNOFFTemplateGenerator,
+)
diff --git a/openmmforcefields/generators/system_generators.py b/openmmforcefields/generators/system_generators.py
index 147eca51..fc058c81 100644
--- a/openmmforcefields/generators/system_generators.py
+++ b/openmmforcefields/generators/system_generators.py
@@ -8,9 +8,8 @@
################################################################################
import logging
-_logger = logging.getLogger("openmmforcefields.system_generators")
-from openmm import app
+_logger = logging.getLogger("openmmforcefields.system_generators")
################################################################################
# System generator base class
@@ -18,13 +17,13 @@
class classproperty(property):
def __get__(self, obj, objtype=None):
- return super(classproperty, self).__get__(objtype)
+ return super().__get__(objtype)
def __set__(self, obj, value):
- super(classproperty, self).__set__(type(obj), value)
+ super().__set__(type(obj), value)
def __delete__(self, obj):
- super(classproperty, self).__delete__(type(obj))
+ super().__delete__(type(obj))
-class SystemGenerator(object):
+class SystemGenerator:
"""
Common interface for generating OpenMM Systems from OpenMM Topology objects
that may contain both biopolymers (with parameters provided by OpenMM) and small molecules
@@ -188,7 +187,9 @@ def __init__(self, forcefields=None, small_molecule_forcefield='openff-1.0.0', f
or nonperiodic_forcefield_kwargs (if it should be applied to non-periodic systems)""")
# Create and cache a residue template generator
- from openmmforcefields.generators.template_generators import SmallMoleculeTemplateGenerator
+ from openmmforcefields.generators.template_generators import (
+ SmallMoleculeTemplateGenerator,
+ )
self.template_generator = None
if small_molecule_forcefield is not None:
for template_generator_cls in SmallMoleculeTemplateGenerator.__subclasses__():
@@ -214,7 +215,9 @@ def __init__(self, forcefields=None, small_molecule_forcefield='openff-1.0.0', f
def SMALL_MOLECULE_FORCEFIELDS(cls):
"""Return a listof available small molecule force fields"""
forcefields = list()
- from openmmforcefields.generators.template_generators import SmallMoleculeTemplateGenerator
+ from openmmforcefields.generators.template_generators import (
+ SmallMoleculeTemplateGenerator,
+ )
for template_generator_cls in SmallMoleculeTemplateGenerator.__subclasses__():
forcefields += template_generator_cls.INSTALLED_FORCEFIELDS
return forcefields
diff --git a/openmmforcefields/generators/template_generators.py b/openmmforcefields/generators/template_generators.py
index 817213a9..cfb27ff8 100644
--- a/openmmforcefields/generators/template_generators.py
+++ b/openmmforcefields/generators/template_generators.py
@@ -11,16 +11,17 @@
# LOGGER
################################################################################
-import os
-import logging
import contextlib
+import logging
+import os
+
_logger = logging.getLogger("openmmforcefields.generators.template_generators")
################################################################################
# Small molecule OpenMM ForceField template generation utilities
################################################################################
-class SmallMoleculeTemplateGenerator(object):
+class SmallMoleculeTemplateGenerator:
"""
Abstract base class for small molecule template generation for OpenMM ForceField.
@@ -218,13 +219,18 @@ def _molecule_has_user_charges(self, molecule):
"""
import numpy as np
- from openmm import unit
- zeros = np.zeros([molecule.n_particles])
- if (molecule.partial_charges is None) or (np.allclose(molecule.partial_charges / unit.elementary_charge, zeros)):
- charges_are_zero = True
- else:
- charges_are_zero = False
- return not charges_are_zero
+ from openff.units import unit
+
+ if molecule.partial_charges is None:
+ return False
+
+ if np.allclose(
+ molecule.partial_charges.m_as(unit.elementary_charge),
+ np.zeros([molecule.n_atoms]),
+ ):
+ return False
+
+ return True
def _generate_unique_atom_names(self, molecule):
"""
@@ -567,6 +573,9 @@ def generate_residue_template(self, molecule, residue_atoms=None):
* Atom names in molecules will be assigned Tripos atom names if any are blank or not unique.
"""
+ import numpy as np
+ from openff.units import unit
+
# Use the canonical isomeric SMILES to uniquely name the template
smiles = molecule.to_smiles()
_logger.info(f'Generating a residue template for {smiles} using {self._forcefield}')
@@ -576,9 +585,10 @@ def generate_residue_template(self, molecule, residue_atoms=None):
# Compute net formal charge
net_charge = molecule.total_charge
- from openmm import unit
+
if type(net_charge) != unit.Quantity:
# openforcefield toolkit < 0.7.0 did not return unit-bearing quantity
+ # how long should openmmforcefields support < 0.7.0?
net_charge = float(net_charge) * unit.elementary_charge
_logger.debug(f'Total charge is {net_charge}')
@@ -590,15 +600,15 @@ def generate_residue_template(self, molecule, residue_atoms=None):
# NOTE: generate_conformers seems to be required for some molecules
# https://github.com/openforcefield/openff-toolkit/issues/492
molecule.generate_conformers(n_conformers=10)
- molecule.compute_partial_charges_am1bcc()
+ molecule.assign_partial_charges(partial_charge_method='am1bcc')
# Geneate a single conformation
_logger.debug(f'Generating a conformer...')
molecule.generate_conformers(n_conformers=1)
# Create temporary directory for running antechamber
- import tempfile
import os
+ import tempfile
tmpdir = tempfile.mkdtemp()
prefix = 'molecule'
input_sdf_filename = os.path.join(tmpdir, prefix + '.sdf')
@@ -627,20 +637,21 @@ def generate_residue_template(self, molecule, residue_atoms=None):
# or pure numbers.
_logger.debug(f'Fixing partial charges...')
_logger.debug(f'{molecule.partial_charges}')
- from openmm import unit
residue_charge = 0.0 * unit.elementary_charge
- total_charge = unit.sum(molecule.partial_charges)
- sum_of_absolute_charge = unit.sum(abs(molecule.partial_charges))
+ total_charge = molecule.partial_charges.sum()
+ sum_of_absolute_charge = np.sum(np.abs(molecule.partial_charges))
charge_deficit = net_charge - total_charge
- if sum_of_absolute_charge / unit.elementary_charge > 0.0:
+ if (sum_of_absolute_charge / unit.elementary_charge).m > 0.0:
# Redistribute excess charge proportionally to absolute charge
- molecule.partial_charges += charge_deficit * abs(molecule.partial_charges) / sum_of_absolute_charge
+ molecule.partial_charges = molecule.partial_charges + charge_deficit * abs(molecule.partial_charges) / sum_of_absolute_charge
_logger.debug(f'{molecule.partial_charges}')
# Generate additional parameters if needed
# TODO: Do we have to make sure that we don't duplicate existing parameters already loaded in the forcefield?
_logger.debug(f'Creating ffxml contents for additional parameters...')
- from inspect import signature # use introspection to support multiple parmed versions
+ from inspect import (
+ signature, # use introspection to support multiple parmed versions
+ )
from io import StringIO
leaprc = StringIO('parm = loadamberparams %s' % frcmod_filename)
import parmed
@@ -664,7 +675,7 @@ def generate_residue_template(self, molecule, residue_atoms=None):
residues = etree.SubElement(root, "Residues")
residue = etree.SubElement(residues, "Residue", name=smiles)
for atom in molecule.atoms:
- atom = etree.SubElement(residue, "Atom", name=atom.name, type=atom.gaff_type, charge=str(atom.partial_charge / unit.elementary_charge))
+ atom = etree.SubElement(residue, "Atom", name=atom.name, type=atom.gaff_type, charge=str(atom.partial_charge.m_as(unit.elementary_charge)))
for bond in molecule.bonds:
if (bond.atom1 in residue_atoms) and (bond.atom2 in residue_atoms):
bond = etree.SubElement(residue, "Bond", atomName1=bond.atom1.name, atomName2=bond.atom2.name)
@@ -718,13 +729,14 @@ def _run_antechamber(self, molecule_filename, input_format='sdf',
frcmod_filename = os.path.abspath( frcmod_filename )
def read_file_contents(filename):
- infile = open(filename, 'r')
+ infile = open(filename)
contents = infile.read()
infile.close()
return contents
# Use temporary directory context to do this to avoid issues with spaces in filenames, etc.
- import tempfile, subprocess
+ import subprocess
+ import tempfile
with tempfile.TemporaryDirectory() as tmpdir:
cwd = os.getcwd()
os.chdir(tmpdir)
@@ -815,7 +827,7 @@ def _read_gaff_atom_types_from_mol2(self, gaff_mol2_filename, molecule):
# 1 C1 1.8850 -1.0360 -0.1120 ca 1 MOL 0.000000
# 012345678901234567890123456789012345678901234567890123456789012345678901234567890
# 0 1 2 3 4 5 6 7 8
- with open(gaff_mol2_filename, 'r') as infile:
+ with open(gaff_mol2_filename) as infile:
line = infile.readline()
# Seek to ATOM block
while line:
@@ -880,7 +892,7 @@ def _check_for_errors(self, outputtext, other_errors=None, ignore_errors=None):
# MixIn for force field template generators that produce OpenMM System objects
################################################################################
-class OpenMMSystemMixin(object):
+class OpenMMSystemMixin:
"""
"""
def clear_system_cache(self):
@@ -937,34 +949,46 @@ def convert_system_to_ffxml(self, molecule, system, improper_atom_ordering='smir
ffxml_contents : str
The OpenMM ffxml contents for the given molecule.
"""
+ # OpenFF Toolkit v0.11.0 removed Atom.element and replced it with Atom.symbol, etc.
+ uses_old_api = hasattr(molecule.atoms[0], "element")
# Generate OpenMM ffxml definition for this molecule
from lxml import etree
root = etree.Element("ForceField")
def as_attrib(quantity):
- """Format openmm.unit.Quantity as XML attribute."""
+ """Format openff.units.Quantity or openmm.unit.Quantity as XML attribute."""
+ import openff.units
+
if isinstance(quantity, str):
return quantity
- elif isinstance(quantity, float) or isinstance(quantity, int):
+ elif isinstance(quantity, (float, int)):
return str(quantity)
+ elif isinstance(quantity, openff.units.Quantity):
+ # TODO: Match behavior of Quantity.value_in_unit_system
+ return str(quantity.m)
else:
- from openmm import unit
- return str(quantity.value_in_unit_system(unit.md_unit_system))
+ from openmm.unit import Quantity as OpenMMQuantity
+ if isinstance(quantity, OpenMMQuantity):
+ from openmm import unit
+ return str(quantity.value_in_unit_system(unit.md_unit_system))
+ else:
+ raise ValueError(f"Found unexpected type {type(quantity)}.")
# Append unique type names to atoms
smiles = molecule.to_smiles()
- for index, particle in enumerate(molecule.particles):
- setattr(particle, 'typename', f'{smiles}${particle.name}#{index}')
+ for index, atom in enumerate(molecule.atoms):
+ setattr(atom, 'typename', f'{smiles}${atom.name}#{index}')
# Generate atom types
atom_types = etree.SubElement(root, "AtomTypes")
- for particle_index, particle in enumerate(molecule.particles):
+ for atom_index, atom in enumerate(molecule.atoms):
# Create a new atom type for each atom in the molecule
- paricle_indices = [particle_index]
- atom_type = etree.SubElement(atom_types, "Type", name=particle.typename,
- element=particle.element.symbol, mass=as_attrib(particle.element.mass))
- atom_type.set('class', particle.typename) # 'class' is a reserved Python keyword, so use alternative API
+ paricle_indices = [atom_index]
+ element_symbol = atom.element.symbol if uses_old_api else atom.symbol
+ atom_type = etree.SubElement(atom_types, "Type", name=atom.typename,
+ element=element_symbol, mass=as_attrib(atom.mass))
+ atom_type.set('class', atom.typename) # 'class' is a reserved Python keyword, so use alternative API
# Compile forces into a dict
forces = dict()
@@ -974,53 +998,53 @@ def as_attrib(quantity):
raise Exception("Two instances of force {force_name} appear in System")
forces[force_name] = force
- def classes(particle_indices):
+ def classes(atom_indices):
"""Build a dict of 'class#=typename' for use in creating XML tags for forces.
Parameters
----------
- particle_indices : list of int
- Particle indices for molecule.particles
+ atom_indices : list of int
+ Particle indices for molecule.atoms
Returns
-------
classmap : dict of str : str
Dict of format { 'class1' : typename1, ... }
"""
- return { f'class{class_index+1}' : molecule.particles[particle_index].typename for class_index,particle_index in enumerate(particle_indices) }
+ return { f'class{class_index+1}' : molecule.atoms[atom_index].typename for class_index,atom_index in enumerate(atom_indices) }
# Lennard-Jones
# TODO: Get coulomb14scale and lj14scale from SMIRNOFF ForceField object,
# though this must match the original AMBER values
nonbonded_types = etree.SubElement(root, "NonbondedForce", coulomb14scale="0.833333", lj14scale="0.5")
etree.SubElement(nonbonded_types, "UseAttributeFromResidue", name="charge")
- for particle_index in range(forces['NonbondedForce'].getNumParticles()):
- charge, sigma, epsilon = forces['NonbondedForce'].getParticleParameters(particle_index)
+ for atom_index in range(forces['NonbondedForce'].getNumParticles()):
+ charge, sigma, epsilon = forces['NonbondedForce'].getParticleParameters(atom_index)
nonbonded_type = etree.SubElement(nonbonded_types, "Atom",
sigma=as_attrib(sigma), epsilon=as_attrib(epsilon))
- nonbonded_type.set('class', molecule.particles[particle_index].typename) # 'class' is a reserved Python keyword, so use alternative API
+ nonbonded_type.set('class', molecule.atoms[atom_index].typename) # 'class' is a reserved Python keyword, so use alternative API
# Bonds
bond_types = etree.SubElement(root, "HarmonicBondForce")
- particle_indices = [-1]*2
+ atom_indices = [-1]*2
for bond_index in range(forces['HarmonicBondForce'].getNumBonds()):
- particle_indices[0], particle_indices[1], length, k = forces['HarmonicBondForce'].getBondParameters(bond_index)
- bond_type = etree.SubElement(bond_types, "Bond", **classes(particle_indices),
+ atom_indices[0], atom_indices[1], length, k = forces['HarmonicBondForce'].getBondParameters(bond_index)
+ bond_type = etree.SubElement(bond_types, "Bond", **classes(atom_indices),
length=as_attrib(length), k=as_attrib(k))
# Angles
angle_types = etree.SubElement(root, "HarmonicAngleForce")
- particle_indices = [-1]*3
+ atom_indices = [-1]*3
for angle_index in range(forces['HarmonicAngleForce'].getNumAngles()):
- particle_indices[0], particle_indices[1], particle_indices[2], angle, k = forces['HarmonicAngleForce'].getAngleParameters(angle_index)
- angle_type = etree.SubElement(angle_types, "Angle", **classes(particle_indices),
+ atom_indices[0], atom_indices[1], atom_indices[2], angle, k = forces['HarmonicAngleForce'].getAngleParameters(angle_index)
+ angle_type = etree.SubElement(angle_types, "Angle", **classes(atom_indices),
angle=as_attrib(angle), k=as_attrib(k))
# Torsions
- def torsion_tag(particle_indices):
+ def torsion_tag(atom_indices):
"""Return 'Proper' or 'Improper' depending on torsion type"""
- atoms = [ molecule.particles[particle_index] for particle_index in particle_indices ]
- # TODO: Check to make sure all particles are in fact atoms and not virtual sites
+ atoms = [ molecule.atoms[atom_index] for atom_index in atom_indices ]
+ # TODO: Check to make sure all atoms are in fact atoms and not virtual sites
if atoms[0].is_bonded_to(atoms[1]) and atoms[1].is_bonded_to(atoms[2]) and atoms[2].is_bonded_to(atoms[3]):
return "Proper"
else:
@@ -1029,39 +1053,38 @@ def torsion_tag(particle_indices):
# Collect torsions
torsions = dict()
for torsion_index in range(forces['PeriodicTorsionForce'].getNumTorsions()):
- particle_indices = [-1]*4
- particle_indices[0], particle_indices[1], particle_indices[2], particle_indices[3], periodicity, phase, k = forces['PeriodicTorsionForce'].getTorsionParameters(torsion_index)
- particle_indices = tuple(particle_indices)
- if particle_indices in torsions.keys():
- torsions[particle_indices].append( (periodicity, phase, k) )
+ atom_indices = [-1]*4
+ atom_indices[0], atom_indices[1], atom_indices[2], atom_indices[3], periodicity, phase, k = forces['PeriodicTorsionForce'].getTorsionParameters(torsion_index)
+ atom_indices = tuple(atom_indices)
+ if atom_indices in torsions.keys():
+ torsions[atom_indices].append( (periodicity, phase, k) )
else:
- torsions[particle_indices] = [ (periodicity, phase, k) ]
+ torsions[atom_indices] = [ (periodicity, phase, k) ]
# Create torsion definitions
torsion_types = etree.SubElement(root, "PeriodicTorsionForce", ordering='smirnoff')
- for particle_indices in torsions.keys():
+ for atom_indices in torsions.keys():
params = dict() # build parameter dictionary
- nterms = len(torsions[particle_indices])
+ nterms = len(torsions[atom_indices])
for term in range(nterms):
- periodicity, phase, k = torsions[particle_indices][term]
+ periodicity, phase, k = torsions[atom_indices][term]
params[f'periodicity{term+1}'] = as_attrib(periodicity)
params[f'phase{term+1}'] = as_attrib(phase)
params[f'k{term+1}'] = as_attrib(k)
- torsion_type = etree.SubElement(torsion_types, torsion_tag(particle_indices), **classes(particle_indices), **params)
+ torsion_type = etree.SubElement(torsion_types, torsion_tag(atom_indices), **classes(atom_indices), **params)
# TODO: Handle virtual sites
- virtual_sites = [ particle_index for particle_index in range(system.getNumParticles()) if system.isVirtualSite(particle_index) ]
+ virtual_sites = [ atom_index for atom_index in range(system.getNumParticles()) if system.isVirtualSite(atom_index) ]
if len(virtual_sites) > 0:
raise Exception('Virtual sites are not yet supported')
# Create residue definitions
- # TODO: Handle non-Atom particles too (virtual sites)
- from openmm import unit
+ # TODO: Handle non-Atom atoms too (virtual sites)
residues = etree.SubElement(root, "Residues")
residue = etree.SubElement(residues, "Residue", name=smiles)
- for particle_index, particle in enumerate(molecule.particles):
- charge, sigma, epsilon = forces['NonbondedForce'].getParticleParameters(particle_index)
- atom = etree.SubElement(residue, "Atom", name=particle.name, type=particle.typename, charge=as_attrib(charge))
+ for atom_index, atom in enumerate(molecule.atoms):
+ charge, sigma, epsilon = forces['NonbondedForce'].getParticleParameters(atom_index)
+ atom = etree.SubElement(residue, "Atom", name=atom.name, type=atom.typename, charge=as_attrib(charge))
for bond in molecule.bonds:
bond = etree.SubElement(residue, "Bond", atomName1=bond.atom1.name, atomName2=bond.atom2.name)
@@ -1235,7 +1258,7 @@ def __init__(self, molecules=None, cache=None, forcefield=None):
@ClassProperty
@classmethod
def INSTALLED_FORCEFIELDS(cls):
- """Return a list of the offxml files shipped with the openfff-forcefields package.
+ """Return a list of the offxml files shipped with the openff-forcefields package.
Returns
-------
@@ -1253,7 +1276,7 @@ def INSTALLED_FORCEFIELDS(cls):
for filename in get_available_force_fields(full_paths=False):
root, ext = os.path.splitext(filename)
# Only add variants without '_unconstrained'
- if '_unconstrained' not in root:
+ if '_unconstrained' in root:
continue
# The OpenFF Toolkit ships two versions of its ff14SB port, one with SMIRNOFF-style
# impropers and one with Amber-style impropers. The latter requires a special handler
@@ -1286,8 +1309,9 @@ def _search_paths(self, filename):
"""
# TODO: Replace this method once there is a public API in the OpenFF toolkit for doing this
- from openff.toolkit.utils import get_data_file_path
- from openff.toolkit.typing.engines.smirnoff.forcefield import _get_installed_offxml_dir_paths
+ from openff.toolkit.typing.engines.smirnoff.forcefield import (
+ _get_installed_offxml_dir_paths,
+ )
# Check whether this could be a file path
if isinstance(filename, str):
@@ -1346,6 +1370,7 @@ def generate_residue_template(self, molecule, residue_atoms=None):
# Determine which molecules (if any) contain user-specified partial charges that should be used
charge_from_molecules = list()
+
if self._molecule_has_user_charges(molecule):
charge_from_molecules = [molecule]
_logger.debug(f'Using user-provided charges because partial charges are nonzero...')
@@ -1559,7 +1584,7 @@ def _get_model_filepath(self, forcefield):
else:
# Identify version number
import re
- m = re.match('espaloma-(\d+\.\d+\.\d+)', forcefield)
+ m = re.match(r'espaloma-(\d+\.\d+\.\d+)', forcefield)
if m is None:
raise ValueError(f'Espaloma model must be filepath or formatted like "espaloma-0.2.2" (found: "{forcefield}")')
version = m.group(1)
@@ -1579,7 +1604,9 @@ def _get_model_filepath(self, forcefield):
# Attempt to retrieve from URL
_logger.info(f'Attempting to retrieve espaloma model from {url}')
- import urllib, urllib.error, urllib.request
+ import urllib
+ import urllib.error
+ import urllib.request
try:
urllib.request.urlretrieve(url, filename=cached_filename)
except urllib.error.URLError as e:
diff --git a/openmmforcefields/tests/__init__.py b/openmmforcefields/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/openmmforcefields/tests/test_amber_import.py b/openmmforcefields/tests/test_amber_import.py
index 16cc7ad9..38024c38 100644
--- a/openmmforcefields/tests/test_amber_import.py
+++ b/openmmforcefields/tests/test_amber_import.py
@@ -2,13 +2,16 @@
Test AMBER forcefield imports.
"""
+import pathlib
+from typing import List
-import os
-import glob
import pytest
from openmmforcefields.utils import get_ffxml_path
-amber_ffxml_filenames = [ os.path.join('amber', os.path.split(filename)[1]) for filename in glob.glob(os.path.join(get_ffxml_path(), 'amber', '*.xml')) ]
+
+amber_ffxml_filenames: List[str] = [
+ 'amber/' + file.name for file in pathlib.Path(get_ffxml_path()).glob("amber/*xml")
+]
@pytest.mark.parametrize("filename", amber_ffxml_filenames, ids=lambda filename : f'Importing ffxml file {filename}')
def test_ffxml_import(filename):
diff --git a/openmmforcefields/tests/test_system_generator.py b/openmmforcefields/tests/test_system_generator.py
index 591b2f49..7e24e40a 100644
--- a/openmmforcefields/tests/test_system_generator.py
+++ b/openmmforcefields/tests/test_system_generator.py
@@ -1,11 +1,16 @@
-import os, sys
-import unittest
+import copy
+import os
import tempfile
-import pytest
+import unittest
-from openmmforcefields.utils import get_data_filename
+import numpy as np
+import openmm
+import pytest
+from openff.toolkit.topology import Molecule
+from openmm.app import LJPME, PME, CutoffNonPeriodic, Modeller, PDBFile
from openmmforcefields.generators import SystemGenerator
+from openmmforcefields.utils import Timer, get_data_filename
CI = ('CI' in os.environ)
@@ -57,12 +62,10 @@ def setUp(self):
#('tyk2', 'Tyk2'),
]:
# Load protein
- from openmm.app import PDBFile
pdb_filename = get_data_filename(os.path.join('perses_jacs_systems', system_name, prefix + '_protein.pdb'))
pdbfile = PDBFile(pdb_filename)
# Load molecules
- from openff.toolkit.topology import Molecule
sdf_filename = get_data_filename(os.path.join('perses_jacs_systems', system_name, prefix + '_ligands_shifted.sdf'))
molecules = Molecule.from_file(sdf_filename, allow_undefined_stereo=True)
@@ -78,6 +81,7 @@ def setUp(self):
# Create structures
import parmed
+
# NOTE: This does not work because parmed does not correctly assign bonds for HID
#protein_structure = parmed.load_file(pdb_filename)
# NOTE: This is the workaround
@@ -100,13 +104,12 @@ def setUp(self):
# DEBUG
for name, testsystem in self.testsystems.items():
- from openmm import app
filename = f'testsystem-{name}.pdb'
print(filename)
structure = testsystem['complex_structures'][0]
#structure.save(filename, overwrite=True)
with open(filename, 'w') as outfile:
- app.PDBFile.writeFile(structure.topology, structure.positions, outfile)
+ PDBFile.writeFile(structure.topology, structure.positions, outfile)
testsystem['molecules'][0].to_file(f'testsystem-{name}-molecule.sdf', file_format="SDF")
testsystem['molecules'][0].to_file(f'testsystem-{name}-molecule.pdb', file_format="PDB")
@@ -132,29 +135,25 @@ def test_barostat(self):
generator = SystemGenerator(forcefields=self.amber_forcefields)
# Create a template barostat
- from openmm import MonteCarloBarostat
- from openmm import unit
+ from openmm import MonteCarloBarostat, unit
pressure = 0.95 * unit.atmospheres
temperature = 301.0 * unit.kelvin
frequency = 23
generator.barostat = MonteCarloBarostat(pressure, temperature, frequency)
# Load a PDB file
- import os
- from openmm.app import PDBFile
+
pdb_filename = get_data_filename(os.path.join('perses_jacs_systems', 'mcl1', 'MCL1_protein.pdb'))
pdbfile = PDBFile(pdb_filename)
# Delete hydrogens from terminal protein residues
# TODO: Fix the input files so we don't need to do this
- from openmm import app
- modeller = app.Modeller(pdbfile.topology, pdbfile.positions)
+ modeller = Modeller(pdbfile.topology, pdbfile.positions)
residues = [residue for residue in modeller.topology.residues() if residue.name != 'UNL']
termini_ids = [residues[0].id, residues[-1].id]
#hs = [atom for atom in modeller.topology.atoms() if atom.element.symbol in ['H'] and atom.residue.name != 'UNL']
hs = [atom for atom in modeller.topology.atoms() if atom.element.symbol in ['H'] and atom.residue.id in termini_ids]
modeller.delete(hs)
- from openmm.app import PDBFile
modeller.addHydrogens()
# Create a System
@@ -203,8 +202,6 @@ def test_forcefield_default_kwargs(self):
SMALL_MOLECULE_FORCEFIELDS = SystemGenerator.SMALL_MOLECULE_FORCEFIELDS if not CI else ['gaff-2.11', 'openff-2.0.0', 'espaloma-0.2.2']
for small_molecule_forcefield in SMALL_MOLECULE_FORCEFIELDS:
# Create a SystemGenerator for this force field
- from simtk import openmm
- from openmm import app
generator = SystemGenerator(forcefields=self.amber_forcefields,
small_molecule_forcefield=small_molecule_forcefield,
forcefield_kwargs=forcefield_kwargs,
@@ -219,8 +216,6 @@ def test_forcefield_default_kwargs(self):
assert forces['NonbondedForce'].getNonbondedMethod() == openmm.NonbondedForce.NoCutoff, "Expected CutoffNonPeriodic, got {forces['NonbondedForce'].getNonbondedMethod()}"
# Create periodic Topology
- import numpy as np
- import copy
box_vectors = unit.Quantity(np.diag([30, 30, 30]), unit.angstrom)
periodic_openmm_topology = copy.deepcopy(nonperiodic_openmm_topology)
periodic_openmm_topology.setPeriodicBoxVectors(box_vectors)
@@ -237,8 +232,7 @@ def test_forcefield_kwargs(self):
# Test exception is raised
with pytest.raises(ValueError) as excinfo:
# Not allowed to specify nonbondedMethod in forcefield_kwargs
- from openmm import app
- generator = SystemGenerator(forcefield_kwargs={'nonbondedMethod':app.PME})
+ generator = SystemGenerator(forcefield_kwargs={'nonbondedMethod':PME})
assert "nonbondedMethod cannot be specified in forcefield_kwargs" in str(excinfo.value)
for name, testsystem in self.testsystems.items():
@@ -248,13 +242,11 @@ def test_forcefield_kwargs(self):
SMALL_MOLECULE_FORCEFIELDS = SystemGenerator.SMALL_MOLECULE_FORCEFIELDS if not CI else ['gaff-2.11', 'openff-2.0.0', 'espaloma-0.2.2']
for small_molecule_forcefield in SMALL_MOLECULE_FORCEFIELDS:
# Create a SystemGenerator for this force field
- from simtk import openmm
- from openmm import app
generator = SystemGenerator(forcefields=self.amber_forcefields,
small_molecule_forcefield=small_molecule_forcefield,
forcefield_kwargs=forcefield_kwargs,
- periodic_forcefield_kwargs={'nonbondedMethod':app.LJPME},
- nonperiodic_forcefield_kwargs={'nonbondedMethod':app.CutoffNonPeriodic},
+ periodic_forcefield_kwargs={'nonbondedMethod':LJPME},
+ nonperiodic_forcefield_kwargs={'nonbondedMethod':CutoffNonPeriodic},
molecules=molecules)
# Parameterize molecules
@@ -266,8 +258,6 @@ def test_forcefield_kwargs(self):
assert forces['NonbondedForce'].getNonbondedMethod() == openmm.NonbondedForce.CutoffNonPeriodic, "Expected CutoffNonPeriodic, got {forces['NonbondedForce'].getNonbondedMethod()}"
# Create periodic Topology
- import numpy as np
- import copy
box_vectors = unit.Quantity(np.diag([30, 30, 30]), unit.angstrom)
periodic_openmm_topology = copy.deepcopy(nonperiodic_openmm_topology)
periodic_openmm_topology.setPeriodicBoxVectors(box_vectors)
@@ -277,8 +267,6 @@ def test_forcefield_kwargs(self):
def test_parameterize_molecules_from_creation(self):
"""Test that SystemGenerator can parameterize pre-specified molecules in vacuum"""
- from openmmforcefields.generators import SystemGenerator
-
for name, testsystem in self.testsystems.items():
print(testsystem)
molecules = testsystem['molecules']
@@ -291,7 +279,6 @@ def test_parameterize_molecules_from_creation(self):
molecules=molecules)
# Parameterize molecules
- from openmmforcefields.utils import Timer
for molecule in molecules:
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as t1:
@@ -305,8 +292,6 @@ def test_parameterize_molecules_from_creation(self):
def test_parameterize_molecules_specified_during_create_system(self):
"""Test that SystemGenerator can parameterize molecules specified during create_system"""
- from openmmforcefields.generators import SystemGenerator
-
for name, testsystem in self.testsystems.items():
molecules = testsystem['molecules']
@@ -317,7 +302,6 @@ def test_parameterize_molecules_specified_during_create_system(self):
small_molecule_forcefield=small_molecule_forcefield)
# Parameterize molecules
- from openmmforcefields.utils import Timer
for molecule in molecules:
openmm_topology = molecule.to_topology().to_openmm()
# Specify molecules during system creation
@@ -325,8 +309,6 @@ def test_parameterize_molecules_specified_during_create_system(self):
def test_add_molecules(self):
"""Test that Molecules can be added to SystemGenerator later"""
- from openmmforcefields.generators import SystemGenerator
-
SMALL_MOLECULE_FORCEFIELDS = SystemGenerator.SMALL_MOLECULE_FORCEFIELDS if not CI else ['gaff-2.11', 'openff-2.0.0', 'espaloma-0.2.2']
for small_molecule_forcefield in SMALL_MOLECULE_FORCEFIELDS:
# Create a SystemGenerator for this force field
@@ -341,7 +323,6 @@ def test_add_molecules(self):
generator.add_molecules(molecules)
# Parameterize molecules
- from openmmforcefields.utils import Timer
for molecule in molecules:
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as t1:
@@ -355,9 +336,6 @@ def test_add_molecules(self):
def test_cache(self):
"""Test that SystemGenerator correctly manages a cache"""
- from openmmforcefields.generators import SystemGenerator
- from openmmforcefields.utils import Timer
-
timing = dict() # timing[(small_molecule_forcefield, smiles)] is the time (in seconds) to parameterize molecule the first time
with tempfile.TemporaryDirectory() as tmpdirname:
# Create a single shared cache for all force fields
@@ -406,8 +384,9 @@ def test_cache(self):
def test_complex(self):
"""Test parameterizing a protein:ligand complex in vacuum"""
- from openmmforcefields.generators import SystemGenerator
for name, testsystem in self.testsystems.items():
+ from openmm import unit
+
print(f'Testing parameterization of {name} in vacuum')
molecules = testsystem['molecules']
# Select a complex from the set
@@ -424,9 +403,7 @@ def test_complex(self):
assert system.getNumParticles() == len(complex_structure.atoms)
# Create solvated structure
- from openmm import app
- from openmm import unit
- modeller = app.Modeller(complex_structure.topology, complex_structure.positions)
+ modeller = Modeller(complex_structure.topology, complex_structure.positions)
modeller.addSolvent(generator.forcefield, padding=0*unit.angstroms, ionicStrength=300*unit.millimolar)
# Create a system with solvent and ions
@@ -434,4 +411,4 @@ def test_complex(self):
assert system.getNumParticles() == len(list(modeller.topology.atoms()))
with open('test.pdb', 'w') as outfile:
- app.PDBFile.writeFile(modeller.topology, modeller.positions, outfile)
+ PDBFile.writeFile(modeller.topology, modeller.positions, outfile)
diff --git a/openmmforcefields/tests/test_template_generators.py b/openmmforcefields/tests/test_template_generators.py
index 24e93947..fca6a582 100644
--- a/openmmforcefields/tests/test_template_generators.py
+++ b/openmmforcefields/tests/test_template_generators.py
@@ -1,14 +1,23 @@
-import os, sys
-import unittest
+import copy
+import logging
+import os
import tempfile
+import unittest
+import numpy as np
+import openmm
+from openff.toolkit import __version__ as toolkit_version
+from openff.toolkit.topology import Molecule
+from openmm.app import PME, ForceField, Modeller, NoCutoff, PDBFile
+from packaging.version import Version
+
+from openmmforcefields.generators import (
+ EspalomaTemplateGenerator,
+ GAFFTemplateGenerator,
+ SMIRNOFFTemplateGenerator,
+)
from openmmforcefields.utils import get_data_filename
-from openmmforcefields.generators import GAFFTemplateGenerator
-from openmmforcefields.generators import SMIRNOFFTemplateGenerator
-from openmmforcefields.generators import EspalomaTemplateGenerator
-
-import logging
_logger = logging.getLogger("openmmforcefields.tests.test_template_generators")
CI = ('CI' in os.environ)
@@ -42,24 +51,23 @@ def filter_molecules(self, molecules):
MAX_ATOMS = 40
molecules = [ molecule for molecule in molecules if molecule.n_atoms < MAX_ATOMS ]
# Cut down number of tests for continuous integration
- import os
MAX_MOLECULES = 50 if not CI else 4
molecules = molecules[:MAX_MOLECULES]
return molecules
def setUp(self):
- # TODO: Harmonize with test_system_generator.py infrastructure
+ from openff.units import unit
+ # TODO: Harmonize with test_system_generator.py infrastructure
# Read test molecules
- from openff.toolkit.topology import Molecule
filename = get_data_filename("minidrugbank/MiniDrugBank-without-unspecified-stereochemistry.sdf")
molecules = Molecule.from_file(filename, allow_undefined_stereo=True)
# DEBUG: Insert acetone perturbed from planarity as first test molecule, since it fails quickly if something is wrong
molecule = Molecule.from_smiles('C=O')
molecule.generate_conformers(n_conformers=1)
- from simtk import unit
+
molecule.conformers[0][0,0] += 0.1*unit.angstroms
molecules.insert(0, molecule)
# DEBUG END
@@ -77,7 +85,7 @@ def test_version(self):
for forcefield in GAFFTemplateGenerator.INSTALLED_FORCEFIELDS:
generator = GAFFTemplateGenerator(forcefield=forcefield)
import re
- result = re.match('^gaff-(?P\d+)\.(?P\d+)$', forcefield)
+ result = re.match(r'^gaff-(?P\d+)\.(?P\d+)$', forcefield)
assert generator.forcefield == forcefield
assert generator.gaff_version == result['major_version'] + '.' + result['minor_version']
assert generator.gaff_major_version == result['major_version']
@@ -108,14 +116,12 @@ def test_add_molecules(self):
# Create a generator that does not know about any molecules
generator = self.TEMPLATE_GENERATOR()
# Create a ForceField
- from openmm.app import ForceField
forcefield = ForceField()
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
# Check that parameterizing a molecule fails
molecule = self.molecules[0]
- from openmm.app import NoCutoff
try:
# This should fail with an exception
openmm_topology = molecule.to_topology().to_openmm()
@@ -131,8 +137,8 @@ def test_add_molecules(self):
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
except Exception as e:
print(forcefield._atomTypes.keys())
- from openmm.app import PDBFile
- PDBFile.writeFile(openmm_topology, molecule.conformers[0])
+ from openff.units.openmm import to_openmm
+ PDBFile.writeFile(openmm_topology, to_openmm(molecule.conformers[0]))
raise e
assert system.getNumParticles() == molecule.n_atoms
@@ -155,11 +161,10 @@ def charges_from_system(self, system):
Returns
-------
- charges : np.array of shape [n_particles]
+ charges : np.array of shape [n_atoms]
The dimensionless partial charges (implicitly in units of elementary_charge)
"""
- import numpy as np
from openmm import unit
system_charges = list()
forces = { force.__class__.__name__ : force for force in system.getForces() }
@@ -185,15 +190,15 @@ def charges_are_equal(self, system, molecule):
result : bool
True if the partial charges are equal, False if not
"""
- assert system.getNumParticles() == molecule.n_particles
+ from openff.units import unit
- system_charges = self.charges_from_system(system)
+ assert system.getNumParticles() == molecule.n_atoms
- from openmm import unit
- molecule_charges = molecule.partial_charges / unit.elementary_charge
+ system_charges: np.ndarray = self.charges_from_system(system)
+ molecule_charges: np.ndarray = molecule.partial_charges.m_as(unit.elementary_charge)
- import numpy as np
result = np.allclose(system_charges, molecule_charges)
+
if not result:
_logger.info('Charges are not equal')
_logger.info(f'system charges : {system_charges}')
@@ -206,13 +211,11 @@ def test_charge(self):
# Create a generator that does not know about any molecules
generator = self.TEMPLATE_GENERATOR()
# Create a ForceField
- from openmm.app import ForceField
forcefield = ForceField()
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
# Check that parameterizing a molecule using user-provided charges produces expected charges
- import numpy as np
from openmm import unit
molecule = self.molecules[0]
# Ensure partial charges are initially zero
@@ -220,7 +223,6 @@ def test_charge(self):
# Add the molecule
generator.add_molecules(molecule)
# Create the System
- from openmm.app import NoCutoff
openmm_topology = molecule.to_topology().to_openmm()
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
# Ensure charges are no longer zero
@@ -228,32 +230,34 @@ def test_charge(self):
def test_charge_from_molecules(self):
"""Test that user-specified partial charges are used if requested"""
+ from openff.units import unit
+
+ if Version(toolkit_version) < Version("0.11.0"):
+ self.skipTest("Test written with new toolkit API")
+
# Create a generator that does not know about any molecules
generator = self.TEMPLATE_GENERATOR()
# Create a ForceField
- from openmm.app import ForceField
forcefield = ForceField()
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
# Check that parameterizing a molecule using user-provided charges produces expected charges
- import numpy as np
- from openmm import unit
+
molecule = self.molecules[0]
- charges = np.random.random([molecule.n_particles])
- total_charge = molecule.total_charge
- if type(total_charge) is unit.Quantity:
- # Handle openforcefield >= 0.7.0
- total_charge /= unit.elementary_charge
- charges += (total_charge - charges.sum()) / molecule.n_particles
- molecule.partial_charges = unit.Quantity(charges, unit.elementary_charge)
- assert (molecule.partial_charges is not None) and not np.all(molecule.partial_charges / unit.elementary_charge == 0)
- # Add the molecule
+
+ # Populate the molecule with arbitrary partial charges that still sum to 0.0
+ molecule.partial_charges = unit.Quantity(
+ np.linspace(-0.5, 0.5, molecule.n_atoms),
+ unit.elementary_charge,
+ )
+
+ assert (molecule.partial_charges is not None) and not np.all(molecule.partial_charges.m_as(unit.elementary_charge) == 0)
+
generator.add_molecules(molecule)
- # Create the System
- from openmm.app import NoCutoff
- openmm_topology = molecule.to_topology().to_openmm()
- system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
+
+ system = forcefield.createSystem(molecule.to_topology().to_openmm(), nonbondedMethod=NoCutoff)
+
assert self.charges_are_equal(system, molecule)
def test_debug_ffxml(self):
@@ -265,12 +269,10 @@ def test_debug_ffxml(self):
molecule = self.molecules[0]
generator = self.TEMPLATE_GENERATOR(molecules=molecule, cache=cache)
# Create a ForceField
- from openmm.app import ForceField
forcefield = ForceField()
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
# Ensure no file is created
- from openmm.app import NoCutoff
openmm_topology = molecule.to_topology().to_openmm()
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
assert not os.path.exists(debug_ffxml_filename)
@@ -292,7 +294,6 @@ def test_debug_ffxml(self):
def test_cache(self):
"""Test template generator cache capability"""
- from openmm.app import ForceField, NoCutoff
with tempfile.TemporaryDirectory() as tmpdirname:
# Create a generator that also has a database cache
cache = os.path.join(tmpdirname, 'db.json')
@@ -325,7 +326,7 @@ def check_cache(generator, n_expected):
db.close()
n_entries = len(db_entries)
assert (n_entries == n_expected), \
- "Expected {} entries but database has {}\n db contents: {}".format(n_expected, n_entries, db_entries)
+ f"Expected {n_expected} entries but database has {n_entries}\n db contents: {db_entries}"
check_cache(generator, len(self.molecules))
@@ -349,13 +350,12 @@ def check_cache(generator, n_expected):
def test_add_solvent(self):
"""Test using openmm.app.Modeller to add solvent to a small molecule parameterized by template generator"""
# Select a molecule to add solvent around
- from openmm.app import NoCutoff, Modeller
+ from openff.units.openmm import to_openmm
from openmm import unit
molecule = self.molecules[0]
openmm_topology = molecule.to_topology().to_openmm()
- openmm_positions = molecule.conformers[0]
+ openmm_positions = to_openmm(molecule.conformers[0])
# Try adding solvent without residue template generator; this will fail
- from openmm.app import ForceField
forcefield = ForceField('tip3p.xml')
# Add solvent to a system containing a small molecule
modeller = Modeller(openmm_topology, openmm_positions)
@@ -374,7 +374,6 @@ def test_add_solvent(self):
def test_jacs_ligands(self):
"""Use template generator to parameterize the Schrodinger JACS set of ligands"""
- from openmm.app import ForceField, NoCutoff
jacs_systems = {
#'bace' : { 'prefix' : 'Bace' },
#'cdk2' : { 'prefix' : 'CDK2' },
@@ -390,7 +389,6 @@ def test_jacs_ligands(self):
# Load molecules
ligand_sdf_filename = get_data_filename(os.path.join('perses_jacs_systems', system_name, prefix + '_ligands.sdf'))
print(f'Reading molecules from {ligand_sdf_filename} ...')
- from openff.toolkit.topology import Molecule
molecules = Molecule.from_file(ligand_sdf_filename, allow_undefined_stereo=True)
# Ensure this is a list
try:
@@ -445,7 +443,6 @@ def test_jacs_complexes(self):
# Read molecules
ligand_sdf_filename = get_data_filename(os.path.join('perses_jacs_systems', system_name, prefix + '_ligands.sdf'))
print(f'Reading molecules from {ligand_sdf_filename} ...')
- from openff.toolkit.topology import Molecule
molecules = Molecule.from_file(ligand_sdf_filename, allow_undefined_stereo=True)
try:
nmolecules = len(molecules)
@@ -457,7 +454,6 @@ def test_jacs_complexes(self):
import parmed
from openmm import unit
protein_pdb_filename = get_data_filename(os.path.join('perses_jacs_systems', system_name, prefix + '_protein.pdb'))
- from openmm.app import PDBFile
print(f'Reading protein from {protein_pdb_filename} ...')
#protein_structure = parmed.load_file(protein_pdb_filename) # NOTE: This mis-interprets distorted geometry and sequentially-numbered residues that span chain breaks
pdbfile = PDBFile(protein_pdb_filename)
@@ -483,7 +479,6 @@ def test_jacs_complexes(self):
generator = self.TEMPLATE_GENERATOR(molecules=molecules, cache=cache)
# Create a ForceField
- from openmm.app import ForceField
forcefield = ForceField(*self.amber_forcefields)
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
@@ -503,17 +498,14 @@ def test_jacs_complexes(self):
#hs = [atom for atom in modeller.topology.atoms() if atom.element.symbol in ['H'] and atom.residue.name != 'UNL']
hs = [atom for atom in modeller.topology.atoms() if atom.element.symbol in ['H'] and atom.residue.id in termini_ids]
modeller.delete(hs)
- from openmm.app import PDBFile
modeller.addHydrogens(forcefield)
# Parameterize protein:ligand complex in vacuum
print(f' Parameterizing {system_name} : {molecule.to_smiles()} in vacuum...')
- from openmm.app import NoCutoff
forcefield.createSystem(modeller.topology, nonbondedMethod=NoCutoff)
# Parameterize protein:ligand complex in solvent
print(f' Parameterizing {system_name} : {molecule.to_smiles()} in explicit solvent...')
- from openmm.app import PME
modeller.addSolvent(forcefield, padding=0*unit.angstroms, ionicStrength=300*unit.millimolar)
forcefield.createSystem(modeller.topology, nonbondedMethod=PME)
@@ -521,6 +513,8 @@ def test_parameterize(self):
"""Test parameterizing molecules with template generator for all supported force fields"""
# Test all supported small molecule force fields
for small_molecule_forcefield in self.TEMPLATE_GENERATOR.INSTALLED_FORCEFIELDS:
+ if "ff14sb" in small_molecule_forcefield:
+ continue
print(f'Testing {small_molecule_forcefield}')
# Create a generator that knows about a few molecules
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
@@ -528,12 +522,11 @@ def test_parameterize(self):
# Check that we have loaded the right force field
assert generator.forcefield == small_molecule_forcefield
# Create a ForceField with the appropriate small molecule force field
- from openmm.app import ForceField
forcefield = ForceField()
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
# Parameterize some molecules
- from openmm.app import NoCutoff
+
from openmmforcefields.utils import Timer
for molecule in self.molecules:
openmm_topology = molecule.to_topology().to_openmm()
@@ -549,7 +542,6 @@ def test_parameterize(self):
def test_multiple_registration(self):
"""Test registering the template generator with multiple force fields"""
generator = self.TEMPLATE_GENERATOR(molecules=self.molecules)
- from openmm.app import ForceField
NUM_FORCEFIELDS = 2 # number of force fields to test
forcefields = list()
for index in range(NUM_FORCEFIELDS):
@@ -560,7 +552,6 @@ def test_multiple_registration(self):
# Parameterize a molecule in each force field instance
molecule = self.molecules[0]
openmm_topology = molecule.to_topology().to_openmm()
- from openmm.app import NoCutoff
for forcefield in forcefields:
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
assert system.getNumParticles() == molecule.n_atoms
@@ -585,11 +576,9 @@ def compute_energy(system, positions):
openmm_forces['total'] is the total force
openmm_forces['components'][forcename] is the force for the specified component force
"""
- import copy
system = copy.deepcopy(system)
for index, force in enumerate(system.getForces()):
force.setForceGroup(index)
- import openmm
platform = openmm.Platform.getPlatformByName('Reference')
integrator = openmm.VerletIntegrator(0.001)
context = openmm.Context(system, integrator, platform)
@@ -624,15 +613,21 @@ def compare_energies(cls, molecule, template_generated_system, reference_system)
System generated by reference parmaeterization engine
"""
+ from openff.units.openmm import to_openmm
# Compute energies
- reference_energy, reference_forces = cls.compute_energy(template_generated_system, molecule.conformers[0])
- template_energy, template_forces = cls.compute_energy(reference_system, molecule.conformers[0])
+ reference_energy, reference_forces = cls.compute_energy(
+ template_generated_system,
+ to_openmm(molecule.conformers[0]),
+ )
+ template_energy, template_forces = cls.compute_energy(
+ reference_system,
+ to_openmm(molecule.conformers[0]),
+ )
from openmm import unit
def write_xml(filename, system):
- import openmm
with open(filename, 'w') as outfile:
print(f'Writing {filename}...')
outfile.write(openmm.XmlSerializer.serialize(system))
@@ -657,7 +652,7 @@ def write_xml(filename, system):
print(f"{'component':24} {'Template (kcal/mol)':>20} {'Reference (kcal/mol)':>20}")
for key in components:
reference_component_energy = reference_energy['components'][key]
- template_component_energy = template_energy['components'][key]
+ template_component_energy = template_energy['components'][key]
print(f'{key:24} {(template_component_energy/unit.kilocalories_per_mole):20.3f} {(reference_component_energy/unit.kilocalories_per_mole):20.3f} kcal/mol')
print(f'{"TOTAL":24} {(template_energy["total"]/unit.kilocalories_per_mole):20.3f} {(reference_energy["total"]/unit.kilocalories_per_mole):20.3f} kcal/mol')
write_xml('reference_system.xml', reference_system)
@@ -665,7 +660,6 @@ def write_xml(filename, system):
raise Exception(f'Energy deviation for {molecule.to_smiles()} ({delta/unit.kilocalories_per_mole} kcal/mol) exceeds threshold ({ENERGY_DEVIATION_TOLERANCE})')
# Compare forces
- import numpy as np
def norm(x):
N = x.shape[0]
return np.sqrt((1.0/N) * (x**2).sum())
@@ -714,7 +708,8 @@ def propagate_dynamics(self, molecule, system):
"""
# Run some dynamics
- import openmm
+ from openff.units.openmm import from_openmm as from_openmm_quantity
+ from openff.units.openmm import to_openmm as to_openmm_quantity
from openmm import unit
temperature = 300 * unit.kelvin
collision_rate = 1.0 / unit.picoseconds
@@ -723,42 +718,56 @@ def propagate_dynamics(self, molecule, system):
integrator = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
platform = openmm.Platform.getPlatformByName('Reference')
context = openmm.Context(system, integrator, platform)
- context.setPositions(molecule.conformers[0])
+ context.setPositions(to_openmm_quantity(molecule.conformers[0]))
integrator.step(nsteps)
# Copy the molecule, storing new conformer
- import copy
new_molecule = copy.deepcopy(molecule)
- new_molecule.conformers[0] = context.getState(getPositions=True).getPositions(asNumpy=True)
- # Clean up
+ new_molecule.conformers[0] = from_openmm_quantity(context.getState(getPositions=True).getPositions())
+
del context, integrator
return new_molecule
def test_INSTALLED_FORCEFIELDS(self):
"""Test INSTALLED_FORCEFIELDS contains expected force fields"""
- assert 'openff-1.1.0' in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
- assert 'smirnoff99Frosst-1.1.0' in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
- assert 'openff_unconstrained-1.1.0' not in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
+ expected_force_fields = [
+ 'openff-1.1.0',
+ 'openff-2.0.0',
+ 'smirnoff99Frosst-1.1.0',
+ 'ff14sb_off_impropers_0.0.3',
+ ]
+ forbidden_force_fields = [
+ 'openff_unconstrained',
+ 'ff14sb_0.0.3',
+ ]
+
+ for expected in expected_force_fields:
+ assert expected in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
+
+ for forbidden in forbidden_force_fields:
+ assert forbidden not in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
def test_energies(self):
"""Test potential energies match between openff-toolkit and OpenMM ForceField"""
- from openff.toolkit.topology import Molecule
- from openmm import unit
+
+ if Version(toolkit_version) < Version("0.11.0"):
+ self.skipTest("Test written with new toolkit API")
+
# Test all supported SMIRNOFF force fields
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
+ if "ff14sb" in small_molecule_forcefield:
+ continue
print(f'Testing energies for {small_molecule_forcefield}...')
# Create a generator that knows about a few molecules
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
generator = SMIRNOFFTemplateGenerator(molecules=self.molecules, forcefield=small_molecule_forcefield)
# Create a ForceField
- import openmm
openmm_forcefield = openmm.app.ForceField()
# Register the template generator
openmm_forcefield.registerTemplateGenerator(generator.generator)
# Parameterize some molecules
for molecule in self.molecules:
# Create OpenMM System using OpenMM app
- from openmm.app import NoCutoff
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
# Retrieve System generated by the SMIRNOFF typing engine
@@ -777,24 +786,23 @@ def test_energies(self):
def test_partial_charges_are_none(self):
"""Test parameterizing a small molecule with `partial_charges=None` instead
of zeros (happens frequently in OFFTK>=0.7.0)"""
- from openff.toolkit.topology import Molecule
molecule = Molecule.from_smiles('C=O')
molecule.generate_conformers(n_conformers=1)
#molecule._partial_charges = None
assert (molecule.partial_charges is None) or np.all(molecule.partial_charges / unit.elementary_charge == 0)
# Test all supported SMIRNOFF force fields
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
+ if "ff14sb" in small_molecule_forcefield:
+ continue
print(f'Testing energies for {small_molecule_forcefield}...')
# Create a generator that knows about a few molecules
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
generator = SMIRNOFFTemplateGenerator(molecules=[molecule], forcefield=small_molecule_forcefield)
# Create a ForceField
- import openmm
openmm_forcefield = openmm.app.ForceField()
# Register the template generator
openmm_forcefield.registerTemplateGenerator(generator.generator)
# Create OpenMM System using OpenMM app
- from openmm.app import NoCutoff
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
smirnoff_system = generator.get_openmm_system(molecule)
@@ -827,8 +835,13 @@ def propagate_dynamics(self, molecule, system):
"""
# Run some dynamics
- import openmm
+ from openff.units.openmm import from_openmm as from_openmm_quantity
+ from openff.units.openmm import to_openmm as to_openmm_quantity
from openmm import unit
+
+ if Version(toolkit_version) < Version("0.11.0"):
+ self.skipTest("Test written with new toolkit API")
+
temperature = 300 * unit.kelvin
collision_rate = 1.0 / unit.picoseconds
timestep = 1.0 * unit.femtoseconds
@@ -836,12 +849,11 @@ def propagate_dynamics(self, molecule, system):
integrator = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
platform = openmm.Platform.getPlatformByName('Reference')
context = openmm.Context(system, integrator, platform)
- context.setPositions(molecule.conformers[0])
+ context.setPositions(to_openmm_quantity(molecule.conformers[0]))
integrator.step(nsteps)
# Copy the molecule, storing new conformer
- import copy
new_molecule = copy.deepcopy(molecule)
- new_molecule.conformers[0] = context.getState(getPositions=True).getPositions(asNumpy=True)
+ new_molecule.conformers[0] = from_openmm_quantity(context.getState(getPositions=True).getPositions())
# Clean up
del context, integrator
@@ -867,8 +879,10 @@ def test_retrieve_forcefields(self):
def test_energies(self):
"""Test potential energies match between openff-toolkit and OpenMM ForceField"""
- from openff.toolkit.topology import Molecule
- from openmm import unit
+
+ if Version(toolkit_version) < Version("0.11.0"):
+ self.skipTest("Test written with new toolkit API")
+
# Test all supported SMIRNOFF force fields
for small_molecule_forcefield in EspalomaTemplateGenerator.INSTALLED_FORCEFIELDS:
print(f'Testing energies for {small_molecule_forcefield}...')
@@ -876,14 +890,12 @@ def test_energies(self):
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
generator = EspalomaTemplateGenerator(molecules=self.molecules, forcefield=small_molecule_forcefield)
# Create a ForceField
- import openmm
openmm_forcefield = openmm.app.ForceField()
# Register the template generator
openmm_forcefield.registerTemplateGenerator(generator.generator)
# Parameterize some molecules
for molecule in self.molecules:
# Create OpenMM System using OpenMM app
- from openmm.app import NoCutoff
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
# Retrieve System generated by Espaloma
@@ -901,7 +913,6 @@ def test_energies(self):
def test_partial_charges_are_none(self):
"""Test parameterizing a small molecule with `partial_charges=None` instead
of zeros (happens frequently in OFFTK>=0.7.0)"""
- from openff.toolkit.topology import Molecule
molecule = Molecule.from_smiles('C=O')
molecule.generate_conformers(n_conformers=1)
#molecule._partial_charges = None
@@ -913,11 +924,9 @@ def test_partial_charges_are_none(self):
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
generator = EspalomaTemplateGenerator(molecules=[molecule], forcefield=small_molecule_forcefield)
# Create a ForceField
- import openmm
openmm_forcefield = openmm.app.ForceField()
# Register the template generator
openmm_forcefield.registerTemplateGenerator(generator.generator)
# Create OpenMM System using OpenMM app
- from openmm.app import NoCutoff
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
smirnoff_system = generator.get_openmm_system(molecule)
diff --git a/openmmforcefields/utils.py b/openmmforcefields/utils.py
index 71a699f4..110f0fe2 100644
--- a/openmmforcefields/utils.py
+++ b/openmmforcefields/utils.py
@@ -1,5 +1,6 @@
-import logging
import contextlib
+import logging
+
_logger = logging.getLogger("openmmforcefields.generators.gaff")
def get_ffxml_path():
@@ -80,7 +81,7 @@ def _wrapper(*args, **kwargs):
return _with_timer
-class Timer(object):
+class Timer:
"""A class with stopwatch-style timing functions.
Examples
@@ -137,7 +138,7 @@ def stop(self, benchmark_id='default'):
try:
t0 = self._t0[benchmark_id]
except KeyError:
- _logger.warning("Can't stop timing for {}".format(benchmark_id))
+ _logger.warning(f"Can't stop timing for {benchmark_id}")
else:
import time
self._t1[benchmark_id] = time.time()
@@ -153,7 +154,7 @@ def partial(self, benchmark_id='default'):
try:
t0 = self._t0[benchmark_id]
except KeyError:
- _logger.warning("Couldn't return partial timing for {}".format(benchmark_id))
+ _logger.warning(f"Couldn't return partial timing for {benchmark_id}")
else:
return time.time() - t0
@@ -172,7 +173,7 @@ def report_timing(self, clear=True):
"""
for benchmark_id, elapsed_time in self._completed.items():
- _logger.debug('{} took {:8.3f}s'.format(benchmark_id, elapsed_time))
+ _logger.debug(f'{benchmark_id} took {elapsed_time:8.3f}s')
if clear is True:
self.reset_timing_statistics()
diff --git a/setup.py b/setup.py
index e9a2b61b..ed1a5beb 100644
--- a/setup.py
+++ b/setup.py
@@ -18,65 +18,50 @@
except:
long_description = "\n".join(short_description[2:])
-try:
- # Symlink converted ffxml directories so we don't need to copy files
- os.makedirs('openmmforcefields/ffxml')
- os.symlink('../../amber/ffxml/', 'openmmforcefields/ffxml/amber')
- os.symlink('../../charmm/ffxml/', 'openmmforcefields/ffxml/charmm')
- os.symlink('../../amber/gaff', 'openmmforcefields/ffxml/amber/gaff')
-
- setup(
- # Self-descriptive entries which should always be present
- name='openmmforcefields',
- author='Chodera lab // MSKCC',
- author_email='john.chodera@choderalab.org',
- description=short_description[0],
- long_description=long_description,
- long_description_content_type="text/markdown",
- keywords = "molecular mechanics, forcefield, OpenMM, AMBER, CHARMM, GAFF",
- url = "http://github.com/choderalab/openmm-forcefields",
- version=versioneer.get_version(),
- cmdclass=versioneer.get_cmdclass(),
- license='MIT',
-
- classifiers=[
- "Development Status :: 3 - Alpha",
- "Topic :: Utilities",
- "License :: OSI Approved :: MIT",
- ],
+setup(
+ # Self-descriptive entries which should always be present
+ name='openmmforcefields',
+ author='Chodera lab // MSKCC',
+ author_email='john.chodera@choderalab.org',
+ description=short_description[0],
+ long_description=long_description,
+ long_description_content_type="text/markdown",
+ keywords = "molecular mechanics, forcefield, OpenMM, AMBER, CHARMM, GAFF",
+ url = "http://github.com/choderalab/openmm-forcefields",
+ version=versioneer.get_version(),
+ cmdclass=versioneer.get_cmdclass(),
+ license='MIT',
- # Don't install as an egg, since OpenMM can't find ffxml files if we do
- zip_safe=False,
+ classifiers=[
+ "Development Status :: 3 - Alpha",
+ "Topic :: Utilities",
+ "License :: OSI Approved :: MIT",
+ ],
- # Which Python importable modules should be included when your package is installed
- # Handled automatically by setuptools. Use 'exclude' to prevent some specific
- # subpackage(s) from being added, if needed
- packages=find_packages(),
+ # Don't install as an egg, since OpenMM can't find ffxml files if we do
+ zip_safe=False,
- # Optional include package data to ship with your package
- # Customize MANIFEST.in if the general case does not suit your needs
- # Comment out this line to prevent the files from being packaged with your software
- include_package_data=True,
+ # Which Python importable modules should be included when your package is installed
+ # Handled automatically by setuptools. Use 'exclude' to prevent some specific
+ # subpackage(s) from being added, if needed
+ packages=find_packages(),
- # Allows `setup.py test` to work correctly with pytest
- setup_requires=[] + pytest_runner,
+ # Optional include package data to ship with your package
+ # Customize MANIFEST.in if the general case does not suit your needs
+ # Comment out this line to prevent the files from being packaged with your software
+ include_package_data=True,
- entry_points={
- 'console_scripts': [],
- 'openmm.forcefielddir' : [
- 'ffxml = openmmforcefields.utils:get_ffxml_path',
- ],
- },
+ # Allows `setup.py test` to work correctly with pytest
+ setup_requires=[] + pytest_runner,
- package_data={
- 'openmmforcefields': ['ffxml/amber/*.xml', 'ffxml/amber/gaff/*.{xml,dat}', 'ffxml/charmm/*.xml']
- },
- )
+ entry_points={
+ 'console_scripts': [],
+ 'openmm.forcefielddir' : [
+ 'ffxml = openmmforcefields.utils:get_ffxml_path',
+ ],
+ },
-finally:
- # TODO: Don't clean these up if `python setup.py develop`
- # Clean up temporary symlinks
- os.unlink('openmmforcefields/ffxml/amber/gaff')
- os.unlink('openmmforcefields/ffxml/amber')
- os.unlink('openmmforcefields/ffxml/charmm')
- os.removedirs('openmmforcefields/ffxml')
+ package_data={
+ 'openmmforcefields': ['ffxml/amber/*.xml', 'ffxml/amber/gaff/*.{xml,dat}', 'ffxml/charmm/*.xml']
+ },
+)