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Update system_generators.py #127

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Jul 17, 2020
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Update system_generators.py #127

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Update system_generators.py
hannahbrucemacdonald Jul 17, 2020
e7b7f27
Update changelog
jchodera Jul 17, 2020
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -269,6 +269,9 @@ See the corresponding directories for information on how to use the provided con

# Changelog

## 0.7.5 Bugfix release
* [(PR #127)](https://github.com/openmm/openmmforcefields/pull/127) Fixes a bug where the wrong path was imported for logging; improves docstrings.

## 0.7.4 Bugfix release to ensure compatibility with openforcefield toolkit 0.7.0
* [(PR #121)](https://github.com/openmm/openmmforcefields/pull/121) Add compatibility with [`openforcefield 0.7.0`](https://github.com/openforcefield/openforcefield/releases/tag/0.7.0)

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11 changes: 8 additions & 3 deletions openmmforcefields/generators/system_generators.py
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Expand Up @@ -8,7 +8,7 @@
################################################################################

import logging
_logger = logging.getLogger("perses.forcefields.system_generators")
_logger = logging.getLogger("openmmforcefields.system_generators")

from simtk.openmm import app

Expand Down Expand Up @@ -54,10 +54,15 @@ class SystemGenerator(object):
nonperiodic_forcefield_kwargs : dict
Keyword arguments fed to ``simtk.openmm.app.ForceField.createSystem()`` during System generation for non-periodic systems.
These keyword arguments can be modified at any time.
template_generator : openmmforcefields.generators.SmallMoleculeTemplateGenerator
The small molecule residue template generator subclass used for small molecules.
barostat : simtk.openmm.MonteCarloBarostat
If not None, this container holds the barostat parameters to use for newly created System objects.
molecules : openforcefield.topology.Molecule or list, optional, default=None
Can alternatively be an object (such as an OpenEye OEMol or RDKit Mol or SMILES string) that can be used to construct a Molecule.
Can also be a list of Molecule objects or objects that can be used to construct a Molecule.
If specified, these molecules will be recognized and parameterized as needed.
The parameters will be cached in case they are encountered again the future.
cache : filename, optional, default=None
If not None, filename for caching small molecule residue templates.
postprocess_system : method
If not None, this method will be called as ``system = postprocess_system(system)`` to post-process the System object for create_system(topology) before it is returned.
"""
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