Coder Social home page Coder Social logo

byun-jinyoung / openff-toolkit Goto Github PK

View Code? Open in Web Editor NEW

This project forked from openforcefield/openff-toolkit

0.0 0.0 0.0 305.13 MB

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

Home Page: http://openforcefield.org

License: MIT License

Ruby 0.01% Python 94.55% Jupyter Notebook 5.44%

openff-toolkit's Introduction

Status GH Actions Status Codecov coverage LGTM analysis
Latest Release Last release tag Commits since release DOI
Communication docs stable Binder dev chat on slack
Foundation license platforms python Funding
Installation Releases Conda Last updated Anaconda Cloud downloads

The Open Force Field toolkit

The Open Force Field Toolkit, built by the Open Force Field Initiative, is a Python toolkit for the development and application of modern molecular mechanics force fields based on direct chemical perception and rigorous statistical parameterization methods.

The toolkit currently covers two main areas we have committed to stably maintain throughout their lifetimes:

Note: Prior to version 0.9.0, this toolkit and its associated repository were named openforcefield and used different import paths. For details on this change and migration instructions, see the release notes of version 0.9.0.

Documentation

Documentation for the Open Force Field Toolkit is hosted at readthedocs. Example notebooks are hosted on binder

How to cite

Please cite the OpenFF Toolkit using the Zenodo record of the latest release or the version that was used. The BibTeX reference of the latest release can be found here.

Installation

The Open Force Field Toolkit (openff-toolkit) is a Python toolkit, and supports Python 3.8 through 3.10.

Installing via conda

Detailed installation instructions can be found here.

Installing from source

If you need to install via source, see the build and run package requirements listed in the development conda recipe.

Force Fields

Two major force field development efforts have been undertaken by the Initiative, with results hosted in separate repositories.

  • The Open Force Fields repository, which features the Parsley and Sage force field lines. These are the Open Force Field Initiative's efforts toward building new force fields. The initial parameters are taken from smirnoff99Frosst, but software and data produced by the Initiative's efforts have been used to refit parameter values and add new SMIRKS-based parameters.
  • The smirnoff99Frosst repository, which is descended from AMBER's parm99 force field as well as Merck-Frosst's parm@frosst. This line of force fields does not aim to alter parameter values, but is instead a test of accurately converting an atom type-based force field to the SMIRNOFF format.

Force fields from both of these packages are available in their respective GitHub repositories and also as conda packages. Tables detailing the individual file names/versions within these force field lines are in the README of each repository. By default, installing the Open Force Field toolkit using conda or the single-file toolkit installers will also install these conda packages. A plugin architecture is provided for other force field developers to produce python/conda packages that can be imported by the Open Force Field Toolkit as well.

Toolkit features

The SMIRKS Native Open Force Field (SMIRNOFF) format

This repository provides tools for using the SMIRKS Native Open Force Field (SMIRNOFF) specification, which currently supports an XML representation for force field definition files.

By convention, files containing XML representations of SMIRNOFF force fields carry .offxml extensions.

Example SMIRNOFF .offxml force field definitions can be found in openff/toolkit/data/test_forcefields/. These force fields are for testing only, and we neither record versions of these files, nor do we guarantee their correctness or completeness.

Working with SMIRNOFF parameter sets

The ForceField class in the OpenFF Toolkit is essentially a drop-in replacement for the OpenMM ForceField class.

# Load a molecule into the OpenFF Molecule object
from openff.toolkit.topology import Molecule
from openff.toolkit.utils import get_data_file_path
sdf_file_path = get_data_file_path('molecules/ethanol.sdf')
molecule = Molecule.from_file(sdf_file_path)

# Create an OpenFF Topology object from the molecule
from openff.toolkit.topology import Topology
topology = Topology.from_molecules(molecule)

# Load the latest OpenFF force field release: version 2.0.0, codename "Sage"
from openff.toolkit.typing.engines.smirnoff import ForceField
forcefield = ForceField('openff-2.0.0.offxml')

# Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
openmm_system = forcefield.create_openmm_system(topology)

Detailed examples of using SMIRNOFF with the toolkit can be found in the documentation.

Frequently asked questions (FAQ)

See FAQ.md for answers to a variety of common problems, such as:

  • Why do I need to provide molecules corresponding to the components of my system, or a Topology with bond orders?
  • Can I use an AMBER, CHARMM, or gromacs topology/coordinate file as a starting point for applying a SMIRNOFF force field?
  • What if I am starting from a PDB file?

Contributors

For a full list of contributors, see the GitHub Contributors page.

openff-toolkit's People

Contributors

j-wags avatar mattwthompson avatar davidlmobley avatar jchodera avatar bannanc avatar andrrizzi avatar trevorgokey avatar dotsdl avatar jaimergp avatar yoshanuikabundi avatar camizanette avatar pavankum avatar cbayly13 avatar joshhorton avatar dependabot[bot] avatar ijpulidos avatar vtlim avatar sukanyasasmal avatar pre-commit-ci[bot] avatar lilyminium avatar simonboothroyd avatar adalke avatar dgasmith avatar jthorton avatar leeping avatar ziyuanzhao2000 avatar proteneer avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.