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parmed

Parameter/topology editor and molecular simulator

https://github.com/parmed/parmed

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    Found 3 DOI reference(s) in README
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    16 of 71 committers (22.5%) from academic institutions
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    Low similarity (18.2%) to scientific vocabulary

Keywords from Contributors

molecular-dynamics molecular-simulation computational-chemistry molecular-dynamics-simulation chemistry mdanalysis trajectory-analysis mosdef molecule-builder mbuild
Last synced: 10 months ago · JSON representation

Repository

Parameter/topology editor and molecular simulator

Basic Info
Statistics
  • Stars: 434
  • Watchers: 30
  • Forks: 160
  • Open Issues: 209
  • Releases: 24
Created over 12 years ago · Last pushed 10 months ago
Metadata Files
Readme

README.md

ParmEd

Cross-program parameter and topology file editor and molecular mechanical simulator engine.

Badges

(Build/Test Status) codecov

Description

ParmEd is a package designed to facilitate creating and easily manipulating molecular systems that are fully described by a common classical force field. Supported force fields include Amber, CHARMM, AMOEBA, and several others that share a similar functional form (e.g., GROMOS).

ParmEd is capable of reading and writing to a wide array of different file formats, like the Amber topology and coordinate files, CHARMM PSF, parameter, topology, and coordinate files, Tinker parameter, topology, and coordinate files, and many others. The expressive central data structure (the Structure class) makes it easy to quickly and safely manipulate a chemical system, its underlying topology, and force field parameters describing its potential energy function.

There are two parts of ParmEd---a documented API that you can incorporate into your own Python scripts and programs, and a GUI/CLI pair of programs that provide a means to quickly perform various modifications to chemical systems for rapid prototyping.

The API also provides bindings to the OpenMM library, permitting you to carry out full molecular dynamics investigations using ParmEd on high-performant hardware, like AMD and NVidia GPUs.

Installing ParmEd

To install ParmEd, either clone this git repository or download the latest release and unpack the resulting tarball. This should create a new ParmEd source code directory. Change to that directory and build ParmEd with the command

sh python setup.py install

Note, if you are using the system Python, you may need to either run the above command as root (e.g., by using sudo) or add the --user flag to install it to your home directory. I would suggest the latter choice.

AMBER user can overwrite installed version by

sh python setup.py install --prefix=$AMBERHOME

Testing ParmEd

In order to automatically run the ParmEd tests, execute the following:

sh cd test py.test .

Examples

```python import parmed as pmd

convert GROMACS topology to AMBER format

gmxtop = pmd.loadfile('pmaawaterFE20mer2.top', xyz='pmaawaterFE20mer2.gro') gmxtop.save('pmaa.top', format='amber') gmxtop.save('pmaa.crd', format='rst7')

convert AMBER topology to GROMACS, CHARMM formats

amber = pmd.load_file('prmtop', 'inpcrd')

Save a GROMACS topology and GRO files

amber.save('gromacs.top') amber.save('gromacs.gro')

Save a CHARMM PSF and crd files

amber.save('charmm.psf') amber.save('charmm.crd')

Save a DLPOLY FIELD and CONFIG files

amber.save('dlpoly.field') amber.save('dlpoly.config')

convert mol2 to pdb file

mol2parm = pmd.loadfile('my.mol2') mol2_parm.save('my.pdb')

and many more

```

Documentation

Want to learn more? Visit the ParmEd documentation page at https://parmed.github.io/ParmEd for examples, descriptions, and API documentation.

Authors and Contributors

The following people have contributed directly to the coding and validation efforts in ParmEd (in alphabetical order). And a special thanks to all of you who helped improve this project either by providing feedback, bug reports, or other general comments!

  • Jason Swails (principal developer) | jason.swails@gmail.com

  • Carlos Hernandez

  • David L. Mobley

  • Hai Nguyen

  • Lee-Ping Wang

  • Pawel Janowski

License

``` LESSER GPL LICENSE INFO

Copyright (C) 2010 - 2014 Jason Swails

This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

The fortranformat package is released under the MIT license, Copyright (C) Brendan Arnold. See fortranformat/__init__.py for more information. ```

For Developers

The standard residue template library is generated from the chemical component database by running the ccd.js script supplied by @dsehnal. Run it using the comments at the top of the file. The chemical component dictionary can be downloaded from https://www.wwpdb.org/data/ccd.

The version used in the current release was downloaded on Jan 23, 2023.

The final file is generated using get_hybridization_from_rdkit.py to add the hybridization information as determined by RDKit.

Citation

If you make use of ParmEd for research and would like to cite your use of it in a research paper, please use the following citation:

https://dx.doi.org/10.1007/s10822-016-9977-1

Owner

  • Name: ParmEd
  • Login: ParmEd
  • Kind: organization

GitHub Events

Total
  • Create event: 3
  • Release event: 1
  • Issues event: 25
  • Watch event: 31
  • Issue comment event: 33
  • Push event: 1
  • Pull request review comment event: 2
  • Pull request review event: 1
  • Pull request event: 8
  • Fork event: 14
Last Year
  • Create event: 3
  • Release event: 1
  • Issues event: 25
  • Watch event: 31
  • Issue comment event: 33
  • Push event: 1
  • Pull request review comment event: 2
  • Pull request review event: 1
  • Pull request event: 8
  • Fork event: 14

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 2,626
  • Total Committers: 71
  • Avg Commits per committer: 36.986
  • Development Distribution Score (DDS): 0.294
Past Year
  • Commits: 23
  • Committers: 12
  • Avg Commits per committer: 1.917
  • Development Distribution Score (DDS): 0.609
Top Committers
Name Email Commits
Jason Swails j****s@g****m 1,853
Hai Nguyen h****p@g****m 184
John Chodera j****a@c****g 127
ChayaSt c****n@c****g 62
Rafal P. Wiewiora r****a@g****m 54
Lee-Ping l****g@s****u 50
Carlos Hernandez c****h@s****u 29
Christoph Klein c****n@m****m 25
Vinicius Wilian D. Cruzeiro v****o@u****u 23
Matthew W. Thompson m****n@v****u 21
peastman p****n@s****u 20
Paul J. van Maaren p****l@v****g 13
Hai Nguyen h****m 11
Brian Radak b****s@g****m 11
Karl Debiec k****c@g****m 10
Thomas Heavey t****y@g****m 10
Pawel Janowski p****k@e****u 8
John Chodera (MSKCC) c****j@m****g 7
HN n****n@g****m 7
Xiaoliang Pan p****l 6
mrshirts m****s@g****m 6
Kristof Farkas-Pall k****4@u****k 5
SGenheden s****n@s****k 5
Christopher Cave-Ayland c****d@s****k 5
Andrew Abi-Mansour a****m@g****m 4
Mario Sergio Valdés Tresanco m****5@g****m 4
Marianne Corvellec m****c@e****g 4
Gaetano Calabro g****o@e****m 3
Jamie Smith j****h@c****m 3
David L. Mobley d****y@g****m 3
and 41 more...
Committer Domains (Top 20 + Academic)
stanford.edu: 3 choderalab.org: 2 me.com: 2 soton.ac.uk: 2 eyesopen.com: 2 ufl.edu: 1 vanderbilt.edu: 1 vanmaaren.org: 1 eden.rutgers.edu: 1 mskcc.org: 1 ucl.ac.uk: 1 ens-lyon.org: 1 crackofdawn.onmicrosoft.com: 1 ketch-linux.cimr.cam.ac.uk: 1 gibarian.attlocal.net: 1 robinbetz.com: 1 entos.ai: 1 lutron.com: 1 rutgers.edu: 1 fu-berlin.de: 1 mst.edu: 1 utexas.edu: 1 nd.edu: 1 msu.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 129
  • Total pull requests: 85
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 months
  • Total issue authors: 106
  • Total pull request authors: 28
  • Average comments per issue: 2.31
  • Average comments per pull request: 1.45
  • Merged pull requests: 62
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 29
  • Pull requests: 14
  • Average time to close issues: about 24 hours
  • Average time to close pull requests: 27 days
  • Issue authors: 21
  • Pull request authors: 8
  • Average comments per issue: 0.66
  • Average comments per pull request: 1.07
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • epretti (5)
  • murfalo (5)
  • xiki-tempula (3)
  • pguillem (3)
  • stefdoerr (3)
  • bradakta (2)
  • mmfarrugia (2)
  • Eduardneu (2)
  • Valdes-Tresanco-MS (2)
  • Kapalisuri (2)
  • OkKakao (2)
  • MattBurn (2)
  • JaimeRubioMartinez (2)
  • ale94mleon (2)
  • slweng0321 (2)
Pull Request Authors
  • swails (30)
  • Valdes-Tresanco-MS (12)
  • nffaruk (8)
  • murfalo (7)
  • ctk3b (3)
  • bradakta (3)
  • njzjz (3)
  • fazledyn-or (3)
  • kbelfon007 (2)
  • ywu (2)
  • chrisjonesBSU (2)
  • bradakstx (2)
  • berkonat (2)
  • jpthompson17 (2)
  • MattBurn (2)
Top Labels
Issue Labels
bug (3) enhancement (2) Major (1)
Pull Request Labels

Packages

  • Total packages: 4
  • Total downloads:
    • pypi 16,524 last-month
  • Total dependent packages: 29
    (may contain duplicates)
  • Total dependent repositories: 78
    (may contain duplicates)
  • Total versions: 25
  • Total maintainers: 1
pypi.org: parmed

Inter-package toolkit for molecular mechanical simulations

  • Versions: 17
  • Dependent Packages: 15
  • Dependent Repositories: 46
  • Downloads: 16,524 Last month
Rankings
Dependent packages count: 0.9%
Dependent repos count: 2.2%
Average: 2.7%
Downloads: 2.7%
Stargazers count: 3.5%
Forks count: 4.1%
Maintainers (1)
swails
Last synced: 10 months ago
proxy.golang.org: github.com/ParmEd/ParmEd
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
proxy.golang.org: github.com/parmed/parmed
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
conda-forge.org: parmed

ParmEd is a package designed to facilitate creating and easily manipulating molecular systems that are fully described by a common classical force field. Supported force fields include Amber, CHARMM, AMOEBA, and several others that share a similar functional form (e.g., GROMOS).

  • Versions: 6
  • Dependent Packages: 14
  • Dependent Repositories: 32
Rankings
Dependent packages count: 4.5%
Dependent repos count: 6.5%
Average: 12.2%
Forks count: 15.7%
Stargazers count: 22.3%
Last synced: 10 months ago

Dependencies

.github/workflows/Test.yaml actions
  • actions/checkout v2 composite
  • codecov/codecov-action v1 composite
  • conda-incubator/setup-miniconda v2 composite