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pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

https://github.com/degrootlab/pmx

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 9 committers (22.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.2%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

Basic Info
  • Host: GitHub
  • Owner: deGrootLab
  • License: lgpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 215 MB
Statistics
  • Stars: 154
  • Watchers: 16
  • Forks: 52
  • Open Issues: 28
  • Releases: 0
Fork of dseeliger/pmx
Created about 9 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

pmx

Introduction

(The 'master' branch is written in Python 2. For Python 3 version and Icolos support use 'develop' branch.)

pmx (formerly pymacs) has started as a small bunch of classes to read structure files such as pdb or gro and trajectory data in gromacs xtc format. Over the years it has been extended towards a versatile (bio-) molecular structure manipulation package with some additional functionalities, e.g. gromacs file parsers and scripts for setup and analysis of free energy calculations.

Citations:

D. Seeliger and Bert L. de Groot, Biophys. J. 98(10):2309-2316 (2010)

V. Gapsys, S. Michielssens, D. Seeliger, B. L. de Groot. J. Comput. Chem. 2014, DOI: 10.1002/jcc.23804

Purpose

I mostly use pmx to write short scripts which perform some changes in pdb files, e.g. changing atom or residue names, applying some geometric transformations or doing some kind of analysis. The critical issue for these things is usually not calculation time but straightforward selection of some atoms/residues of interest, quick file parsing and data visualization, which renders a well-organized data structure and easy programming style more important than computation performance. Hence, and ideal task for Python.

Installation

Checkout the source code and run the usual python installation git clone https://github.com/deGrootLab/pmx pmx cd pmx The 'master' branch is written in Python 2. For Python 3 version and Icolos support use 'develop' branch; to switch to 'develop' branch type: git checkout develop For installation type the command: python setup.py install or pip install .

Software Requirements

Getting Started

Once installed, you can access the scripts via the command line tool pmx. Type pmx -h to view the help message. The command pmx gmxlib will help you locate the pmx force field libraries, which are placed in the data folder where pmx was installed.

pmx stores structure data in Python classes. The "Model" class is the uppermost class which contains severals lists of Atoms, Molecules and Chains. The following script reads a pdb file, prints some atom properties and writes the structure in gro format.

pmx data structure

The figure above shows the most important data structure. A "Model" instance contains list of chains, residues and atoms. A "Chain" instance of residues and atoms and a "Molecule" instance of a list of atoms only. Check the example scripts for how to navigate trough particular storage classes.

pmx Modules

pmx currently contains the following modules. Click on the links below for a (short) documentation

pmx Classes (the most important ones)

Using pmx

Owner

  • Name: deGrootLab
  • Login: deGrootLab
  • Kind: organization

GitHub Events

Total
  • Issues event: 7
  • Watch event: 22
  • Issue comment event: 3
  • Push event: 14
  • Pull request event: 4
  • Fork event: 6
Last Year
  • Issues event: 7
  • Watch event: 22
  • Issue comment event: 3
  • Push event: 14
  • Pull request event: 4
  • Fork event: 6

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 347
  • Total Committers: 9
  • Avg Commits per committer: 38.556
  • Development Distribution Score (DDS): 0.579
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Vytautas Gapsys v****s@v****n 146
Vytautas Gapsys v****s@m****e 67
Matteo Aldeghi m****h@m****e 54
Vytautas Gapsys v****s@g****e 43
Servaas s****s@g****m 20
dseelig s****t@g****m 8
Daniel Seeliger s****d@b****m 5
Servaas Michielssens s****e@s****n 3
Daniel Seeliger s****d@b****m 1
Committer Domains (Top 20 + Academic)
mpibpc.mpg.de: 2 bibciw20lx.eu.boehringer.com: 1 smichie.mpibpc.intern: 1 bibciw19lx.eu.boehringer.com: 1 gwdg.de: 1 vgapsys.mpibpc.intern: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 41
  • Total pull requests: 31
  • Average time to close issues: 7 days
  • Average time to close pull requests: 4 months
  • Total issue authors: 24
  • Total pull request authors: 12
  • Average comments per issue: 1.8
  • Average comments per pull request: 0.61
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 3
  • Average time to close issues: 2 days
  • Average time to close pull requests: 5 months
  • Issue authors: 6
  • Pull request authors: 2
  • Average comments per issue: 0.88
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • noahharrison64 (4)
  • matteoaldeghi (4)
  • pbuslaev (3)
  • Lyn-666 (2)
  • DreamCykl (2)
  • aixintiankong (1)
  • ksy141 (1)
  • qqq12a (1)
  • DJNovack (1)
  • JiangXu123 (1)
  • stain (1)
  • aminsagar (1)
  • almeida85 (1)
  • woefulblock401 (1)
  • bertadenes (1)
Pull Request Authors
  • pbuslaev (5)
  • zetadin (5)
  • matteoaldeghi (4)
  • foxtran (2)
  • alexxy (2)
  • aizvorski (2)
  • xiaoyongzhu (2)
  • h-mnzlr (1)
  • noahharrison64 (1)
  • lmacaya (1)
  • tlhr (1)
  • jharrymoore (1)
Top Labels
Issue Labels
develop_branch (4) enhancement (2)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 84 last-month
  • Total docker downloads: 46
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 13
  • Total maintainers: 3
pypi.org: pmx-biobb

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

  • Versions: 12
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 77 Last month
  • Docker Downloads: 46
Rankings
Docker downloads count: 3.2%
Dependent packages count: 4.8%
Forks count: 6.3%
Stargazers count: 6.8%
Average: 11.0%
Dependent repos count: 21.6%
Downloads: 23.0%
Maintainers (2)
andriopau gbayarri
Last synced: 11 months ago
pypi.org: pmx

Python Toolbox structure file editing and writing simulation setup/analysis tools

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 7 Last month
Rankings
Forks count: 6.3%
Stargazers count: 6.8%
Dependent packages count: 10.1%
Average: 20.5%
Dependent repos count: 21.6%
Downloads: 58.0%
Maintainers (1)
MatteoAldeghi
Last synced: 11 months ago

Dependencies

setup.py pypi
  • matplotlib >=2.2
  • numpy >=1.14
  • scipy >=1.1