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distruct

https://github.com/kit-mbs/distruct

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 5 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: KIT-MBS
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 514 KB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Created over 7 years ago · Last pushed about 6 years ago
Metadata Files
Readme License

README.md

diSTruct

python package name: distruct Implementation of Maxent-stress Optimization of Biomolecular systems.

diSTruct is in essence an implementation of the MaxEnt-Stress graph drawing algorithm (Gansner, E.; Hu, Y. and North, S. C.: "A Maxent-Stress Model for Graph Layout" in IEE Trans. Vis. Comput. Graph. 2013) for generating biomolecular structures from distance constraints.

Requirements

The actual structure generation in diSTruct is build on the MaxEnt-stress graph drawing implementation in NetworKit.

It aims to conveniently combine this with the PDB module in Biopython.

It also depends on lxml and requires Cython.

Installation Instructions

First install NetworKit following the instructions in their homepage. Make sure you can import networkit without error. Sometimes there are issues with automatically installing all dependenicies. Simply install missing packages manually.

Install Cython, Biopython and lxml. Install diSTruct with

pip install distruct

Publications

Please cite 

@article{10.1093/bioinformatics/btz578,
    author = {Taubert, Oskar and Reinartz, Ines and Meyerhenke, Henning and Schug, Alexander},
    title = "{diSTruct v1.0: generating biomolecular structures from distance constraints}",
    journal = {Bioinformatics},
    year = {2019},
    month = {07},
    abstract = "{The distance geometry problem is often encountered in molecular biology and the life sciences at large, as a host of experimental methods produce ambiguous and noisy distance data. In this note, we present diSTruct; an adaptation of the generic MaxEnt-Stress graph drawing algorithm to the domain of biological macromolecules. diSTruct is fast, provides reliable structural models even from incomplete or noisy distance data and integrates access to graph analysis tools.diSTruct is written in C++, Cython and Python 3. It is available from https://github.com/KIT-MBS/distruct.git or in the Python package index under the MIT license.Supplementary data are available at Bioinformatics online.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btz578},
    url = {https://doi.org/10.1093/bioinformatics/btz578},
    note = {btz578},
    eprint = {http://oup.prod.sis.lan/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz578/29161648/btz578.pdf},
}

Tests

To run the python tests install pytest an run python -m pytest in /path/to/distruct/tests

Owner

  • Name: Multiscale Biomolecular Simulation
  • Login: KIT-MBS
  • Kind: organization
  • Location: Karlsruhe

Biophysics group at the Steinbuch Centre for Computing at the Karlsruhe Institute of Technology

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 265
  • Total Committers: 4
  • Avg Commits per committer: 66.25
  • Development Distribution Score (DDS): 0.249
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Oskar Taubert o****t@k****u 199
Oskar Taubert u****x@s****u 54
Oskar Taubert o****t@g****e 11
oskar-taubert o****t@g****e 1
Committer Domains (Top 20 + Academic)
gmx.de: 2 student.kit.edu: 1 kit.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: about 2 years
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 1.33
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wjxts (2)
  • drewaight (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 47 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 15
  • Total maintainers: 1
pypi.org: distruct

a package to generate 3d molecular structures from distance constraints

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 47 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Average: 22.3%
Forks count: 22.6%
Stargazers count: 27.8%
Downloads: 29.6%
Maintainers (1)
taubert
Last synced: 12 months ago

Dependencies

requirements.txt pypi
  • biopython *
  • lxml *
  • networkit ==7.0
  • numpy *
setup.py pypi
  • numpy *