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The pdb2sql Python Package

The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queries - Published in JOSS (2020)

https://github.com/deeprank/pdb2sql

Science Score: 100.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 7 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    1 of 11 committers (9.1%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords from Contributors

convolutional-neural-networks graph-neural-networks protein-protein-interfaces single-residue-variants structural-biology molecular-dynamics
Last synced: 6 months ago · JSON representation ·

Repository

Fast and versatile biomolecular structure PDB file parser using SQL queries

Basic Info
Statistics
  • Stars: 24
  • Watchers: 3
  • Forks: 11
  • Open Issues: 8
  • Releases: 11
Created over 8 years ago · Last pushed almost 3 years ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Zenodo

README.md

PDB2SQL

PyPI DOI RSD Build_Test Coverage Status Codacy Badge Documentation Status DOI

pdb2sql is a Python package that leverage SQL queries to parse, manipulate and process PDB files. It provides:

  • a powerful pdb2sql object to convert PDB data in SQL database
  • strcuture transformation functions (rotations, translations...)
  • useful capablities to
    • calculate structure interface (contact atoms and residues)
    • calculate structure similarity (iRMSD, lRMSD, FNAT, DockQ...)

Installation

pip install pdb2sql

Documentation

The documentation of the package alongside small tutorial can be found at : - https://pdb2sql.readthedocs.io

Quick Example

pdb2sql easily allows to load a PDB file in an object. Once loaded, the data can be parsed using SQL queries. To facilitate the adoption of the tool simple methods have been developped to wrap the SQL queries in simple methods. For example obtaining the positions of all carbon, nitrogen and oxygen atoms of chain A from all residues but VAL and LEU, one can use :

python from pdb2sql import pdb2sql pdb = pdb2sql('1AK4.pdb') atoms = pdb.get('x,y,z', name = ['C','N', 'O'], no_resName = ['VAL','LEU'], chainID = 'A')

Owner

  • Name: DeepRank
  • Login: DeepRank
  • Kind: organization

JOSS Publication

The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queries
Published
May 28, 2020
DOI
Volume 5, Issue 49, Page 2077
Authors
Nicolas Renaud ORCID
Netherlands eScience Center, Science Park 140 1098 XG Amsterdam, the Netherlands
Cunliang Geng ORCID
Netherlands eScience Center, Science Park 140 1098 XG Amsterdam, the Netherlands
Editor
Lorena Pantano ORCID
Tags
Bioinformatics PDB files
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

# YAML 1.2
---
abstract: "Fast and versatile biomolecular structure PDB file parser using SQL queries."
authors:
  -
    affiliation: "Netherlands eScience Center"
    family-names: Renaud
    given-names: Nicolas
    orcid: "https://orcid.org/0000-0001-9589-2694"
  -
    affiliation: "Netherlands eScience Center"
    family-names: Geng
    given-names: Cunliang
    orcid: "https://orcid.org/0000-0002-1409-8358"
cff-version: 1.2.0
doi: "10.5281/zenodo.3232887"
keywords:
  - "pdb parser"
  - "protein structure"
  - biomolecule
  - bioinformatics
  - CAPRI
license: "Apache-2.0"
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/DeepRank/pdb2sql"
title: pdb2sql
...

GitHub Events

Total
  • Issues event: 1
Last Year
  • Issues event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 353
  • Total Committers: 11
  • Avg Commits per committer: 32.091
  • Development Distribution Score (DDS): 0.397
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Cunliang Geng c****g@e****l 213
NicoRenaud n****d@g****m 120
manonreau m****u@g****m 9
Li Xue m****e@g****m 2
Jurriaan H. Spaaks j****s@e****l 2
Daniel S. Katz d****z@i****g 2
joaomcteixeira j****a@g****m 1
dependabot-preview[bot] 2****] 1
Dario Marzella 5****a 1
Abel Soares Siqueira n****1@g****m 1
Manon F. Réau m****u@i****x 1
Committer Domains (Top 20 + Academic)
esciencecenter.nl: 2 int1.bullx: 1 ieee.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 45
  • Total pull requests: 44
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 13
  • Total pull request authors: 11
  • Average comments per issue: 1.76
  • Average comments per pull request: 1.18
  • Merged pull requests: 39
  • Bot issues: 1
  • Bot pull requests: 1
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • LilySnow (10)
  • CunliangGeng (8)
  • NicoRenaud (7)
  • joaomcteixeira (5)
  • JoaoRodrigues (4)
  • DarioMarzella (3)
  • FarzanehParizi (2)
  • Smarti92 (1)
  • taras-stx (1)
  • hanjialu0810 (1)
  • DTRademaker (1)
  • dependabot-preview[bot] (1)
  • reneejoosten (1)
Pull Request Authors
  • CunliangGeng (21)
  • NicoRenaud (11)
  • manonreau (2)
  • DTRademaker (2)
  • jspaaks (2)
  • DarioMarzella (1)
  • joaomcteixeira (1)
  • dependabot-preview[bot] (1)
  • LilySnow (1)
  • danielskatz (1)
  • abelsiqueira (1)
Top Labels
Issue Labels
stale (11)
Pull Request Labels
stale (5) dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 423 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 9
  • Total versions: 10
  • Total maintainers: 2
pypi.org: pdb2sql

PDB parser using SQL queries

  • Versions: 10
  • Dependent Packages: 2
  • Dependent Repositories: 9
  • Downloads: 423 Last month
Rankings
Dependent packages count: 3.1%
Dependent repos count: 4.9%
Average: 8.7%
Forks count: 10.2%
Downloads: 11.5%
Stargazers count: 13.6%
Maintainers (2)
CunliangGeng nico_reno
Last synced: 6 months ago

Dependencies

setup.py pypi
  • numpy *
  • pandas *
.github/workflows/build_test.yml actions
  • actions/checkout v2 composite
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.github/workflows/cffconvert.yml actions
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  • citation-file-format/cffconvert-github-action 2.0.0 composite
.github/workflows/publish_pypi.yml actions
  • actions/checkout master composite
  • actions/setup-python v3 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/stale_issue_pr.yml actions
  • actions/stale v5.0.0 composite