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biobb-structure-checking

https://github.com/bioexcel/biobb_structure_checking

Science Score: 54.0%

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
  • ○
    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 (12.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: bioexcel
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Size: 5.57 MB
Statistics
  • Stars: 12
  • Watchers: 4
  • Forks: 1
  • Open Issues: 4
  • Releases: 1
Created about 7 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License Citation

README.md

biobbstructurechecking

Introduction

Biobbstructurechecking provides a series of functions to check the quality of a 3D structure intended to facilitate the setup of a molecular dynamics simulation of protein or nucleic acids systems.

Biobbstructurechecking package allows to configure the system (selection of model/chains,alternative location, addition of disulfide bonds and hydrogen atoms, side chain mutations), to detect and fix structure errors (missing side chain atoms, backbone breaks, amide assignments, incorrect chirality). It works with structures obtained from the Protein Data Bank or user provided.

The Biobbstructurechecking package provides a command line utility (check_structure) and a python API.

The latest documentation of this package can be found in our readthedocs site: latest package documentation.

Version

v3.15.6 March 2025

Requirements

  • Biopython ### Optional requirements
  • psutil (required for --debug, included in conda pkg.)
  • Modeller (required for some functionalities, not included in conda pkg.)
  • jupyter & nglview (required for demonstration notebooks, not included in conda pkg.)

Installation

Using PIP:

Important: PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA.

Using ANACONDA:

Copyright & Licensing

This software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the BSC (https://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (https://bioexcel.eu/). BioExcel is funded by the European Union Horizon 2020 program under grant agreements 823830, 675728 and by the EuroHPC Joint Undertaking and Sweden, Netherlands, Germany, Spain, Finland and Norway under grant agreement 101093290 funded by the European Commission.

Licensed under the GNU Lesser General Public License v2.1.

Owner

  • Name: BioExcel
  • Login: bioexcel
  • Kind: organization

Center of Excellence for Computational Biomolecular Research

Citation (CITATION.cff) 

abstract: "BioExcel Building Blocks (BioBB) library. BioBB's are built as Python wrappers to provide an interoperable architecture. BioBB's have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments."
authors:
  - affiliation: "Barcelona Supercomputing Center (BSC)"
    family-names: "Andrio"
    given-names: "Pau"
    orcid: "https://orcid.org/0000-0003-2116-3880"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Hospital"
    given-names: "Adam"
    orcid: "https://orcid.org/0000-0002-8291-8071"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Bayarri"
    given-names: "Genís"
    orcid: "https://orcid.org/0000-0003-0513-0288"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "García"
    given-names: "Agustín"
    orcid: "https://orcid.org/0009-0002-2159-965X"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Chaves"
    given-names: "Rubén"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University of Barcelona (UB)"
    family-names: "Orozco"
    given-names: "Modesto"
    orcid: "https://orcid.org/0000-0002-8608-3278"
  - affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
    family-names: "Gelpí"
    given-names: "Josep Ll."
    orcid: "https://orcid.org/0000-0002-0566-7723"
    email: "gelpi@ub.edu"
cff-version: 1.2.0
date-released: "2019-09-10"
keywords:
  - "BioExcel"
  - "BioBB"
  - "Bioinformatics"
  - "Computational Biology"
  - "Biomolecular Workflows"
license: "Apache-2.0"
message: "If you use this dataset, please cite it using the metadata from this file."
repository-code: "https://github.com/bioexcel/biobb"
title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
doi: "10.1038/s41597-019-0177-4"
url: "https://mmb.irbbarcelona.org/biobb/"
version: 5.0.0
preferred-citation:
  type: "article"
  authors:
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Andrio"
      given-names: "Pau"
      orcid: "https://orcid.org/0000-0003-2116-3880"
    - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
      family-names: "Hospital"
      given-names: "Adam"
      orcid: "https://orcid.org/0000-0002-8291-8071"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Conejero"
      given-names: "Javier"
      orcid: "https://orcid.org/0000-0001-6401-6229"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Jordà"
      given-names: "Luis"
      orcid: "https://orcid.org/0000-0002-9407-9703"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Del Pino"
      given-names: "Marc"
      orcid: "https://orcid.org/0000-0001-5565-7577"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Laia"
      given-names: "Codó"
      orcid: "https://orcid.org/0000-0002-6797-8746"
    - affiliation: "University of Manchester (UOM)"
      family-names: "Soiland-Reyes"
      given-names: "Stian"
      orcid: "https://orcid.org/0000-0001-9842-9718"
    - affiliation: "University of Manchester (UOM)"
      family-names: "Goble"
      given-names: "Carole"
      orcid: "https://orcid.org/0000-0003-1219-2137"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Lezzi"
      given-names: "Daniele"
      orcid: "https://orcid.org/0000-0001-5081-7244"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Badia"
      given-names: "Rosa M"
      orcid: "https://orcid.org/0000-0003-2941-5499"
    - affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University  of Barcelona (UB)"
      family-names: "Orozco"
      given-names: "Modesto"
      orcid: "https://orcid.org/0000-0002-8608-3278"
    - affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
      family-names: "Gelpí"
      given-names: "Josep Ll."
      orcid: "https://orcid.org/0000-0002-0566-7723"
      email: "gelpi@ub.edu"
  doi: "10.1038/s41597-019-0177-4"
  journal: "Nature Scientific Data"
  month: 9
  start: 169
  title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
  issue: 1
  volume: 6
  year: 2019

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 1
  • Push event: 16
Last Year
  • Issues event: 2
  • Issue comment event: 1
  • Push event: 16

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 715
  • Total Committers: 4
  • Avg Commits per committer: 178.75
  • Development Distribution Score (DDS): 0.078
Top Committers
Name Email Commits
Josep Ll. Gelpi g****i@u****u 659
Pau Andrio a****u@g****m 54
root r****t@p****u 1
dependabot[bot] 4****]@u****m 1
Committer Domains (Top 20 + Academic)
portjlg5.ub.edu: 1 ub.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 11
  • Total pull requests: 16
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 3 months
  • Total issue authors: 7
  • Total pull request authors: 3
  • Average comments per issue: 1.45
  • Average comments per pull request: 0.19
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 0
  • Average comments per issue: 0.33
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jlgelpi (5)
  • PauAndrio (1)
  • B-omics (1)
  • PabloNA97 (1)
  • pgbarletta (1)
  • ovavourakis (1)
  • adamhospital (1)
Pull Request Authors
  • jlgelpi (12)
  • dependabot[bot] (3)
  • iwatobipen (1)
Top Labels
Issue Labels
enhancement (5) stale (5)
Pull Request Labels
dependencies (3)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 1,918 last-month
  • Total docker downloads: 25
  • Total dependent packages: 3
  • Total dependent repositories: 1
  • Total versions: 37
  • Total maintainers: 3
pypi.org: biobb-structure-checking

BioBB_structure_checking performs MDWeb structure checking tool set as a command line utility.

  • Versions: 37
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 1,918 Last month
  • Docker Downloads: 25
Rankings
Dependent packages count: 2.4%
Docker downloads count: 3.9%
Average: 13.8%
Downloads: 14.4%
Stargazers count: 17.7%
Dependent repos count: 21.5%
Forks count: 22.6%
Maintainers (3)
andriopau gbayarri gelpi
Last synced: 10 months ago

Dependencies

biobb_structure_checking/docs/requirements.txt pypi
  • docutils ==0.17.1
  • numpy ==1.22.0
setup.py pypi
  • biopython ==1.79
  • numpy *
  • psutil *