biobb-structure-utils

Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues.

https://github.com/bioexcel/biobb_structure_utils

Science Score: 77.0%

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

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: nature.com, zenodo.org
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Committers with academic emails
1 of 3 committers (33.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (7.8%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: bioexcel
License: apache-2.0
Language: Python
Default Branch: master
Homepage: https://mmb.irbbarcelona.org/biobb/
Size: 11.7 MB

Statistics

Stars: 2
Watchers: 5
Forks: 3
Open Issues: 1
Releases: 0

Created over 6 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

README.md

biobbstructureutils

Introduction

Biobbstructureutils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v5.1.0 2025.1

Installation

Using PIP:

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

Installation:

pip install "biobb_structure_utils>=5.1.0"

Usage: Python API documentation

Using ANACONDA:

Installation:

conda install -c bioconda "biobb_structure_utils>=5.1.0"

Usage: With conda installation BioBBs can be used with the Python API documentation and the Command Line documentation

Using DOCKER:

Installation:

docker pull quay.io/biocontainers/biobb_structure_utils:5.1.0--pyhdfd78af_0

Usage:

docker run quay.io/biocontainers/biobb_structure_utils:5.1.0--pyhdfd78af_0 <command>

Using SINGULARITY:

MacOS users: it's strongly recommended to avoid Singularity and use Docker as containerization system.

Installation:

singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.1.0--pyhdfd78af_0

Usage:

singularity exec biobb_structure_utils.sif <command>

The command list and specification can be found at the Command Line documentation.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

Acknolegements

This software uses functions to read and modify GRO files based in the GROPY library created by Zhikun Cai (caizkun@gmail.com) under the MIT. In this project GROPY has been adapted to Python 3 and our own needs.

Owner

Name: BioExcel
Login: bioexcel
Kind: organization

Website: https://bioexcel.eu/
Repositories: 50
Profile: https://github.com/bioexcel

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: 1
Issue comment event: 4
Push event: 51
Pull request event: 1
Fork event: 1
Create event: 2

Last Year

Issues event: 1
Issue comment event: 4
Push event: 51
Pull request event: 1
Fork event: 1
Create event: 2

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 134
Total Committers: 3
Avg Commits per committer: 44.667
Development Distribution Score (DDS): 0.157

Top Committers

Name	Email	Commits
gbayarri	g**i@i**g	113
Pau Andrio	a**u@g**m	20
Josep Ll. Gelpi	g**i@u**u	1

Committer Domains (Top 20 + Academic)

ub.edu: 1 irbbarcelona.org: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 15
Total pull requests: 1
Average time to close issues: 2 months
Average time to close pull requests: 20 days
Total issue authors: 7
Total pull request authors: 1
Average comments per issue: 1.6
Average comments per pull request: 4.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 20 days
Issue authors: 1
Pull request authors: 1
Average comments per issue: 2.0
Average comments per pull request: 4.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

gbayarri (4)
PauAndrio (3)
jlgelpi (3)
adamhospital (2)
ndonyapour (1)
PabloNA97 (1)
pgbarletta (1)

Pull Request Authors

PabloNA97 (2)

Top Labels

Issue Labels

stale (3) enhancement (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 338 last-month
Total docker downloads: 25

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 23
Total maintainers: 2

pypi.org: biobb-structure-utils

biobb_structure_utils is the Biobb module collection to perform basic manipulations on 3d structures.

Homepage: https://github.com/bioexcel/biobb_structure_utils
Documentation: http://biobb-structure-utils.readthedocs.io/en/latest/
License: Apache Software License
Latest release: 5.1.0
published 9 months ago

Versions: 23
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 338 Last month
Docker Downloads: 25

Rankings

Docker downloads count: 3.9%

Dependent packages count: 10.1%

Downloads: 15.2%

Average: 16.3%

Forks count: 19.1%

Dependent repos count: 21.6%

Stargazers count: 27.8%

Maintainers (2)

andriopau gbayarri

Last synced: 7 months ago

Dependencies

setup.py pypi

biobb_common ==3.7.0
biobb_structure_checking ==3.9.11

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.github/workflows/linting_and_testing.yml actions

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biobb_structure_utils/docs/requirements.txt pypi

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