buildH

buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters - Published in JOSS (2021)

https://github.com/patrickfuchs/buildh

Science Score: 95.0%

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Published in Journal of Open Source Software

Keywords

lipids molecular-dynamics-simulation order-parameters python united-atom

Last synced: 4 months ago · JSON representation

Repository

:computer: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.

Basic Info

Host: GitHub
Owner: patrickfuchs
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://buildh.readthedocs.io/
Size: 27.5 MB

Statistics

Stars: 14
Watchers: 4
Forks: 7
Open Issues: 4
Releases: 8

Topics

lipids molecular-dynamics-simulation order-parameters python united-atom

Created almost 7 years ago · Last pushed about 3 years ago

Metadata Files

Readme Changelog Contributing License Code of conduct Authors Codemeta Zenodo

buildH

buildH_logo

Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters

Features

buildH can : - Reconstruct hydrogens from a united-atom structure file (pdb, gro) or trajectory (e.g. xtc). - Calculate the order parameters based on the reconstructed hydrogens. - Write new structure trajectory files with the reconstructed hydrogens.

buildH works in two modes : 1. A slow mode when an output trajectory (in xtc format) is requested by the user. In this case, the whole trajectory including newly built hydrogens are written to this trajectory. 2. A fast mode without any output trajectory.

In both modes, the order parameters are calculated. All calculations are accelerated with Numba. As a CPU cost indication, running buildH on a trajectory of 2500 frames with 128 POPC (without trajectory output) takes ~ 7' on a single core Xeon @ 3.60GHz.

Requirements

Python >= 3.6 is mandatory for running buildH.

buildH is written in Python 3 and needs the modules numpy, pandas, MDAnalysis and Numba.

Installation

Pip

A simple installation with pip will do the trick:

python3 -m pip install buildh

All dependencies (modules) will be installed automatically by pip.

Conda

buildH is also available through the Bioconda channel:

conda install buildh -c bioconda -c conda-forge

More details on installation here.

For installing a development version, see here.

Running buildH

Once installed, a simple invocation of the buildH command will run the program ($ represents the Unix prompt):

$ buildH usage: buildH [-h] -c COORD [-t TRAJ] -l LIPID [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP [-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-pi PICKLE] [-igch3] buildH: error: the following arguments are required: -c/--coord, -l/--lipid, -d/--defop

The minimal command for running buildH can resemble this:

$ buildH -c start_128popc.pdb -t popc0-25ns_dt1000.xtc -l Berger_POPC -d Berger_POPC.def

The different arguments mean the following: -c start_128popc.pdb is a pdb file with 128 POPC molecules, -t popc0-25ns_dt1000.xtc is a trajectory with 25 frames, -l Berger_POPC indicates the united-atom force field and the type of lipid to be analyzed, -d Berger_POPC.def indicates what C-H are considered for H building and order parameter calculation (the structure and trajectory files can be found here). The def file can be found here. The final order parameters averaged over the trajectory will be written to the default output name OP_buildH.out

Other detailed examples and Jupyter Notebooks can be found in the documentation at Read the Docs.

Important: sometimes, when performing MD, some molecules are split over periodic boundary conditions (PBC). buildH takes as input whole structures (pdb, gro, xtc, etc.). If broken molecules are supplied, it will most likely generate nonsense results. So it is up to the user to take care of making molecules whole before running buildH (e.g. by using a tool like trjconv in GROMACS with flag -pbc mol).

Invoking buildH with the -h flag will display some help to the screen and tell which lipids are supported.

$ buildH -h usage: buildH [-h] [-v] -c COORD [-t TRAJ] -l LIPID [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP [-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-igch3] [...] The list of supported lipids (-l option) are: Berger_CHOL, Berger_DOPC, Berger_DPPC, Berger_POP, Berger_POPC, Berger_PLA, Berger_POPE, Berger_POPS, CHARMM36UA_DPPC, CHARMM36UA_DPUC, CHARMM36_POPC, GROMOS53A6L_DPPC, GROMOSCKP_POPC, GROMOSCKP_POPS. More documentation can be found at https://buildh.readthedocs.io.

Documentation

The full documentation is available at Read the Docs.

Contributors

Hubert Santuz
Amélie Bâcle
Pierre Poulain
Patrick Fuchs

License

buildH is licensed under the BSD License.

Contributing

If you want to report a bug, request a feature, or propose an improvement use the GitHub issue system.

Please, see also the CONTRIBUTING file.

Note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms. See the CODEOFCONDUCT file.

Citing buildH

If you use buildH for your research, please cite :

Santuz et al., (2021). buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters. Journal of Open Source Software, 6(65), 3521, https://doi.org/10.21105/joss.03521

Owner

Name: Patrick Fuchs
Login: patrickfuchs
Kind: user
Location: Paris
Company: Université Paris Cité

Website: https://www.dsimb.inserm.fr/~fuchs/
Repositories: 2
Profile: https://github.com/patrickfuchs

Maître de conférences à Université Paris Cité

JOSS Publication

buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters

Published

September 19, 2021

DOI

10.21105/joss.03521

Volume 6, Issue 65, Page 3521

Authors

Hubert Santuz

CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, F-75005 Paris, France, Institut de Biologie Physico-Chimique–Fondation Edmond de Rothschild, PSL Research University, Paris, France

Amélie Bacle

Laboratoire Coopératif "Lipotoxicity and Channelopathies - ConicMeds", Université de Poitiers, F-86000 Poitiers, France

Pierre Poulain

Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France

Patrick F.j. Fuchs

Sorbonne Université, Ecole Normale Supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), F-75005 Paris, France, Université de Paris, UFR Sciences du Vivant, F-75013 Paris, France

Editor

Richard Gowers

CodeMeta (codemeta.json)

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  "dateCreated": "2019-03-06",
  "datePublished": "2019-06-21",
  "dateModified": "2021-05-21",
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GitHub Events

Total

Last Year

Committers

Last synced: 5 months ago

All Time

Total Commits: 530
Total Committers: 6
Avg Commits per committer: 88.333
Development Distribution Score (DDS): 0.643

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Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
patrickfuchs	p**s@u**r	189
Hubert	h**z@g**m	130
patrickfuchs	p**s@u**t	115
Pierre Poulain	p**n@c**t	85
ABacle	a**e@g**m	10
readthedocs-assistant	9****t	1

Committer Domains (Top 20 + Academic)

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Total pull requests: 46
Average time to close issues: 2 months
Average time to close pull requests: 1 day
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Average comments per issue: 3.02
Average comments per pull request: 2.72
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patrickfuchs (26)
pierrepo (14)
lilyminium (5)
HubLot (4)
ojeda-e (2)
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larabort (1)

Pull Request Authors

HubLot (20)
pierrepo (19)
patrickfuchs (6)
readthedocs-assistant (1)

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documentation (14) enhancement (5) packaging (5) paper (3) bug (3) Registry & archive (2)

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Total packages: 1
Total downloads:
- pypi 118 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 7
Total maintainers: 3

pypi.org: buildh

Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.

Homepage: https://github.com/patrickfuchs/buildH
Documentation: https://buildh.readthedocs.io/
License: BSD 3-Clause License
Latest release: 1.6.1
published almost 4 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 118 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 13.3%

Stargazers count: 16.1%

Average: 18.5%

Dependent repos count: 21.5%

Downloads: 31.5%

Maintainers (3)

pierrepo Hub patrickfuchs

Last synced: 4 months ago

Dependencies

requirements.txt pypi

MDAnalysis *
numba *
numpy *
pandas *

.github/workflows/archive-to-software-heritage.yml actions

sdruskat/swh-save-action v1.0.1 composite

.github/workflows/code.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/docs.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/publish-to-pypi.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
pypa/gh-action-pypi-publish master composite

binder/environment.yml conda

bump2version
jupyterlab
matplotlib
myst-parser
nbsphinx
pip
pycodestyle
pydocstyle
pylint
pytest
python 3.8.*
python-build
sphinx
twine

buildH

Science Score: 95.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

buildH

Features

Requirements

Installation

Pip

Conda

Running buildH

Documentation

Contributors

License

Contributing

Citing buildH

Owner

JOSS Publication

buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters

Authors

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