mdakit_sasa

Toolkit to calculate the surface accessible area of a molecular dynamic trajectory

https://github.com/pegerto/mdakit_sasa

Science Score: 67.0%

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
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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 1 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (6.6%) to scientific vocabulary

Keywords

molecular-dynamics molecular-dynamics-simulation protein-structure

Last synced: 7 months ago · JSON representation ·

Repository

Toolkit to calculate the surface accessible area of a molecular dynamic trajectory

Basic Info

Host: GitHub
Owner: pegerto
License: gpl-2.0
Language: Python
Default Branch: main
Homepage: https://mdakit-sasa.readthedocs.io/en/latest/index.html
Size: 149 KB

Statistics

Stars: 5
Watchers: 3
Forks: 2
Open Issues: 7
Releases: 11

Topics

molecular-dynamics molecular-dynamics-simulation protein-structure

Created over 2 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Authors

mdakit-sasa

This kit allows the calculation of a solvent-accessible-surface area of a trajectory

mdakit-sasa is bound by a Code of Conduct.

Installation

To build mdakit-sasa from source, we highly recommend using virtual environments. If possible, we strongly recommend that you use Anaconda as your package manager. Below we provide instructions both for conda and for pip.

With conda

Ensure that you have conda installed.

Create a virtual environment and activate it:

conda create --name mdakit_sasa conda activate mdakit_sasa

Install the development and documentation dependencies:

conda env update --name mdakit_sasa --file devtools/conda-envs/test_env.yaml conda env update --name mdakit_sasa --file docs/requirements.yaml

Build this package from source:

pip install -e .

If you want to update your dependencies (which can be risky!), run:

conda update --all

And when you are finished, you can exit the virtual environment with:

conda deactivate

With pip

To build the package from source, run:

pip install .

If you want to create a development environment, install the dependencies required for tests and docs with:

pip install ".[test,doc]"

Copyright

The mdakit-sasa source code is hosted at https://github.com/pegerto/mdakit_sasa and is available under the GNU General Public License, version 2 (see the file LICENSE).

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdakit-sasa in published work.

Owner

Name: Pegerto
Login: pegerto
Kind: user

Website: http://pegerto.com
Repositories: 18
Profile: https://github.com/pegerto

Citation (CITATION.cff)

cff-version: 1.2.0
title: mdakit-sasa
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Pegerto
    family-names: Fernandez
    affiliation: 'Brunel University, London'
    orcid: 'https://orcid.org/0000-0001-8186-8431'
  - given-names: Alessandro
    family-names: Pandini
    affiliation: 'Brunel University, London'
    orcid: 'https://orcid.org/0000-0002-4158-233X'
identifiers:
  - type: doi
    value: 10.5281/zenodo.10182425
abstract: >-
  This MDAKit allows for the computation of Solvent
  Accessible Surface Area (SASA) through MDAnalysis,
  leveraging the essential role of FreeSASA in performing
  the calculation.
license: GPL-2.0

GitHub Events

Total

Issues event: 1
Watch event: 1

Last Year

Issues event: 1
Watch event: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 1
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 1
Total 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

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
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

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