Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/ajax23/porems

Pore generator for molecular simulations.

https://github.com/ajax23/porems

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 61 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: acs.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (18.2%) to scientific vocabulary

Keywords

functionalization generator gromacs molecular-dynamics molecular-simulations pore
Last synced: 6 months ago · JSON representation

Repository

Pore generator for molecular simulations.

Basic Info
Statistics
  • Stars: 7
  • Watchers: 1
  • Forks: 4
  • Open Issues: 2
  • Releases: 10
Topics
functionalization generator gromacs molecular-dynamics molecular-simulations pore
Created over 6 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.md

PyPI Version License: GPL v3 DOI Build Status codecov

Documentation

Online documentation is available at ajax23.github.io/PoreMS.

The docs include an example for generating molecules and pores, and an API reference. Visit process for an overview of the programs operating principle.

An examplary workflow has been provided for using the PoreMS package to create a pore system and run molecular dynamics simulation using Gromacs.

Dependencies

PoreMS supports Python 3.5+.

Installation requires numpy, pandas and matplotlib.

Installation

The latest stable release (and older versions) can be installed from PyPI:

pip install porems

You may instead want to use the development version from Github:

pip install git+https://github.com/ajax23/porems.git#egg=porems

pip install git+https://github.com/ajax23/porems.git@develop#egg=porems

Or download the repository and install in the top directory via:

pip install .

Testing

To test porems, run the test in the test directory.

Development

PoreMS development takes place on Github: www.github.com/Ajax23/PoreMS

Please submit any reproducible bugs you encounter to the issue tracker.

How to Cite PoreMS

When citing PoreMS please use the following: Kraus et al., Molecular Simulation, 2021, DOI: 10.1080/08927022.2020.1871478

Additionaly, to assure reproducability of the generated pore systems, please cite the Zenodo DOI corresponding to the used PoreMS version. (Current DOI is listed in the badges.)

Published Work

  • Probst et al., 2025. Ring-Expansion Metathesis Polymerization under Confinement. Journal of the American Chemical Society, doi:doi.org/10.1021/jacs.4c18171
    • Data-Repository: doi:
  • Högler et al., 2024. Influence of Ionic Liquid Film Thickness and Flow Rate on Macrocyclization Efficiency and Selectivity in Supported Ionic Liquid-Liquid Phase Catalysis. Chemistry – A European Journal, doi:doi.org/10.1002/chem.202403237
  • Nguyen et al., 2024. Effects of Surfaces and Confinement on Formic Acid Dehydrogenation Catalyzed by an Immobilized Ru–H Complex: Insights from Molecular Simulation and Neutron Scattering. ACS Catalysis, doi:doi.org/10.1021/acscatal.4c02626
  • Kraus et al., 2023. Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models. The Journal of Physical Chemistry C, doi:10.1021/acs.jpcc.3c01974.
  • Kraus and Hansen, 2022. An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica. Adsorption, doi:10.1007/s10450-022-00356-w.
  • Kraus et al., 2021. PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions. Molecular Simulation, 47(4), pp.306-316, doi:10.1080/08927022.2020.1871478.
  • Ziegler et al., 2021. Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N-Heterocyclic Carbene Complexes. ACS Catalysis, 11(18), pp. 11570-11578, doi:10.1021/acscatal.1c03057
  • Kobayashi et al., 2021. Confined Ru-catalysts in a Two-phase Heptane/Ionic Liquid Solution: Modeling Aspects. ChemCatChem, 13(2), pp.739-746, doi:10.1002/cctc.202001596.
  • Ziegler et al., 2019. Olefin Metathesis in Confined Geometries: A Biomimetic Approach toward Selective Macrocyclization. Journal of the American Chemical Society, 141(48), pp.19014-19022, doi:10.1021/jacs.9b08776.

Owner

  • Name: Hamzeh Kraus
  • Login: Ajax23
  • Kind: user

GitHub Events

Total
  • Create event: 2
  • Issues event: 1
  • Release event: 1
  • Watch event: 3
  • Delete event: 1
  • Push event: 11
  • Pull request event: 4
Last Year
  • Create event: 2
  • Issues event: 1
  • Release event: 1
  • Watch event: 3
  • Delete event: 1
  • Push event: 11
  • Pull request event: 4

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 272
  • Total Committers: 3
  • Avg Commits per committer: 90.667
  • Development Distribution Score (DDS): 0.382
Top Committers
Name Email Commits
ajax23 h****s@w****e 168
ajax23 g****b@k****e 81
Ajax23 A****3@u****m 23
Committer Domains (Top 20 + Academic)
kraushh.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 13
  • Total pull requests: 19
  • Average time to close issues: 3 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 7
  • Total pull request authors: 2
  • Average comments per issue: 0.69
  • Average comments per pull request: 0.89
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 minutes
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Ajax23 (6)
  • jsgonzlez661 (1)
  • davidemarchiUPO (1)
  • mgeier (1)
  • CalenLev (1)
  • kamikahzadi (1)
  • adsavoy (1)
Pull Request Authors
  • Ajax23 (19)
  • marc310896 (2)
Top Labels
Issue Labels
enhancement (4) help wanted (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 1,478 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 17
  • Total maintainers: 1
proxy.golang.org: github.com/ajax23/porems
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 8.4%
Forks count: 9.8%
Average: 10.5%
Dependent repos count: 10.6%
Stargazers count: 13.4%
Last synced: 7 months ago
pypi.org: porems

Pore Generator for Molecular Simulations.

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 1,478 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 16.9%
Dependent repos count: 21.5%
Stargazers count: 23.1%
Average: 26.8%
Downloads: 62.2%
Maintainers (1)
Ajax23
Last synced: 6 months ago

Dependencies

docsrc/requirements.txt pypi
  • numpydoc *
  • sphinx ==1.6.6
  • sphinx_bootstrap_theme *
requirements.txt pypi
  • pandas *
  • pyyaml *
  • seaborn *
setup.py pypi
  • pandas *
  • pyyaml *
  • seaborn *
.github/workflows/workflow.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite