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molify: Molecular Structure Interface

molify: Molecular Structure Interface - Published in JOSS (2025)

https://github.com/zincware/molify

Science Score: 87.0%

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    CITATION.cff file
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    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
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    Links to: joss.theoj.org, zenodo.org
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    Published in Journal of Open Source Software

Keywords

ase packmol rdkit
Last synced: 2 months ago · JSON representation

Repository

Create atomistic structures with ASE, rdkit and packmol

Basic Info
Statistics
  • Stars: 17
  • Watchers: 1
  • Forks: 1
  • Open Issues: 6
  • Releases: 15
Topics
ase packmol rdkit
Created over 2 years ago · Last pushed 3 months ago
Metadata Files
Readme Contributing License

README.md

zincware codecov PyPI version DOI Docs status Ask DeepWiki

molify - Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX

Installation via pip install molify. For more information please visit the documentation.

A common use case is to create 3D structures from SMILES strings. This can be achieved using the molify.rdkit2ase function.

```py import ase from rdkit import Chem from molify import rdkit2ase, ase2rdkit

mol = Chem.MolFromSmiles("O") atoms: ase.Atoms = rdkit2ase(mol) mol = ase2rdkit(atoms) ```

Because this is such a common use case, there is a convenience function molify.smiles2atoms that combines the two steps.

```py import ase from molify import smiles2atoms

atoms: ase.Atoms = smiles2atoms("O")

print(atoms)

Atoms(symbols='OH2', pbc=False) ```

Packmol Interface

Given the molecular units, you can build periodic boxes with a given density using the molify.pack function.

The molify package ships with an installation of packmol. If you like packmol, give it a star on GitHub!

```py from molify import pack, smiles2conformers

water = smiles2conformers("O", 2) ethanol = smiles2conformers("CCO", 5) density = 1000 # kg/m^3 box = pack([water, ethanol], [7, 5], density) print(box)

Atoms(symbols='C10H44O12', pbc=True, cell=[8.4, 8.4, 8.4]) ```

Many additional features are described in the documentation.

Owner

  • Name: Zincware
  • Login: zincware
  • Kind: organization
  • Email: zincwarecode@gmail.com
  • Location: Germany

Open source software organisation hosting software built for computational physics and chemistry.

JOSS Publication

molify: Molecular Structure Interface
Published
December 12, 2025
DOI
Volume 10, Issue 116, Page 8829
Authors
Fabian Zills ORCID
Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany
Editor
Lucy Whalley ORCID
Tags
cheminformatics MLIPs ASE RDKit PACKMOL NetworkX
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GitHub Events

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  • Issues event: 2
  • Delete event: 3
  • Issue comment event: 5
  • Push event: 9
  • Pull request review comment event: 2
  • Pull request event: 2
  • Create event: 2
Last Year
  • Issues event: 2
  • Delete event: 3
  • Issue comment event: 5
  • Push event: 9
  • Pull request review comment event: 2
  • Pull request event: 2
  • Create event: 2

Issues and Pull Requests

Last synced: 2 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 minutes
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 3,269 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
pypi.org: molify

Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 3,269 Last month
Rankings
Dependent packages count: 8.4%
Average: 27.9%
Dependent repos count: 47.5%
Last synced: 3 months ago