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moly

Molecular Visualization powered by Plotly

https://github.com/vhchavez/moly

Science Score: 54.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.7%) to scientific vocabulary

Keywords

jupyter molecular-structures plotly
Last synced: 6 months ago · JSON representation ·

Repository

Molecular Visualization powered by Plotly

Basic Info
  • Host: GitHub
  • Owner: VHchavez
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 1.59 MB
Statistics
  • Stars: 18
  • Watchers: 1
  • Forks: 4
  • Open Issues: 10
  • Releases: 2
Topics
jupyter molecular-structures plotly
Created about 6 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Code of conduct Citation

README.md

moly

GitHub Workflow Status LGTM Grade GitHub

Try it now:

Features:

Geometry
Volumes from Cube Files

Supports:

xyz files
Psi4 geometries
QCElemental molecules

Installation

  • git: git clone https://github.com/VHchavez/moly.git cd moly pip install .
  • pip: pip install moly
  • conda: coming soon!


  • ### Basic Geometry Define a figure and add molecules to it.

import moly fig = moly.Figure() molecule = moly.Molecule.from_file("caffeine.xyz") fig.add_molecule("caffeine", molecule) fig.show()


  • ### Basic Layering Geometries can be brought from different sources and be thrown in the same figure ``` #Molecules from QCArchive

import qcportal as ptl client = ptl.FractalClient()

Get molecule from QCArchive

ds = client.getcollection("ReactionDataset", "S22") dimers = ds.getmolecules() ammonia_dimer = dimers.loc['Ammonia Dimer', 'molecule'][0]

Different surfaces are available.

Resolution can be increased if saving figure is desired.

fig = moly.Figure(figsize=(800,800), surface="shiny") fig.addmolecule("dimer", ammoniadimer) fig.addmolecule("bucky ball", moly.Molecue.fromfile("bucky.xyz")) fig.show() ```

Copyright

Copyright (c) 2020, VH Chavez

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.
Victor H. Chavez was supported by a fellowship from The Molecular Sciences Software Institute under NSF grant OAC-1547580.

Owner

  • Name: Victor Hugo
  • Login: VHchavez
  • Kind: user
  • Location: Santa Fe, NM
  • Company: Cadence Design Systems

Software Scientist.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Chávez"
  given-names: "Victor H."
  orcid: "https://orcid.org/0000-0003-3765-2961"
title: "moly: Molecular Visualization in Jupyter"
version: 0.1.1
date-released: 2018-02-18
url: "https://github.com/VHchavez/moly"

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 166
  • Total Committers: 3
  • Avg Commits per committer: 55.333
  • Development Distribution Score (DDS): 0.343
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Victor H. Chavez g****5@p****u 109
Victor Hugo 5****z 53
Billy Doyle d****8@g****m 4
Committer Domains (Top 20 + Academic)
purdue.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 12
  • Total pull requests: 5
  • Average time to close issues: 15 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 2.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dgasmith (5)
  • VHchavez (4)
  • billy-doyle (2)
  • Sulstice (1)
Pull Request Authors
  • billy-doyle (3)
  • VHchavez (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 44 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 1
pypi.org: moly
  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 44 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.6%
Average: 23.1%
Downloads: 37.5%
Maintainers (1)
VHchavez
Last synced: 6 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v1 composite
  • codecov/codecov-action v1 composite
.github/workflows/pypi.yml actions
  • actions/checkout v1 composite
  • codecov/codecov-action v1 composite
  • pypa/gh-action-pypi-publish master composite
setup.py pypi
  • numpy *
  • plotly >=4.0.0
  • qcelemental *