/moly

Molecular Visualization powered by Plotly

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause


moly

Molecular visualization in Jupyter.



(Package is under development!)

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.get_collection("ReactionDataset", "S22")
dimers = ds.get_molecules()
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.add_molecule("dimer", ammonia_dimer)
fig.add_molecule("bucky ball", moly.Molecue.from_file("bucky.xyz"))
fig.show()

Copyright

Copyright (c) 2020, VH Chavez

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.