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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.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.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.