Molecular visualization in Jupyter.

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(Package is under development!)

Features:

Geometry
Volumes (Density, MOs, ESP)

Supports:

xyz files
Psi4 geometries
QCElemental molecules
Cube files

Installation

• pip:

  pip install moly
  

• conda:

  coming soon!
  

• Basic Geometry

*Define a figure and add molecules to it.

import moly
caffeine = moly.molecule_factory("xyz", file='/caffeine.xyz')
fig = moly.Figure()
fig.add_molecule(caffeine)
fig.show()

Produces

• Basic Cube file

Geometry and volumentric information can extracted from cube files.

formal = moly.molecule_factory("Cube", file='orbitals.cube')
fig = moly.Figure()
fig.add_molecule(formal)
fig.add_blob(iso=0.05)
fig.show()

Produces

• Basic Layering

Geometries can be brought from different sources and be thrown in the same figure

#Implementation with 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]

#Molecules
ammonia_dimer = moly.molecule_factory("QC", molecule=ammonia_dimer)
bucky = moly.molecule_factory("xyz", file='bucky.xyz')

#Figure, resolution and surface material can be changed
fig = moly.Figure(resolution=(800,800), surface="shiny")
fig.add_molecule(ammonia_dimer)
fig.add_molecule(bucky)
fig.show()

Produces

Copyright

Copyright (c) 2020, VH Chavez

Acknowledgements

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