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Project description
Molecular visualization in Jupyter (Package 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.
Victor H. Chavez was supported by a fellowship from The Molecular Sciences Software Institute under NSF grant OAC-1547580.
Project details
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