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VHchavez authored Feb 19, 2020
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<p align="center">
<br>
<img src="media/title.png" alt="moly" height=300> <br><br>
Molecular visualization in Jupyter.<br><br>
<a href="https://travis-ci.com/VHChavez/moly"><img src="https://travis-ci.com/VHChavez/moly.svg?branch=master" /></a>
<a href="https://lgtm.com/projects/g/VHchavez/moly/context:python"><img src="https://img.shields.io/lgtm/grade/python/g/VHchavez/moly.svg?logo=lgtm&logoWidth=18" /></a>
<a href="https://opensource.org/licenses/BSD-3-Clause"><img src="https://img.shields.io/badge/License-BSD%203--Clause-blue.svg" /></a>
<br>
</p>

---

Molecular visualization in Jupyter Notebooks.
<br>
(Package is still under development!)


### Features:
Geometry
Volumes (Density, MOs, ESP)
Volumes (Density, MOs, ESP)

### Supports:
xyz files
Psi4 geometries
QCElemental molecules
Cube files
xyz files
Psi4 geometries
QCElemental molecules
Cube files

### Installation
* pip:
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<br>
### Basic Geometry
* ### Basic Geometry
*Define a figure and add elements to it. These can be molecues:*
```
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<br>
### Basic Cube file
* ### Basic Cube file
*Geometry and volumentric information can extracted from cube files.*
```
formal = moly.molecule_factory("Cube", file='orbitals.cube')
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<img src="/media/formaldehyde.png" alt="formal" height=300> <br>
### Basic Layering
* ### Basic Layering
*Geometries can be brought from different sources and be thrown in the same figure*
```
#Implementation with QCArchive
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### Copyright
#### Copyright
Copyright (c) 2020, VH Chavez
#### Acknowledgements
##### Acknowledgements
Project based on the
[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.

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