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Merge pull request #61 from xiaoruiDong/docs
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Huge Improvement of Documentation
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xiaoruiDong authored Sep 11, 2023
2 parents 9f6f3de + 2a0e19f commit 8f16e96
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4 changes: 4 additions & 0 deletions docs/source/_static/custom.css
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.social-icon {
height: 1rem;
width: auto;
}
28 changes: 22 additions & 6 deletions docs/source/conf.py
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# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import datetime
import os
import sys
sys.path.insert(0, os.path.abspath('../../'))
import sphinx_rtd_theme

# -- Project information -----------------------------------------------------

project = 'RDMC'
copyright = '2020, Xiaorui Dong'
author = 'Xiaorui Dong'
copyright = f'2020-{datetime.datetime.now().year}, Xiaorui Dong'
author = 'Xiaorui Dong, Lagnajit Pattanaik, Shih-Cheng Li, ' \
'Kevin Spiekermann, Hao-Wei Pang, and William H. Green'

# The full version, including alpha/beta/rc tags
release = '0.1'
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# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

html_theme = 'pydata_sphinx_theme'
html_theme_options = {
"icon_links": [
{
"name": "GitHub",
"url": "https://github.com/xiaoruidong/rdmc",
"icon": "fa-brands fa-square-github",
"type": "fontawesome",
},
]
}

# Make the `Returns` in docstring behave like `Args`
napoleon_custom_sections = [('Returns', 'params_style')]

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_css_files = [
'custom.css',
]

# -- Packages that are not importable from the default environment ---------

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107 changes: 96 additions & 11 deletions docs/source/index.rst
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RDMC Documentation
===================

**RDMC (RDkit Molecule and Conformer)** is A light-weight wrapper for **RDKit** Molecule and Conformer related operations. RDkit is great! I like its versatility and speed, but
personally, I find learning to use RDKit is not easy. I usually have to go back and forth to check if RDKit has certain methods and how to use them,
since those molecule operations are usually located in different modules. I wrote this tiny thing majorly aiming to make my life easier and to
provide a convenient tool so that users can just import a single module / class instead of remembering which method in what module.
**RDMC (Reaction Data and Molecular Conformer)** is an open-source lightweight software package specialized in handling Reaction Data and Molecular (including transition states) Conformers.

To start with, simply try::
It contains various modules and classes (e.g., ``RDKitMol``, ``Reaction``, ``view``) helpful for relevant tasks to make conversion, visualization, manipulation, and analysis of molecules easier.
It also provides solutions to pipelining tasks to achieve high-throughput generating and processing of large amount of molecule/reaction data. It is written in Python and has dependencies only
on popular packages (i.e., ``numpy``, ``scipy``, ``matplotlib``, ``rdkit``, ``openbabel``, ``py3dmol``, ``ase``, ``networkx``, ``cclib``), and you can easily incorporate it into your own Python scripts.

from rdmc.mol import RDKitMol
The source code of the RDMC software package is hosted on GitHub, and its binary distribution is available on Anaconda Cloud. The easiest way to install RDMC is to use ``conda`` or ``mamba``::

and see what you can do with this ``RDKitMol`` class!
conda install -c xiaoruidong rdmc

Or

.. code-block:: bash
mamba install -c xiaoruidong rdmc
``conda`` can be installed by via `Anaconda <https://www.anaconda.com/download/>`_ and, ``mamba`` can be installed via `Mambaforge <https://github.com/conda-forge/miniforge#mambaforge>`_.

You can also install RDMC from the source code:

.. code-block:: bash
git clone https://github.com/xiaoruidong/rdmc
cd RDMC
conda env create -f environment.yml
conda activate rdmc
python -m pip install --no-deps -vv ./
To start with, simply try:

.. code-block:: python
from rdmc import RDKitMol, Reaction
mol = RDKitMol('CCO')
rxn = Reaction('CCO>>CC(=O)O')
And see what the ``mol`` and ``rxn`` are capable of! The full lists of APIs of :obj:`RDKitMol <rdmc.mol.RDKitMol>` and :obj:`Reaction <rdmc.reaction.Reaction>` are provided in this documentation.

We also provided a few notebooks (available in ``\ipython`` and `Colab <https://drive.google.com/drive/folders/1bHSChJOocycE5ZfbnGkocX4-OFVDhShW?usp=sharing>`_) to demonstrate the usage of RDMC. Please feel invited to try them out!

RDMC is developed by

- Xiaorui Dong (|github_xiaorui|_ \| |linkedin_xiaorui|_ \| |gs_xiaorui|_),
- Dr. Lagnajit Pattanaik (|github_lucky|_ \| |linkedin_lucky|_ \| |gs_lucky|_),
- Dr. Shih-Cheng Li (|github_shihcheng|_ \| |linkedin_shihcheng|_ \| |gs_shihcheng|_),
- Dr. Kevin Spiekermann (|github_kevin|_ \| |linkedin_kevin|_ \| |gs_kevin|_),
- Hao-Wei Pang (|github_haowei|_ \| |linkedin_haowei|_ \| |gs_haowei|_),
- Prof. William H. Green (|linkedin_bill|_ \| |gs_bill|_)

at `Green Research Group <https://greengroup.mit.edu>`_ at `Massachusetts Institute of Technology (MIT) <https://www.mit.edu>`_.
For any questions while using RDMC, please contact us via the `GitHub issue page <https://github.com/xiaoruiDong/RDMC/issues>`_ or email us at `[email protected] <mailto:[email protected]>`_.

Contents
========
.. toctree::
:maxdepth: 2

rdmc
license
reference/rdmc
reference/credits
reference/cite
reference/license


Indices and tables
APIs
===================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


.. |github| image:: _static/GitHub_icon.svg
:class: social-icon
.. |github_xiaorui| replace:: |github|
.. _github_xiaorui: https://github.com/xiaoruiDong
.. |github_lucky| replace:: |github|
.. _github_lucky: https://github.com/PattanaikL
.. |github_shihcheng| replace:: |github|
.. _github_shihcheng: https://github.com/shihchengli
.. |github_kevin| replace:: |github|
.. _github_kevin: https://github.com/kspieks
.. |github_haowei| replace:: |github|
.. _github_haowei: https://github.com/hwpang

.. |linkedin| image:: _static/LinkedIn_icon.svg
:class: social-icon
.. |linkedin_xiaorui| replace:: |linkedin|
.. _linkedin_xiaorui: https://www.linkedin.com/in/xiaorui-dong/
.. |linkedin_lucky| replace:: |linkedin|
.. _linkedin_lucky: https://www.linkedin.com/in/lagnajit-pattanaik-94a564108/
.. |linkedin_shihcheng| replace:: |linkedin|
.. _linkedin_shihcheng: https://www.linkedin.com/in/shih-cheng-li-564006207/
.. |linkedin_kevin| replace:: |linkedin|
.. _linkedin_kevin: https://www.linkedin.com/in/kspiekermann/
.. |linkedin_haowei| replace:: |linkedin|
.. _linkedin_haowei: https://www.linkedin.com/in/hao-wei-pang/
.. |linkedin_bill| replace:: |linkedin|
.. _linkedin_bill: https://www.linkedin.com/in/william-green-63a9a218/

.. |google_scholar| image:: _static/Google_Scholar_icon.svg
:class: social-icon
.. |gs_xiaorui| replace:: |google_scholar|
.. _gs_xiaorui: https://scholar.google.com/citations?hl=en&user=r5Wz41EAAAAJ
.. |gs_lucky| replace:: |google_scholar|
.. _gs_lucky: https://scholar.google.com/citations?hl=en&user=bVT6lpwAAAAJ
.. |gs_shihcheng| replace:: |google_scholar|
.. _gs_shihcheng: https://scholar.google.com/citations?hl=en&user=kc_rvjoAAAAJ
.. |gs_kevin| replace:: |google_scholar|
.. _gs_kevin: https://scholar.google.com/citations?hl=en&user=qg2LmbgAAAAJ
.. |gs_haowei| replace:: |google_scholar|
.. _gs_haowei: https://scholar.google.com/citations?hl=en&user=hmkEmtcAAAAJ
.. |gs_bill| replace:: |google_scholar|
.. _gs_bill: https://scholar.google.com/citations?hl=en&user=PGQTLWwAAAAJ
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How to cite RDMC
================

Text form

.. code-block:: tex

Dong, X., Pattanaik, L., Li, S.-C., Spiekermann, K., Pang, H.-W., Green, William H (2023). RDMC: Reaction Data and Molecular Conformer (Version 0.1.0) [Computer software]. https://github.com/xiaoruiDong/RDMC


BibTeX form

.. code-block:: tex

@misc{RDMC,
author = {Dong, Xiaorui and Pattanaik, Lagnajit and Li, Shih-Cheng and Spiekermann, Kevin and Pang, Hao-Wei and Green, William H.},
title = {RDMC: Reaction Data and Molecular Conformer Software Package, version 0.1.0},
year = {2023},
publisher = {GitHub},
howpublished = {\url{https://github.com/xiaoruiDong/RDMC}}}

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rdmc.conformer_generation.align
=================================

.. automodule:: rdmc.conformer_generation.align
:members:
:undoc-members:
:show-inheritance:
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rdmc.conformer_generation.embedders
===================================

.. automodule:: rdmc.conformer_generation.embedders
:members:
:undoc-members:
:show-inheritance:
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Embedding Geometries
=====================

.. toctree::
:maxdepth: 2

embedders
align
ts_guessers
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rdmc.conformer_generation.ts_guessers
======================================

.. automodule:: rdmc.conformer_generation.ts_guessers
:members:
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Geometry Optimization
=====================

.. toctree::
:maxdepth: 2

optimizers
ts_optimizers
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rdmc.conformer_generation.optimizers
=====================================

.. automodule:: rdmc.conformer_generation.optimizers
:members:
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rdmc.conformer_generation.ts_optimizers
=======================================

.. automodule:: rdmc.conformer_generation.ts_optimizers
:members:
:undoc-members:
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rdmc.conformer_generation
==========================

.. automodule:: rdmc.conformer_generation
:members:
:undoc-members:
:show-inheritance:

.. toctree::
:maxdepth: 2

embedding_geometries/index
geometry_optimization/index
postprocessing/index
workflow/index
utils
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Postprocessing
=====================

.. toctree::
:maxdepth: 2

verifiers
ts_verifiers
pruners
solvation
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rdmc.conformer_generation.pruners
=======================================

.. automodule:: rdmc.conformer_generation.pruners
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rdmc.conformer_generation.solvation
=======================================

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rdmc.conformer_generation.ts_verifiers
=======================================

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rdmc.conformer_generation.verifiers
=======================================

.. automodule:: rdmc.conformer_generation.verifiers
:members:
:undoc-members:
:show-inheritance:
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Utils
=====================================

.. automodule:: rdmc.conformer_generation.utils
:members:
:undoc-members:
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rdmc.conformer_generation.generators
=====================================

.. automodule:: rdmc.conformer_generation.generators
:members:
:undoc-members:
:show-inheritance:
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Workflow
=====================

.. toctree::
:maxdepth: 2

generators
ts_generators
metrics
sampler
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