working on rst

docs/cctk.rst

@@ -11,14 +11,6 @@ Subpackages
 Submodules
 ----------
 
-cctk.DEPRECATED\_cctk module
-----------------------------
-
-.. automodule:: cctk.DEPRECATED_cctk
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 cctk.ensemble module
 --------------------
 

docs/index.rst

@@ -10,6 +10,10 @@ Welcome to cctk's documentation!
    :maxdepth: 4
    :caption: Contents:
 
+   intro
+   molecule
+   file_io
+   groups
    cctk
 
 

docs/intro.rst

@@ -0,0 +1,70 @@
+====
+cctk
+====
+
+computational chemistry toolkit
+====
+
+Overview:
+____
+
+*cctk* is an open-source Python 3 package designed to automate generation and analysis of computational chemistry files. 
+
+Potential uses for *cctk* include:
+
+- Monitoring one or many geometry optimizations.
+- Extracting geometry from output files, changing geometric parameters, and creating new input files.
+- Calculating molecular properties (e.g. NICS) along a reaction coordinate.
+- Screening different functionals and basis sets.
+- Generating potential energy surfaces in one or more dimensions (e.g. More O'Ferrall-Jencks plots).
+
+Compatible Filetypes:
+____
+
+Currently *cctk* supports:
+
+- Gaussian 16 ``.out`` (read) and ``.gjf`` (read/write).
+- ``.xyz`` (read/write)
+- ``.mol2`` (read)
+- ``.mae`` (read)
+- Orca ``.inp`` (write)
+
+We hope to add more filetypes in future releases. 
+
+Installation:
+____
+
+*cctk* requires ``numpy``, ``networkx``, and ``importlib_resources``. A full list of requirements can be found in ``env.yml``.
+
+**Installing with a working Python 3.7+ environment:**
+
+Simply run:
+
+``$ pip install cctk``
+
+**Installing without a working Python 3.7+ environment:**
+
+If you have a different version of Python (e.g. Python 2.7), you can use a ``conda`` environment to run *cctk* without breaking existing packages.
+
+1. Install ``conda``/``miniconda``.
+2. Use ``env.yml`` to create a Conda environment called ``cctk`` and install *cctk*:
+
+``$ cd cctk
+$ conda env create -f env.yml``
+
+Now, run ``conda activate cctk`` to enter the ``cctk`` Python environment (and ``conda deactivate`` to leave). (More complete guides to ``conda`` usage can be found elsewhere.)
+
+Authors:
+____
+*cctk* was written by Corin Wagen and Eugene Kwan at the Department of Chemistry and Chemical Biology at Harvard University. 
+Please email ``cwagen@g.harvard.edu`` with any questions or bug reports; we will do our best!
+
+How to Cite:
+____
+Wagen, C.C.; Kwan, E.E. *cctk* 2020, www.github.com/ekwan/cctk.
+
+License:
+____
+This project is licensed under the Apache License, Version 2.0.
+
+*Copyright 2020 by Corin Wagen and Eugene Kwan*