Initial documentation upload

Author: Kessler

README.md

@@ -1,2 +1,111 @@
-# alvaDescPy
-Python wrapper for alvaDesc software
+[![UML Energy & Combustion Research Laboratory](http://faculty.uml.edu/Hunter_Mack/uploads/9/7/1/3/97138798/1481826668_2.png)](http://faculty.uml.edu/Hunter_Mack/)
+
+# alvaDescPy: A Python wrapper for alvaDesc software
+
+[![GitHub version](https://badge.fury.io/gh/ecrl%2Falvadescpy.svg)](https://badge.fury.io/gh/ecrl%2Falvadescpy)
+[![PyPI version](https://badge.fury.io/py/alvadescpy.svg)](https://badge.fury.io/py/alvadescpy)
+[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/ecrl/alvadescpy/master/LICENSE.txt)
+
+alvaDescPy provides a Python wrapper for the [alvaDesc](https://www.alvascience.com/alvadesc/) molecular descriptor calculation software. It was created to allow direct access to the alvaDesc command-line interface via Python.
+
+## Installation
+
+Installation via pip:
+
+```
+$ pip install alvadescpy
+```
+
+Installation via cloned repository:
+
+```
+$ git clone https://github.com/ecrl/alvadescpy
+$ cd alvadescpy
+$ python setup.py install
+```
+
+There are currently no additional dependencies for alvaDescPy, however it requires a valid, licensed installation of [alvaDesc](https://www.alvascience.com/alvadesc/).
+
+## Basic Usage
+
+alvaDescPy assumes the location of alvaDesc's command-line interface is located at ```C:\Program Files\Alvascience\alvaDesc\alvaDescCLI.exe```. If alvaDesc is located in a different location, you can change the path:
+
+```python
+from alvadescpy import ALVADESC_PATH
+
+ALVADESC_PATH = '\\path\\to\\alvaDescCLI.exe'
+```
+
+alvaDescPy provides direct access to all alvaDesc command line arguments via the "alvadesc" function:
+
+```python
+from alvadescpy import alvadesc
+
+# providing an XML script file
+alvadesc(script='my_script.xml')
+
+# supplying a SMILES string returns a list of descriptors
+descriptors = alvadesc(ismiles='CCC', descriptors='ALL')
+
+# a Python dictionary is returned if labels are desired
+descriptors = alvadesc(ismiles='CCC', descriptors='ALL', labels=True)
+
+# specific descriptors can be calculated
+descriptors = alvadesc(ismiles='CCC', descriptors=['MW', 'AMW'], labels=True)
+
+# input/output files (and input type) can be specified
+alvadesc(
+    input_file='mols.mdl',
+    inputtype='MDL',
+    descriptors='ALL',
+    output='descriptors.txt'
+)
+
+# various fingerprints can be calculated
+ecfp = alvadesc(ismiles='CCC', ecfp=True)
+pfp = alvadesc(ismiles='CCC', pfp=True)
+maccsfp = alvadesc(ismiles='CCC', pfp=True)
+
+# fingerprint hash size, min/max fragment length, bits/pattern and other
+#   options can be specified
+ecfp = alvadesc(
+    ismiles='CCC',
+    ecfp=True,
+    fpsize=2048,
+    fpmin=1,
+    fpmax=4,
+    bits=4,
+    fpoptions='- Additional Options -'
+)
+
+# alvaDesc uses a number of threads equal to the maximum number of CPUs, but
+#   can be changed
+descriptors=alvadesc(ismiles='CCC', descriptors='ALL', threads=4)
+```
+
+alvaDescPy also provides the "smiles_to_descriptors" function:
+
+```python
+from alvadescpy import smiles_to_descriptors
+
+# returns a list of descriptor values
+descriptors = smiles_to_descriptors('CCC', descriptors='ALL')
+
+# returns a dictionary of descriptor labels, values
+descriptors = smiles_to_descriptors('CCC', descriptors='ALL', labels=True)
+
+# returns a dictionary containing MW, AMW labels, values
+descriptors = smiles_to_descriptors(
+    'CCC',
+    descriptors=['MW', 'AMW'],
+    labels=True
+)
+```
+
+## Contributing, Reporting Issues and Other Support
+
+To contribute to alvaDescPy, make a pull request. Contributions should include tests for new features added, as well as extensive documentation.
+
+To report problems with the software or feature requests, file an issue. When reporting problems, include information such as error messages, your OS/environment and Python version.
+
+For additional support/questions, contact Travis Kessler (Travis_Kessler@student.uml.edu).