alvaDescPy: A Python wrapper for alvaDesc software

alvaDescPy provides a Python wrapper for the alvaDesc molecular descriptor calculation software. It was created to allow direct access to the alvaDesc command-line interface via Python.

Important Notice:

Please note that alvaDescPy is an independent project and was not developed by Alvascience. You can find the official alvaDesc Python interface on Alvascience website: https://www.alvascience.com/python-alvadesc/.

Installation

Installation via pip:

$ pip install alvadescpy

Installation via cloned repository:

$ git clone https://github.com/ecrl/alvadescpy
$ cd alvadescpy
$ pip install .

There are currently no additional dependencies for alvaDescPy, however it requires a valid, licensed installation of alvaDesc.

Basic Usage

alvaDescPy assumes the location of alvaDesc's command-line interface is located at your OS's default location. If alvaDesc is located in a different location, you can change the path:

fromalvadescpyimportCONFIGCONFIG['alvadesc_path'] ='\\path\\to\\alvaDescCLI'

alvaDescPy provides direct access to all alvaDesc command line arguments via the "alvadesc" function:

fromalvadescpyimportalvadesc# providing an XML script filealvadesc(script='my_script.xml')
# supplying a SMILES string returns a list of descriptorsdescriptors=alvadesc(ismiles='CCC', descriptors='ALL')
# a Python dictionary is returned if labels are desireddescriptors=alvadesc(ismiles='CCC', descriptors='ALL', labels=True)
# specific descriptors can be calculateddescriptors=alvadesc(ismiles='CCC', descriptors=['MW', 'AMW'], labels=True)
# input/output files (and input type) can be specifiedalvadesc(
input_file='mols.mdl',
inputtype='MDL',
descriptors='ALL',
output='descriptors.txt'
)
# various fingerprints can be calculatedecfp=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 specifiedecfp=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 changeddescriptors=alvadesc(ismiles='CCC', descriptors='ALL', threads=4)

alvaDescPy also provides the "smiles_to_descriptors" function:

fromalvadescpyimportsmiles_to_descriptors# returns a list of descriptor valuesdescriptors=smiles_to_descriptors('CCC', descriptors='ALL')
# returns a dictionary of descriptor labels, valuesdescriptors=smiles_to_descriptors('CCC', descriptors='ALL', labels=True)
# returns a dictionary containing MW, AMW labels, valuesdescriptors=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).