DESCRIPTION
===========
The molecular descriptors are widely used in the field of QSAR analysis.
The current project is designed to implement some of widely used descriptors.
Currently, the follwoing types of descriptors are available by `tools/calcDescriptors.exe`
1. constitutional (38)
2. electrostatic (64)
3. geometrical (14)
4. physico-chemical (1)
5. quantum-chemical (156)
6. topological (38)
For quantum-chemical descriptors, the Mopac output file is needed. For convenience,
the python script `tools/runMopac.py` is written to do semi-empirical QC calculation using
Mopac with necessary keywords.
While, the python script `tools/fingerprints.py` based on RDKit provides a convenient way
to generate fingerprints, e.g. ECFP, FCFP, MACCS.
Please refer to the `DEPENDENCE` section for the dependent libraries.
DEPENDENCE
==========
1. OpenBabel
- We use OpenBabel, which is the popular open source chemistry toolbox, to parse
molecule files. And the current program is compiled using OpenBabel version 2.3.2.
- main page: http://openbabel.org/wiki/Main_Page
sourceforge: http://sourceforge.net/projects/openbabel/
2. MOPAC7
- MOPAC7 is a semi-empirical quantum-mechanics code written by James J. P. Stewart
and co-workers. The purpose of this project is to maintain MOPAC7 as a stand-alone
program as well as a library that provides the functionality of MOPAC7 to other programs.
(copied from http://sourceforge.net/projects/mopac7/)
- sourceforge: http://sourceforge.net/projects/mopac7/
- the 'tools/mopac7.exe' is compiled from the source code using VS 2010.
3. RDKit
- a toolkit for cheminformatics and machine learning software.
- it has corresponding functions to generate fingerprints, and the python script
`tools/fingrprint.py` is just written to make it more convient.
- main page: http://www.rdkit.org/
sourceforge: http://sourceforge.net/projects/rdkit/
ATTENTION
=========
1. OpenBabel 2.3.2 should be installed in order to run `tools/calcDescriptors.exe`
2. the python wrappers of RDKit should be installed in order to run `tools/fingerprint.py`
CONTACT
=======
Xiaomin Luo
Professor at Shanghai Institute of Materia Medica, Chinese Academy of Sciences.
E-mail: xmluo@simm.ac.cn
Jianlong Peng
Ph.D. candidate
E-mail: pjlxsda@163.com; jlpeng1201@gmail.com
WEBSITE
=======
www.dddc.ac.cn/admetus