chemdescriptor 0.1.0

A standalone module to help generate molecular descriptors from various cheminformatics software

chemdescriptor - Molecular descriptor generator

Generic molecular descriptor generator wrapper around various software packages to simplify the process of getting descriptors

To install

Type:

pip install chemdescriptor

Requirements

1. Pandas
2. ChemAxon descriptors
   • Working copy of ChemAxon cxcalc
3. RDKit descriptors
   • RDKit installed

Usage

Currently only supports ChemAxon cxcalc and RDKit. The module can be expanded to cover other generators as well. Example input files can be found in the examples/ folder of this repo as well as the pip installed package.

CXCalc

Important! The code requires an environment variable CXCALC_PATH to be set, which points to the folder where cxcalc is installed!

Command Line

chemdescriptor-cx -m /path/to/SMILES/file -d /path/to/descriptor/whitelist/json -p 6.8 7.0 7.2 -o output.csv

usage: chemdescriptor-cx [-h] -m MOLECULE -d DESCRIPTORS -p PH [PH ...]
                         [-c COMMANDS] [-pc PHCOMMANDS] -o OUTPUT

optional arguments:
  -h, --help            show this help message and exit
  -m MOLECULE, --molecule MOLECULE
                        Path to input SMILES file
  -d DESCRIPTORS, --descriptors DESCRIPTORS
                        Path to descriptor white list json file
  -p PH [PH ...], --pH PH [PH ...]
                        List of pH values at which to calculate descriptors
  -c COMMANDS, --commands COMMANDS
                        Optional command stems for descriptors in json format
  -pc PHCOMMANDS, --phcommands PHCOMMANDS
                        Optional command stems for pH dependent descriptorsin
                        json format
  -o OUTPUT, --output OUTPUT
                        Path to output file

In code

Set CXCALC_PATH

import os
os.environ['CXCALC_PATH'] = '/path/to/cxcalc'

Import the generator class

from chemdescriptor import ChemAxonDescriptorGenerator

Instantiate a generator

cag = ChemAxonDescriptorGenerator('/path/to/SMILES/file',
                                  '/path/to/descriptor/whitelist/json',
                                  ph_values=[6, 7, 8],
                                  command_stems=None,
                                  ph_command_stems=None)

Generate csv output cag.generate('output.csv', dataframe=False, lec=False)

Optional keyword arguments for generate include dataframe boolean (default False) which returns a pandas dataframe in addition to writing a csv if True and lec boolean (default False) which converts the Smiles code to an intermediate "Low Energy Conformer (LEC)" representation before generating descriptors. A license is most likely required to generate LECs.

Notes:

Input SMILES file has a SMILES code in each line.

Descriptor whitelist is a json file of the form:

{
    "descriptors": [
        "refractivity",
        "maximalprojectionarea",
        "maximalprojectionradius",
        "maximalprojectionsize",
        "minimalprojectionarea",
        "minimalprojectionradius",
        "minimalprojectionsize"
    ],
    "ph_descriptors": [
        "avgpol",
        "molpol",
        "vanderwaals",
        "asa",
        "asa+",
        "asa-",
        "asa_hydrophobic",
        "asa_polar",
        "hbda_acc",
        "hbda_don",
        "polar_surface_area"
    ]
}

chemdescriptor expects 2 keys where "descriptors" are generic and "ph_descriptors" are ph dependent descriptors

2 optional dictionaries can be passed to the ChemAxonDescriptorGenerator, "command_stems" and "ph_command_stems". These dictionaries "translate" the above descriptors into commands that ChemAxon cxcalc can understand.

For example, if no value is passed to the ph_command_stems, the following dictionary is used:

_default_ph_command_stems = {
        'avgpol': 'avgpol',
        'molpol': 'molpol',
        'vanderwaals': 'vdwsa',
        'asa': ['molecularsurfacearea', '-t', 'ASA'],
        'asa+': ['molecularsurfacearea', '-t', 'ASA+'],
        'asa-': ['molecularsurfacearea', '-t', 'ASA-'],
        'asa_hydrophobic': ['molecularsurfacearea', '-t', 'ASA_H'],
        'asa_polar': ['molecularsurfacearea', '-t', 'ASA_P'],
        'hbda_acc': 'acceptorcount',
        'hbda_don': 'donorcount',
        'polar_surface_area': 'polarsurfacearea',
    }

Note that commands with multiple words are entries in a list. For example, the command

molecularsurfacearea -t ASA

is represented in the dictionary as ['molecularsurfacearea', '-t', 'ASA']

RDKit

Much easier to use. Only needs a list of descriptors similar to cxcalc.

To Do

[ ] Test on different machines

[ ] Get feedback on what needs to be changed/improved

[ ] Expand to cover other descriptor generators