chemdescriptor 0.2.0

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: git clone https://github.com/darkreactions/chemdescriptor

cd chemdescriptor

git checkout cxcalc_rewrite

pip install .

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] -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
  -o OUTPUT, --output OUTPUT
                        Path to output file

In code

The package will initially search cxcalc executable in the PATH variable if not will fall back to CXCALC_PATH

Set CXCALC_PATH

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

Import the generator class

from chemdescriptor.generator.chemaxon import ChemAxonDescriptorGenerator as CAG

Import SMILES and whitelist

with open('/path/to/SMILES/file', 'r') as f:
    smiles_list = f.read().splitlines()

with open('/path/to/descriptor/whitelist/json', 'r') as f:
    whitelist = json.load(f)

Instantiate a generator. smiles_list is a list of smiles and whitelist is a dictionary of keys in the command_dict logfile is the path to a log which contains information such as the final cxcalc command, columns that were renamed and other errors for debugging

cag = CAG(smiles_list,
          whitelist,
          ph_values=[6, 7, 8],
          command_dict={},
          logfile='/path/to/logfile')

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:

Descriptor whitelist is a python dictionary 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 in the whitelist where "descriptors" are generic and "ph_descriptors" are ph dependent descriptors

An optional dictionary can be passed to the ChemAxonDescriptorGenerator, "command_dict" which "translates" the above descriptor names into commands that ChemAxon cxcalc can understand.

It also consists of column names that will be added to the final output.

Note: If the command_dict is not given or is empty, a default command dict is used whose definition is here

An example of a command_dict is:

command_dict = {
    "descriptors": {
        "atomcount_c": {
            "command": [
                "atomcount",
                "-z",
                "6"
            ],
            "column_names": [
                "_feat_AtomCount_C"
            ]
        },
        "wateraccessiblesurfacearea": {
            "command": [
                "wateraccessiblesurfacearea"
            ],
            "column_names": [
                "_feat_ASA",
                "_feat_ASA+",
                "_feat_ASA-",
                "_feat_ASA_H",
                "_feat_ASA_P"
            ]
        }
    "ph_descriptors": {
        "acceptorcount": {
            "command": [
                "acceptorcount"
            ],
            "column_names": [
                "_feat_Hacceptorcount"
            ]
        },
        "donorcount": {
            "command": [
                "donorcount"
            ],
            "column_names": [
                "_feat_Hdonorcount"
            ]
        }
    }

command_dict consists of 2 dictionaries with keys descriptors and ph_descriptors. Within each dictionary are descriptor names referred in the whitelist.

Under each descriptor, two lists are required command and column_names

Command refers to the command line options for cxcalc as documented here Note: that commands with multiple words are entries in a list. For example, the command atomcount -z 6 is represented in the dictionary as ['atomcount', '-z', '6']

column_names is a list of names the user wants to rename the cxcalc generated csv column names.

Certain commands generate multiple columns for example, wateraccessiblesurfacearea generates 5 columns. Therefore, the column_names list becomes

"column_names": [
                "_feat_ASA",
                "_feat_ASA+",
                "_feat_ASA-",
                "_feat_ASA_H",
                "_feat_ASA_P"
            ]

Note : If the number of columns generated by cxcalc do not match the expected count, none of the column names are renamed.

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