conformer

Conformation generator with RDKit

This is a modified code of https://github.com/iwatobipen/rdk_confgen.git (https://iwatobipen.wordpress.com/)

Description

• This is simple script for generating conformers and tautomer from single molfiles
• This script generates conformers with MMFF94s/UFF FF which is implemented in rdkit

Requirements

• RDKit
• os
• datetime
• argparse

Install

$ git clone https://github.com/spectroscop/conformer.git
$ cd conformer
$ pip install -e .

Basic usage

• User need to prepare input molfile as a template.
• Then run conformer command (with deafault settings)

$ python conformer.py -i ./sample/ligand.mol -o ./sample
## UFF
$ python conformer.py -i ./sample/ligand.mol -o ./sample -f UFF
## tautomer 
$ python conformer.py -i ./sample/ligand.mol -o ./sample -t true
## stereomer 
$ python conformer.py -i ./sample/ligand.mol -o ./sample/ -s true 
## RMSD
$ python conformer.py -i ./sample/ligand.mol -o ./sample -r 0.9
## macrocycle
$ python conformer.py -i ./sample/ligand.mol -o ./sample -c 30
## number of conformers per structure
$ python conformer.py -i ./sample/ligand.mol -o ./sample -m true
## not write FF energy
$ python conformer.py -i ./sample/ligand.mol -o ./sample -a false

Useful informations

• Coformer Generation using RDKit
• Freely Available Conformer Generation Methods: How Good Are They?