PatWalters’s gists

PatWalters / split_complex.py

Last active August 30, 2024 14:57

Split a protein-ligand complex into protein and ligands and assign ligand bond orders using SMILES strings from Ligand Expo

	#!/usr/bin/env python

	# Split a protein-ligand complex into protein and ligands and assign ligand bond orders using SMILES strings from Ligand Export
	# Code requires Python 3.6

	import sys
	from prody import *
	import pandas as pd
	from rdkit import Chem
	from rdkit.Chem import AllChem

PatWalters / split_complex_v2.py

Created October 2, 2018 01:20

An improved script to extract a ligand from a protein-ligand complex and assign bond orders

	#!/usr/bin/env python

	import sys
	from prody import *
	from rdkit import Chem
	from rdkit.Chem import AllChem
	from io import StringIO
	import pypdb

PatWalters / dupe.py

Last active January 14, 2023 01:12

Compare two SMILES or SD files to identify duplicate structures. Duplicates are identified by comparing InChI keys

	#!/usr/bin/env python

	import sys
	import os
	from rdkit import Chem


	def molecule_supplier_from_name(input_file_name):
	ext = os.path.splitext(input_file_name)[-1]
	if ext == ".smi":

PatWalters / remove_dupe_confs.py

Last active February 20, 2019 01:05

PatWalters / rescale_bonds.ipynb

Created May 23, 2019 14:56

Rescale the bonds in a template molecule so that structures created by rdDepictor.GenerateDepictionMatching2DStructure appear reasonable

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