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Patrick Walters PatWalters

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PatWalters / split_complex.py
Last active September 20, 2023 02:34
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
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
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
PatWalters / remove_dupe_confs.py
Last active February 20, 2019 01:05
#!/usr/bin/env python
import sys
from rdkit import Chem
from tqdm import tqdm
import pandas as pd
import math
def in_place_rmsd(mol_1, mol_2):
@PatWalters
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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@PatWalters
PatWalters / wine_with_stats.ipynb
Created May 19, 2020 01:19
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@PatWalters
PatWalters / compare_rocs_plec.ipynb
Created May 30, 2020 19:45
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@PatWalters
PatWalters / rule_of_five.ipynb
Last active May 31, 2020 02:13
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@PatWalters
PatWalters / ChEMBL_examples.ipynb
Last active August 31, 2020 23:47
A few ChEMBL query examples
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@PatWalters
PatWalters / chembl_drugs.smi
Last active August 31, 2020 23:56
Compare some similarity metrics
Br.CC(NC(C)(C)C)C(=O)c1cccc(Cl)c1 675686
Br.Cc1ccc(Sc2ccccc2N3CCNCC3)c(C)c1 1379657
Br.CN(C)CCCC1(OCc2cc(ccc12)C#N)c3ccc(F)cc3 674732
Br.CN1CCC[C@@H]1Cc2c[nH]c3ccc(CCS(=O)(=O)c4ccccc4)cc23 674954
Br.COc1ccc2CN(C)CC[C@@]34C=C[C@H](O)C[C@@H]3Oc1c24 443255
Br.NC(=O)C([C@@H]1CCN(CCc2ccc3OCCc3c2)C1)(c4ccccc4)c5ccccc5 674886
BrCCC(=O)N1CCN(CC1)C(=O)CCBr 453722
C#CCN[C@@H]1CCc2ccccc12 75752
c1ccc2[nH]c(nc2c1)c3cscn3 26590
C1CN2C[C@@H](N=C2S1)c3ccccc3 384948