minimum number of ligand atoms is 3
Browse files- get_pdb_ids.py +0 -14
- parse_complexes.py +5 -1
- split_complex.py +0 -123
get_pdb_ids.py
DELETED
@@ -1,14 +0,0 @@
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from rcsbsearch import Terminal
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from rcsbsearch import rcsb_attributes as attrs
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# Create terminals for each query
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q1 = attrs.rcsb_entry_info.nonpolymer_entity_count > 0
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q2 = attrs.rcsb_entry_info.polymer_entity_count_protein > 0
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q3 = Terminal('chem_comp.formula_weight','greater_or_equal',150,service='text_chem')
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# combined using bitwise operators (&, |, ~, etc)
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query = q1 & q2 & q3 # AND of all queries
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# Call the query to execute it
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for assemblyid in query("entry"):
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print(assemblyid)
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parse_complexes.py
CHANGED
@@ -26,6 +26,9 @@ import os
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# minimum molecular weight to consider sth a ligand
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mol_wt_cutoff = 100
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# all punctuation
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punctuation_regex = r"""(\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""
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@@ -148,8 +151,9 @@ def process_entry(df_dict, pdb_fn):
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mol, template = process_ligand(ligand, res, df_dict)
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mol_wt = ExactMolWt(template)
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if mol_wt >= mol_wt_cutoff:
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ligand_mols.append(mol)
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ligand_names.append(res)
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# minimum molecular weight to consider sth a ligand
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mol_wt_cutoff = 100
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# minimum number of atoms
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min_atoms = 3
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# all punctuation
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punctuation_regex = r"""(\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""
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mol, template = process_ligand(ligand, res, df_dict)
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mol_wt = ExactMolWt(template)
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natoms = template.GetNumAtoms()
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if mol_wt >= mol_wt_cutoff and natoms >= min_atoms:
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ligand_mols.append(mol)
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ligand_names.append(res)
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split_complex.py
DELETED
@@ -1,123 +0,0 @@
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#!/usr/bin/env python
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# Split a protein-ligand complex into protein and ligands and assign ligand bond orders using SMILES strings from Ligand Export
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# Code requires Python 3.6
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import sys
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from prody import *
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import pandas as pd
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from rdkit import Chem
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from rdkit.Chem import AllChem
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from io import StringIO
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import requests
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def read_ligand_expo():
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"""
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Read Ligand Expo data, try to find a file called
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Components-smiles-stereo-oe.smi in the current directory.
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If you can't find the file, grab it from the RCSB
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:return: Ligand Expo as a dictionary with ligand id as the key
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"""
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file_name = "Components-smiles-stereo-oe.smi"
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try:
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df = pd.read_csv(file_name, sep="\t",
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header=None,
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names=["SMILES", "ID", "Name"])
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except FileNotFoundError:
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url = f"http://ligand-expo.rcsb.org/dictionaries/{file_name}"
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print(url)
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r = requests.get(url, allow_redirects=True)
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open('Components-smiles-stereo-oe.smi', 'wb').write(r.content)
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df = pd.read_csv(file_name, sep="\t",
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header=None,
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names=["SMILES", "ID", "Name"])
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df.set_index("ID", inplace=True)
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return df.to_dict()
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def get_pdb_components(pdb_id):
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"""
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Split a protein-ligand pdb into protein and ligand components
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:param pdb_id:
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:return:
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"""
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pdb = parsePDB(pdb_id)
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protein = pdb.select('protein')
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ligand = pdb.select('not protein and not water')
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return protein, ligand
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def process_ligand(ligand, res_name, expo_dict):
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"""
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Add bond orders to a pdb ligand
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1. Select the ligand component with name "res_name"
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2. Get the corresponding SMILES from the Ligand Expo dictionary
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3. Create a template molecule from the SMILES in step 2
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4. Write the PDB file to a stream
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5. Read the stream into an RDKit molecule
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6. Assign the bond orders from the template from step 3
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:param ligand: ligand as generated by prody
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:param res_name: residue name of ligand to extract
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:param expo_dict: dictionary with LigandExpo
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:return: molecule with bond orders assigned
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"""
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output = StringIO()
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sub_mol = ligand.select(f"resname {res_name}")
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sub_smiles = expo_dict['SMILES'][res_name]
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template = AllChem.MolFromSmiles(sub_smiles)
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writePDBStream(output, sub_mol)
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pdb_string = output.getvalue()
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rd_mol = AllChem.MolFromPDBBlock(pdb_string)
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new_mol = AllChem.AssignBondOrdersFromTemplate(template, rd_mol)
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return new_mol
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def write_pdb(protein, pdb_name):
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"""
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Write a prody protein to a pdb file
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:param protein: protein object from prody
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:param pdb_name: base name for the pdb file
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:return: None
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"""
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output_pdb_name = f"{pdb_name}_protein.pdb"
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writePDB(f"{output_pdb_name}", protein)
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print(f"wrote {output_pdb_name}")
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def write_sdf(new_mol, pdb_name, res_name):
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"""
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Write an RDKit molecule to an SD file
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:param new_mol:
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:param pdb_name:
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:param res_name:
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:return:
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"""
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outfile_name = f"{pdb_name}_{res_name}_ligand.sdf"
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writer = Chem.SDWriter(f"{outfile_name}")
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writer.write(new_mol)
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print(f"wrote {outfile_name}")
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def main(pdb_name):
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"""
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Read Ligand Expo data, split pdb into protein and ligands,
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write protein pdb, write ligand sdf files
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:param pdb_name: id from the pdb, doesn't need to have an extension
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:return:
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"""
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df_dict = read_ligand_expo()
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protein, ligand = get_pdb_components(pdb_name)
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write_pdb(protein, pdb_name)
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res_name_list = list(set(ligand.getResnames()))
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for res in res_name_list:
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new_mol = process_ligand(ligand, res, df_dict)
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write_sdf(new_mol, pdb_name, res)
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if __name__ == "__main__":
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if len(sys.argv) == 2:
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main(sys.argv[1])
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else:
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print("Usage: {sys.argv[1]} pdb_id", file=sys.stderr)
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