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#!/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
from io import StringIO
import requests
def read_ligand_expo():
"""
Read Ligand Expo data, try to find a file called
Components-smiles-stereo-oe.smi in the current directory.
If you can't find the file, grab it from the RCSB
:return: Ligand Expo as a dictionary with ligand id as the key
"""
file_name = "Components-smiles-stereo-oe.smi"
try:
df = pd.read_csv(file_name, sep="\t",
header=None,
names=["SMILES", "ID", "Name"])
except FileNotFoundError:
url = f"http://ligand-expo.rcsb.org/dictionaries/{file_name}"
print(url)
r = requests.get(url, allow_redirects=True)
open('Components-smiles-stereo-oe.smi', 'wb').write(r.content)
df = pd.read_csv(file_name, sep="\t",
header=None,
names=["SMILES", "ID", "Name"])
df.set_index("ID", inplace=True)
return df.to_dict()
def get_pdb_components(pdb_id):
"""
Split a protein-ligand pdb into protein and ligand components
:param pdb_id:
:return:
"""
pdb = parsePDB(pdb_id)
protein = pdb.select('protein')
ligand = pdb.select('not protein and not water')
return protein, ligand
def process_ligand(ligand, res_name, expo_dict):
"""
Add bond orders to a pdb ligand
1. Select the ligand component with name "res_name"
2. Get the corresponding SMILES from the Ligand Expo dictionary
3. Create a template molecule from the SMILES in step 2
4. Write the PDB file to a stream
5. Read the stream into an RDKit molecule
6. Assign the bond orders from the template from step 3
:param ligand: ligand as generated by prody
:param res_name: residue name of ligand to extract
:param expo_dict: dictionary with LigandExpo
:return: molecule with bond orders assigned
"""
output = StringIO()
sub_mol = ligand.select(f"resname {res_name}")
sub_smiles = expo_dict['SMILES'][res_name]
template = AllChem.MolFromSmiles(sub_smiles)
writePDBStream(output, sub_mol)
pdb_string = output.getvalue()
rd_mol = AllChem.MolFromPDBBlock(pdb_string)
new_mol = AllChem.AssignBondOrdersFromTemplate(template, rd_mol)
return new_mol
def write_pdb(protein, pdb_name):
"""
Write a prody protein to a pdb file
:param protein: protein object from prody
:param pdb_name: base name for the pdb file
:return: None
"""
output_pdb_name = f"{pdb_name}_protein.pdb"
writePDB(f"{output_pdb_name}", protein)
print(f"wrote {output_pdb_name}")
def write_sdf(new_mol, pdb_name, res_name):
"""
Write an RDKit molecule to an SD file
:param new_mol:
:param pdb_name:
:param res_name:
:return:
"""
outfile_name = f"{pdb_name}_{res_name}_ligand.sdf"
writer = Chem.SDWriter(f"{outfile_name}")
writer.write(new_mol)
print(f"wrote {outfile_name}")
def main(pdb_name):
"""
Read Ligand Expo data, split pdb into protein and ligands,
write protein pdb, write ligand sdf files
:param pdb_name: id from the pdb, doesn't need to have an extension
:return:
"""
df_dict = read_ligand_expo()
protein, ligand = get_pdb_components(pdb_name)
write_pdb(protein, pdb_name)
res_name_list = list(set(ligand.getResnames()))
for res in res_name_list:
new_mol = process_ligand(ligand, res, df_dict)
write_sdf(new_mol, pdb_name, res)
if __name__ == "__main__":
if len(sys.argv) == 2:
main(sys.argv[1])
else:
print("Usage: {sys.argv[1]} pdb_id", file=sys.stderr)
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