|
|
|
|
|
|
|
|
|
|
|
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) |
|
|