minimum number of ligand atoms is 3

get_pdb_ids.py

@@ -1,14 +0,0 @@
-from rcsbsearch import Terminal
-from rcsbsearch import rcsb_attributes as attrs
-
-# Create terminals for each query
-q1 = attrs.rcsb_entry_info.nonpolymer_entity_count > 0
-q2 = attrs.rcsb_entry_info.polymer_entity_count_protein > 0
-q3 = Terminal('chem_comp.formula_weight','greater_or_equal',150,service='text_chem')
-
-# combined using bitwise operators (&, |, ~, etc)
-query = q1 & q2 & q3  # AND of all queries
-
-# Call the query to execute it
-for assemblyid in query("entry"):
-    print(assemblyid)

parse_complexes.py

@@ -26,6 +26,9 @@ import os
 # minimum molecular weight to consider sth a ligand
 mol_wt_cutoff = 100
 
+# minimum number of atoms
+min_atoms = 3
+
 # all punctuation
 punctuation_regex  = r"""(\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""
 
@@ -148,8 +151,9 @@ def process_entry(df_dict, pdb_fn):
                 mol, template = process_ligand(ligand, res, df_dict)
 
                 mol_wt = ExactMolWt(template)
+                natoms = template.GetNumAtoms()
 
-                if mol_wt >= mol_wt_cutoff:
+                if mol_wt >= mol_wt_cutoff and natoms >= min_atoms:
                     ligand_mols.append(mol)
                     ligand_names.append(res)
 

split_complex.py

@@ -1,123 +0,0 @@
-#!/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)