Hi Maciek, I want to create PLEC vectors without using OpenBabel at

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Calculating PLEC by bypassing completely OpenBabel,about oddt/oddt

mwojcikowski commented on June 25, 2024

Hi Thomas,

In oddt we have created additional module for such operations in RDKit in oddt.toolkits.extras.rdkit.fixer. Note it requires Chem.Mol, not oddt.Molecule.

from oddt.toolkits.extras.rdkit.fixer import ExtractPocketAndLigand
mol = Chem.MolFromPDBFile("complex_forscoring_frm.1.min.pdb", sanitize=False)
pocket, ligand = ExtractPocketAndLigand(mol, cutoff=12., ligand_residue='LIG')

Pocket and ligand are still Chem.Mol objects, which you can convert back to ODDT:

oddt_pocket = oddt.toolkit.Molecule(pocket)

If you wish to get wole protein you can set high cutoff.

oddt/oddt/toolkits/extras/rdkit/fixer.py

Lines 166 to 196 in 8cf5558

    
           def ExtractPocketAndLigand(mol, cutoff=12., expandResidues=True, 
        
                                      ligand_residue=None, ligand_residue_blacklist=None, 
        
                                      append_residues=None): 
        
               """Function extracting a ligand (the largest HETATM residue) and the protein 
        
               pocket within certain cutoff. The selection of pocket atoms can be expanded 
        
               to contain whole residues. The single atom HETATM residues are attributed 
        
               to pocket (metals and waters) 
        
               Parameters 
        
               ---------- 
        
                   mol: rdkit.Chem.rdchem.Mol 
        
                       Molecule with a protein ligand complex 
        
                   cutoff: float (default=12.) 
        
                       Distance cutoff for the pocket atoms 
        
                   expandResidues: bool (default=True) 
        
                       Expand selection to whole residues within cutoff. 
        
                   ligand_residue: string (default None) 
        
                       Residue name which explicitly pint to a ligand(s). 
        
                   ligand_residue_blacklist: array-like, optional (default None) 
        
                       List of residues to ignore during ligand lookup. 
        
                   append_residues: array-like, optional (default None) 
        
                       List of residues to append to pocket, even if they are HETATM, such 
        
                       as MSE, ATP, AMP, ADP, etc. 
        
               Returns 
        
               ------- 
        
                   pocket: rdkit.Chem.rdchem.RWMol 
        
                       Pocket constructed of protein residues/atoms around ligand 
        
                   ligand: rdkit.Chem.rdchem.RWMol 
        
                       Largest HETATM residue contained in input molecule 
        
               """

from oddt.

tevang commented on June 25, 2024

Hi Maciek,

I wrote the following function in line with your suggestion, but I get an error.

import oddt
from oddt.fingerprints import PLEC
from oddt.toolkits.extras.rdkit.fixer import ExtractPocketAndLigand
from rdkit import Chem


def calc_PLEC(complex_pdb, ligand_resname='LIG', cutoff=12.0, depth_ligand=2, depth_protein=4, distance_cutoff=4.5,
                        size=16384, count_bits=True, sparse=False, ignore_hoh=True):
    mol = Chem.MolFromPDBFile(complex_pdb, sanitize=False)
    pocket, ligand = ExtractPocketAndLigand(mol, cutoff=cutoff, ligand_residue=ligand_resname)
    oddt_protein = oddt.toolkit.Molecule(pocket)
    oddt_ligand = oddt.toolkit.Molecule(ligand)
    return PLEC(oddt_ligand, oddt_protein, depth_ligand=depth_ligand, depth_protein=depth_protein,
                    distance_cutoff=distance_cutoff,
                    size=size, count_bits=count_bits, sparse=sparse, ignore_hoh=ignore_hoh)

calc_PLEC('complex_forscoring_frm.1.min.pdb')

The input PDB file is this complex_forscoring_frm.1.min.pdb.gz and the error I get is the following:

RuntimeError: Pre-condition Violation
	RingInfo not initialized
	Violation occurred on line 66 in file Code/GraphMol/RingInfo.cpp
	Failed Expression: df_init
	RDKIT: 2019.03.4
	BOOST: 1_70

Do I need to upgrade RDKit or is it due to something else?

from oddt.

mwojcikowski commented on June 25, 2024

@tevang It looks like you need to sanitize the molecule first. Or at least generate rings with Chem.FastFindRings(...)

from oddt.

tevang commented on June 25, 2024

@mwojcikowski I use the following workaround that - at least seemingly - does not require sanitization or ring generation. Does it produce correct PLEC fingerprints?

def split_complex_pdb(complex_pdb, ligand_resname='LIG'):
    protein_f = open(complex_pdb.replace('.pdb', '_prot.pdb'), 'w')
    ligand_f = open(complex_pdb.replace('.pdb', '_lig.pdb'), 'w')
    with open(complex_pdb, 'r') as f:
        for line in f:
            if line[17:20] == ligand_resname:
                ligand_f.write(line)
            else:
                protein_f.write(line)
    protein_f.close()
    ligand_f.close()
    return protein_f.name, ligand_f.name


protein_pdb, ligand_pdb = split_complex_pdb(complex_pdb, ligand_resname)
oddt_protein = oddt.toolkit.Molecule(list(oddt.toolkit.readfile('pdb', protein_pdb, sanitize=False))[0])
oddt_ligand = oddt.toolkit.Molecule(list(oddt.toolkit.readfile('pdb', ligand_pdb, sanitize=False))[0])
plec_vector = PLEC(oddt_ligand, oddt_protein, depth_ligand=2, depth_protein=4, distance_cutoff=4.5,
                    size=16384, count_bits=True, sparse=False, ignore_hoh=True)

from oddt.

tevang commented on June 25, 2024

@mwojcikowski essentially my query is whether I am getting correct PLEC vectors without sanitizing the ligands or generating rings with FastFindRings() as you stated. Otherwise, it works.

from oddt.

mwojcikowski commented on June 25, 2024

@tevang I would say that sanitization is highly recommended. That said being consistent is the key for most use cases, so you might get away with it. Keep in mind that the input is also important (e.g. kekulization), that is why sanitization helps normalising the data.

from oddt.

Calculating PLEC by bypassing completely OpenBabel about oddt HOT 6 OPEN

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	def ExtractPocketAndLigand(mol, cutoff=12., expandResidues=True,
	ligand_residue=None, ligand_residue_blacklist=None,
	append_residues=None):
	"""Function extracting a ligand (the largest HETATM residue) and the protein
	pocket within certain cutoff. The selection of pocket atoms can be expanded
	to contain whole residues. The single atom HETATM residues are attributed
	to pocket (metals and waters)

	Parameters
	----------
	mol: rdkit.Chem.rdchem.Mol
	Molecule with a protein ligand complex
	cutoff: float (default=12.)
	Distance cutoff for the pocket atoms
	expandResidues: bool (default=True)
	Expand selection to whole residues within cutoff.
	ligand_residue: string (default None)
	Residue name which explicitly pint to a ligand(s).
	ligand_residue_blacklist: array-like, optional (default None)
	List of residues to ignore during ligand lookup.
	append_residues: array-like, optional (default None)
	List of residues to append to pocket, even if they are HETATM, such
	as MSE, ATP, AMP, ADP, etc.

	Returns
	-------
	pocket: rdkit.Chem.rdchem.RWMol
	Pocket constructed of protein residues/atoms around ligand
	ligand: rdkit.Chem.rdchem.RWMol
	Largest HETATM residue contained in input molecule
	"""