atom/score_protein_with_ligand.py

Show how to score a number of ligand conformations loaded from a file against a protein loaded from a pdb.

## \example atom/score_protein_with_ligand.py
# Show how to score a number of ligand conformations loaded from a file
# against a protein loaded from a pdb.

import IMP.atom

m = IMP.kernel.Model()
IMP.base.set_check_level(IMP.base.NONE)
protein = IMP.atom.read_pdb(IMP.atom.get_example_path('1d3d-protein.pdb'), m)
protein_atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE)
ligands = IMP.atom.read_mol2(IMP.atom.get_example_path('1d3d-ligands.mol2'), m)
# create the score which applies to a pair of atoms
ps = IMP.atom.ProteinLigandAtomPairScore()
ps.set_was_used(True)
# label each atom of the protein with the type needed for scoring
IMP.atom.add_protein_ligand_score_data(protein)
for l in ligands.get_children():
    # compute the atom type for each ligand atom
    IMP.atom.add_protein_ligand_score_data(l)
    score = 0
    ligand_atoms = IMP.atom.get_by_type(l, IMP.atom.ATOM_TYPE)
    for pa in protein_atoms:
        for la in ligand_atoms:
            # check if the atoms are close enough together
            if IMP.core.get_distance(IMP.core.XYZ(pa), IMP.core.XYZ(la)) < 15:
                # score one pair of atoms
                score += ps.evaluate((pa, la), None)
    print "score for ", l.get_name(), "is", score