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IMP Reference Guide  2.20.2
The Integrative Modeling Platform
score_protein_with_ligand.py
1 ## \example atom/score_protein_with_ligand.py
2 # Show how to score a number of ligand conformations loaded from a file
3 # against a protein loaded from a pdb.
4 
5 from __future__ import print_function
6 import IMP.atom
7 import sys
8 
9 IMP.setup_from_argv(sys.argv, "score protein with ligand")
10 
11 m = IMP.Model()
12 IMP.set_check_level(IMP.NONE)
13 protein = IMP.atom.read_pdb(IMP.atom.get_example_path('1d3d-protein.pdb'), m)
14 protein_atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE)
15 ligands = IMP.atom.read_mol2(IMP.atom.get_example_path('1d3d-ligands.mol2'), m)
16 # create the score which applies to a pair of atoms
18 ps.set_was_used(True)
19 # label each atom of the protein with the type needed for scoring
21 for cl in ligands.get_children():
22  # compute the atom type for each ligand atom
24  score = 0
25  ligand_atoms = IMP.atom.get_by_type(cl, IMP.atom.ATOM_TYPE)
26  for pa in protein_atoms:
27  for la in ligand_atoms:
28  # check if the atoms are close enough together
30  # score one pair of atoms
31  score += ps.evaluate_index(m,
32  (pa.get_particle_index(),
33  la.get_particle_index()), None)
34  print("score for ", cl.get_name(), "is", score)
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
double get_distance(XYZR a, XYZR b)
Compute the sphere distance between a and b.
Definition: XYZR.h:89
void read_pdb(TextInput input, int model, Hierarchy h)
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
void add_protein_ligand_score_data(Hierarchy h)
Functionality for loading, creating, manipulating and scoring atomic structures.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:72