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IMP Reference Guide  2.11.1
The Integrative Modeling Platform
assess_dope.py
1 ## \example atom/assess_dope.py
2 # The script shows how to assess a protein conformation using DOPE.
3 
4 from __future__ import print_function
5 import IMP
6 import IMP.atom
7 import IMP.container
8 import sys
9 
10 IMP.setup_from_argv(sys.argv, "assess dope")
11 
12 def create_representation():
13  m = IMP.Model()
14  mp0 = IMP.atom.read_pdb(IMP.atom.get_example_path(
15  '1fdx.B99990001.pdb'), m, IMP.atom.NonWaterNonHydrogenPDBSelector())
16  prot = IMP.atom.get_by_type(mp0, IMP.atom.CHAIN_TYPE)[0]
17  return (m, prot)
18 
19 
20 def add_dope(m, prot):
21  ps = IMP.atom.get_by_type(prot, IMP.atom.ATOM_TYPE)
22  for p in ps:
23  if not IMP.atom.Atom.get_is_setup(p):
24  print("Huh?", p)
25  dpc = IMP.container.ClosePairContainer(ps, 15.0, 0.0)
26 # exclude pairs of atoms belonging to the same residue
27 # for consistency with MODELLER DOPE score
28  f = IMP.atom.SameResiduePairFilter()
29  dpc.add_pair_filter(f)
30  IMP.atom.add_dope_score_data(prot)
31  dps = IMP.atom.DopePairScore(15.0)
32 # dps= IMP.membrane.DopePairScore(15.0, IMP.membrane.get_data_path("dope_scorehr.lib"))
33  d = IMP.container.PairsRestraint(dps, dpc)
34  return d
35 
36 print("creating representation")
37 (m, prot) = create_representation()
38 
39 print("creating DOPE score function")
40 d = add_dope(m, prot)
41 
42 IMP.set_check_level(IMP.USAGE)
43 print("DOPE SCORE ::", d.evaluate(False))
IMP::atom::NonWaterNonHydrogenPDBSelector
Select non water and non hydrogen atoms.
Definition: pdb.h:245
IMP::atom::Atom::get_is_setup
static bool get_is_setup(const IMP::ParticleAdaptor &p)
Definition: atom/Atom.h:241
IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
IMP::container
Various classes to hold sets of particles.
IMP::atom::get_example_path
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
IMP::container::ClosePairContainer
Return all close unordered pairs of particles taken from the SingletonContainer.
Definition: ClosePairContainer.h:63
IMP::atom::read_pdb
void read_pdb(TextInput input, int model, Hierarchy h)
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72
IMP::atom::add_dope_score_data
void add_dope_score_data(atom::Hierarchy h)
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::container::PairsRestraint
Applies a PairScore to each Pair in a list.
Definition: PairsRestraint.h:34
IMP::set_check_level
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73