doc/ref/load__protein__restrain__bonds_8py_source.html

 ## \example atom/load_protein_restrain_bonds.py

 # Load a protein from a PDB file and then restrain all the bonds to have their

 # current length.

 #


 from __future__ import print_function

 import IMP.atom

 import IMP.container

 import sys


 IMP.setup_from_argv(sys.argv, "load protein restrain bonds")


 m = IMP.Model()

 prot = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m)

 IMP.atom.add_bonds(prot)

 bds = IMP.atom.get_internal_bonds(prot)

 bl = IMP.container.ListSingletonContainer(m, bds)

 h = IMP.core.Harmonic(0, 1)

 bs = IMP.atom.BondSingletonScore(h)

 br = IMP.container.SingletonsRestraint(bs, bl)

 print(br.evaluate(False))

IMP::container::SingletonsRestraint
Applies a SingletonScore to each Singleton in a list.
Definition: SingletonsRestraint.h:34

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_internal_bonds
Bonds get_internal_bonds(Hierarchy mhd)
Get the bonds internal to this tree.

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::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::container::ListSingletonContainer
Store a list of ParticleIndexes.
Definition: ListSingletonContainer.h:33

IMP::atom::BondSingletonScore
Score the bond based on a UnaryFunction,.
Definition: BondSingletonScore.h:27

IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.

IMP::atom::add_bonds
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())

IMP::core::Harmonic
Harmonic function (symmetric about the mean)
Definition: core/Harmonic.h:24