IMP  2.3.1
The Integrative Modeling Platform
load_protein_restrain_bonds.py
1 ## \example atom/load_protein_restrain_bonds.py
2 # Load a protein from a PDB file and then restrain all the bonds to have their
3 # current length.
4 #
5 
6 import IMP.atom
7 import IMP.container
8 m = IMP.kernel.Model()
9 prot = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m)
10 IMP.atom.add_bonds(prot)
11 bds = IMP.atom.get_internal_bonds(prot)
12 bl = IMP.container.ListSingletonContainer(bds)
13 h = IMP.core.Harmonic(0, 1)
14 bs = IMP.atom.BondSingletonScore(h)
15 br = IMP.container.SingletonsRestraint(bs, bl)
16 m.add_restraint(br)
17 print m.evaluate(False)
IMP::container::SingletonsRestraint
Applies a SingletonScore to each Singleton in a list.
Definition: SingletonsRestraint.h:34
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 path to installed example data for this module.
IMP::container::ListSingletonContainer
Store a kernel::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::read_pdb
void read_pdb(base::TextInput input, int model, Hierarchy h)
IMP::atom::add_bonds
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73
IMP::core::Harmonic
Harmonic function (symmetric about the mean)
Definition: core/Harmonic.h:24