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IMP Reference Guide  2.23.0
The Integrative Modeling Platform
version 2.23.0
spb_representation.h
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1 /**
2  * \file IMP/spb/spb_representation.h
3  * \brief SPB Representation
4  *
5  * Copyright 2007-2022 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPSPB_SPB_REPRESENTATION_H
10 #define IMPSPB_SPB_REPRESENTATION_H
11 
12 #include <IMP/spb/spb_config.h>
13 #include <IMP/container/ListSingletonContainer.h>
14 #include <IMP/core/MonteCarlo.h>
15 #include <IMP/atom/Hierarchy.h>
16 #include <IMP/atom/Molecule.h>
17 
18 IMPSPB_BEGIN_NAMESPACE
19 
20 IMPSPBEXPORT atom::Hierarchies create_representation(
21  Model *m, RestraintSet *allrs, spb::SPBParameters mydata,
22  container::ListSingletonContainer *CP_ps,
23  container::ListSingletonContainer *IL2_ps, core::MonteCarloMovers &mvs,
24  Particle *SideXY, Particle *SideZ, int iseed);
25 
26 IMPSPBEXPORT atom::Molecule create_protein(
27  Model *m, RestraintSet *allrs, std::string name, double mass, int nbeads,
28  display::Color color, int copy, double kappa, algebra::Vector3D x0,
29  bool use_connectivity, int start_residue = 1, int length = -1);
30 
31 IMPSPBEXPORT atom::Molecule create_protein(
32  Model *m, std::string name, std::string filename, int nbeads,
33  display::Color colore, int copy, algebra::Vector3D x0, int offset = 0,
34  bool makerigid = true);
35 
36 IMPSPBEXPORT atom::Molecule create_merged_protein(
37  Model *m, RestraintSet *allrs, std::string name, atom::Molecules proteins,
38  int copy, double kappa, double dist = -1.0);
39 
40 IMPSPBEXPORT void recenter_rb(core::RigidBody &rb, core::XYZRs &rbps,
41  algebra::Vector3D x0,
42  bool coiledcoil = false);
43 
44 IMPSPBEXPORT atom::Molecules create_coiled_coil(
45  Model *m, std::string name, std::string filename_A, std::string filename_B,
46  int nbeads, display::Color colore, int copy, algebra::Vector3D x0,
47  int offset = 0);
48 
49 IMPSPBEXPORT void load_restart(atom::Hierarchies &all_mol,
50  spb::SPBParameters mydata);
51 
52 IMPSPBEXPORT atom::Molecule create_GFP(
53  Model *m, std::string name, int copy,
54  container::ListSingletonContainer *lsc, algebra::Vector3D x0,
55  core::MonteCarloMovers &mvs, spb::SPBParameters mydata,
56  Particle *SideXY, Particle *SideZ);
57 
58 IMPSPB_END_NAMESPACE
59 
60 #endif /* IMPSPB_SPB_REPRESENTATION_H */
IMP::core::MonteCarloMovers
IMP::Vector< IMP::Pointer< MonteCarloMover > > MonteCarloMovers
Definition: MonteCarloMover.h:119
ListSingletonContainer.h
Store a list of ParticleIndexes.
MonteCarlo.h
Simple Monte Carlo optimizer.
Molecule.h
A decorator for Molecules.
Hierarchy.h
Decorator for helping deal with a hierarchy of molecules.
IMP::atom::create_protein
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
IMP::algebra::Vector3D
VectorD< 3 > Vector3D
Definition: VectorD.h:408