IMP logo
IMP Reference Guide  2.13.0
The Integrative Modeling Platform
helpers.h
Go to the documentation of this file.
1 /**
2  * \file IMP/kinematics/helpers.h
3  * \brief
4  *
5  * \authors Dina Schneidman
6  * Copyright 2007-2020 IMP Inventors. All rights reserved.
7  *
8  */
9 
10 #ifndef IMPKINEMATICS_HELPERS_H
11 #define IMPKINEMATICS_HELPERS_H
12 
13 #include "kinematics_config.h"
14 
15 #include <IMP/atom/Atom.h>
16 #include <IMP/atom/Residue.h>
17 
18 #include <boost/algorithm/string.hpp>
19 
20 IMPKINEMATICS_BEGIN_NAMESPACE
21 
22 IMPKINEMATICSEXPORT
23 IMP::atom::Atom find_atom(const IMP::ParticlesTemp& atoms, int input_index);
24 
25 IMPKINEMATICSEXPORT
26 IMP::atom::Residue find_residue(const IMP::ParticlesTemp& residues,
27  int res_index, std::string chain);
28 
29 IMPKINEMATICSEXPORT
30 IMP::atom::Atom get_ca_atom(const IMP::ParticlesTemp& atoms,
31  int residue_index, std::string chain_id);
32 
33 IMPKINEMATICSEXPORT
34 void read_connect_chains_file(const std::string& file_name,
35  const IMP::ParticlesTemp& atoms,
36  std::vector<IMP::atom::Atoms>& connect_atoms);
37 
38 IMPKINEMATICSEXPORT
39 void read_angle_file(const std::string& file_name,
40  const IMP::ParticlesTemp& residues,
41  const IMP::ParticlesTemp& atoms,
42  IMP::atom::Residues& flexible_residues,
43  std::vector<IMP::atom::Atoms>& dihedral_angles);
44 
45 IMPKINEMATICSEXPORT
47 
48 IMPKINEMATICSEXPORT
49 void add_missing_bonds(IMP::ParticlesTemp& atoms, IMP::ParticlesTemp& bonds);
50 
51 IMPKINEMATICS_END_NAMESPACE
52 
53 #endif /* IMPKINEMATICS_HELPERS_H */
Simple atom decorator.
A decorator for wrapping a particle representing a molecular bond.
A decorator for a particle representing an atom.
Definition: atom/Atom.h:234
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
A decorator for Residues.
A decorator for a residue.
Definition: Residue.h:135