IMP  2.3.0
The Integrative Modeling Platform
coarse_molecule.h
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1 /**
2  * \file IMP/multifit/coarse_molecule.h
3  * \brief coarsen molecule by clustering
4  *
5  * Copyright 2007-2014 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPMULTIFIT_COARSE_MOLECULE_H
10 #define IMPMULTIFIT_COARSE_MOLECULE_H
11 
12 #include <IMP/atom/Hierarchy.h>
13 #include <IMP/em/DensityMap.h>
14 #include <IMP/multifit/multifit_config.h>
15 
16 IMPMULTIFIT_BEGIN_NAMESPACE
17 
18 //! Coarsen a molecule based on atom clustering
19 /**
20 \param[in] mh the molecule to coarsen
21 \param[in] num_beads the output number of beads
22 \param[in] mdl model to add the new molecule to
23 \param[in] bead_radius bead radius
24 \param[in] add_conn_restraint if true a connectivity restraint
25  between the particles of the new molecule is added
26  */
27 IMPMULTIFITEXPORT
29  const atom::Hierarchy &mh, int num_beads, kernel::Model *mdl,
30  float bead_radius, bool add_conn_restraint = false);
31 
32 //! Coarsen molecules based on atom clustering
33 /**
34 \param[in] mhs the molecules to coarsen
35 \param[in] frag_len the number of beads for each molecule will be
36  its number of residues / frag_len
37 \param[in] mdl model to add the new molecule to
38 \param[in] bead_radius bead radius
39 \param[in] add_conn_restraint if true a connectivity restraint
40  between the particles of the new molecule is added
41  */
42 IMPMULTIFITEXPORT
44  const atom::Hierarchies &mhs, int frag_len, kernel::Model *mdl,
45  float bead_radius, bool add_conn_restraint = false);
46 
47 //! Coarsen a density map based on voxels clustering
48 /**
49 \param[in] dmap the density map to coarsen
50 \param[in] dens_threshold use only voxels above this
51  threshold for clustering
52 \param[in] num_beads the number of beads
53 \param[in] mdl model to add the new molecule to
54 \param[in] bead_radius bead radius
55  */
56 IMPMULTIFITEXPORT
57 atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap,
58  float dens_threshold,
59  int num_beads,
60  kernel::Model *mdl,
61  float bead_radius);
62 
63 IMPMULTIFIT_END_NAMESPACE
64 
65 #endif /* IMPMULTIFIT_COARSE_MOLECULE_H */
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, kernel::Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.
Class for handling density maps.
Decorator for helping deal with a hierarchy of molecules.
IMP::kernel::Model Model
atom::Hierarchy create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, kernel::Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen a molecule based on atom clustering.
atom::Hierarchies create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, kernel::Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen molecules based on atom clustering.