IMP  2.0.0
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 2007-2013 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
28 atom::Hierarchy create_coarse_molecule_from_molecule(
29  const atom::Hierarchy &mh,int num_beads,
30  Model *mdl,
31  float bead_radius,
32  bool add_conn_restraint = false);
33 
34 //! Coarsen molecules based on atom clustering
35 /**
36 \param[in] mhs the molecules to coarsen
37 \param[in] frag_len the number of beads for each molecule will be
38  its number of residues / frag_len
39 \param[in] mdl model to add the new molecule to
40 \param[in] bead_radius bead radius
41 \param[in] add_conn_restraint if true a connectivity restraint
42  between the particles of the new molecule is added
43  */
44 IMPMULTIFITEXPORT
45 atom::Hierarchies create_coarse_molecules_from_molecules(
46  const atom::Hierarchies &mhs,
47  int frag_len,
48  Model *mdl,
49  float bead_radius,
50  bool add_conn_restraint = false);
51 
52 //! Coarsen a density map based on voxels clustering
53 /**
54 \param[in] dmap the density map to coarsen
55 \param[in] dens_threshold use only voxels above this
56  threshold for clustering
57 \param[in] num_beads the number of beads
58 \param[in] mdl model to add the new molecule to
59 \param[in] bead_radius bead radius
60  */
61 IMPMULTIFITEXPORT
62 atom::Hierarchy create_coarse_molecule_from_density(
63  em::DensityMap *dmap,
64  float dens_threshold,
65  int num_beads,
66  Model *mdl,
67  float bead_radius);
68 
69 IMPMULTIFIT_END_NAMESPACE
70 
71 #endif /* IMPMULTIFIT_COARSE_MOLECULE_H */