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IMP Reference Guide  2.5.0
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 2007-2015 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 \deprecated_at{2.5} Unused and will be removed.
21 \param[in] mh the molecule to coarsen
22 \param[in] num_beads the output number of beads
23 \param[in] mdl model to add the new molecule to
24 \param[in] bead_radius bead radius
25 \param[in] add_conn_restraint if true a connectivity restraint
26  between the particles of the new molecule is added
27  */
28 IMPMULTIFITEXPORT
29 IMPMULTIFIT_DEPRECATED_FUNCTION_DECL(2.5)
31  const atom::Hierarchy &mh, int num_beads, Model *mdl,
32  float bead_radius, bool add_conn_restraint = false);
33 
34 //! Coarsen molecules based on atom clustering
35 /**
36 \deprecated_at{2.5} Unused and will be removed.
37 \param[in] mhs the molecules to coarsen
38 \param[in] frag_len the number of beads for each molecule will be
39  its number of residues / frag_len
40 \param[in] mdl model to add the new molecule to
41 \param[in] bead_radius bead radius
42 \param[in] add_conn_restraint if true a connectivity restraint
43  between the particles of the new molecule is added
44  */
45 IMPMULTIFITEXPORT
46 IMPMULTIFIT_DEPRECATED_FUNCTION_DECL(2.5)
48  const atom::Hierarchies &mhs, int frag_len, Model *mdl,
49  float bead_radius, bool add_conn_restraint = false);
50 
51 //! Coarsen a density map based on voxels clustering
52 /**
53 \param[in] dmap the density map to coarsen
54 \param[in] dens_threshold use only voxels above this
55  threshold for clustering
56 \param[in] num_beads the number of beads
57 \param[in] mdl model to add the new molecule to
58 \param[in] bead_radius bead radius
59  */
60 IMPMULTIFITEXPORT
61 atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap,
62  float dens_threshold,
63  int num_beads,
64  Model *mdl,
65  float bead_radius);
66 
67 IMPMULTIFIT_END_NAMESPACE
68 
69 #endif /* IMPMULTIFIT_COARSE_MOLECULE_H */
atom::Hierarchies create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen molecules based on atom clustering.
atom::Hierarchy create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false)
Coarsen a molecule based on atom clustering.
Class for handling density maps.
Decorator for helping deal with a hierarchy of molecules.
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.