| Bsoft 2.0.5 Bernard's software package

mol_monte.h
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1
9 #include "rwmolecule.h"
10 #include "rwimg.h"
11 #include "rwmodel.h"
12 #include "rwmd.h"
13
14
15 // Function prototypes
16 Bmolgroup* monte_carlo_metropolis(Bmolgroup* molgroup, Bmd* md, Bimage* map,
17 double beta, double max_angle, double max_shift,
18 long max_iter, int rigid,
19 double (Efunc)(Bmolgroup*, Bimage*, Bmd*),
20 int (Tfunc)(Bmolgroup*, double, double));
21 Bmolgroup* molgroup_generate_masked_grid_list(Bmolgroup* molgroup, Bimage* pmask,
22 Vector3<double> grid_sampling, Bstring filename);
23 Bmodel* molgroup_generate_masked_grid_list(Bmolgroup* molgroup,
24 Vector3<double> grid_sampling, Bimage* pmask);
25 Bmolgroup* molgroup_generate_orientation_list(Bmolgroup* molgroup,
26 double angle_step, Bstring filename, int whole);
27 Bmodel* molgroup_generate_orientation_list(Bmolgroup* molgroup, double angle_step);
28 Bmolgroup* mcm_molecule_list(Bmolgroup* molgroup, Bmd* md, Bimage* map, double beta,
29 double max_angle, double max_shift, long max_iter, int rigid);
30 int mcm_molecule_groups(Bmolgroup* molgroup, Bmodel* model, Bmd* md, Bimage* map, double beta,
31 double max_angle, double max_shift, long max_iter, int rigid);
32 int mcm_molecule_list(Bmolgroup* molgroup, Bmodel* model, Bmd* md, Bimage* map, double beta,
33 double max_angle, double max_shift, long max_iter, int rigid);
34 int molgroup_set_box_to_map_boundaries(Bmolgroup* molgroup, Bimage* map);
35 long molgroup_test_if_within_box(Bmolgroup* molgroup, Vector3<double> min, Vector3<double> max);
36 double monte_rigid_body_fit_energy(Bmolgroup* molgroup, Bimage* map, Bmd* md);
37 double monte_atom_fit_energy(Bmolgroup* molgroup, Bimage* map, Bmd* md);
38 double monte_bond_fit_energy(Bmolgroup* molgroup, Bimage* map, Bmd* md);
39 double molgroup_atom_overlap(Bmolgroup* molgroup, Bmd* md);
40 int molgroup_rigid_body_transform(Bmolgroup* molgroup, double max_angle, double shift_std);
41 int molgroup_move_atoms_down_energy(Bmolgroup* molgroup, double max_angle, double max_shift);
42
monte_atom_fit_energy
double monte_atom_fit_energy(Bmolgroup *molgroup, Bimage *map, Bmd *md)
Calculates the potential energy for fitting atoms to a map.
Definition: mol_monte.cpp:693
monte_carlo_metropolis
Bmolgroup * monte_carlo_metropolis(Bmolgroup *molgroup, Bmd *md, Bimage *map, double beta, double max_angle, double max_shift, long max_iter, int rigid, double(Efunc)(Bmolgroup *, Bimage *, Bmd *), int(Tfunc)(Bmolgroup *, double, double))
Definition: mol_monte.cpp:71
molgroup_test_if_within_box
long molgroup_test_if_within_box(Bmolgroup *molgroup, Vector3< double > min, Vector3< double > max)
Tests if a molecule overlaps with a defined box.
Definition: mol_monte.cpp:626
Bmd
Definition: rwmd.h:56
mcm_molecule_list
Bmolgroup * mcm_molecule_list(Bmolgroup *molgroup, Bmd *md, Bimage *map, double beta, double max_angle, double max_shift, long max_iter, int rigid)
molgroup_generate_orientation_list
Bmolgroup * molgroup_generate_orientation_list(Bmolgroup *molgroup, double angle_step, Bstring filename, int whole)
Generates multiple versions of a molecule at different locations.
Definition: mol_monte.cpp:386
monte_bond_fit_energy
double monte_bond_fit_energy(Bmolgroup *molgroup, Bimage *map, Bmd *md)
Calculates the potential energy for fitting bonds to a map.
Definition: mol_monte.cpp:725
molgroup_set_box_to_map_boundaries
int molgroup_set_box_to_map_boundaries(Bmolgroup *molgroup, Bimage *map)
Sets the box in a molgroup to that defined by the map boundaries.
Definition: mol_monte.cpp:604
Bimage
General image parameter class.
Definition: Bimage.h:163
molgroup_move_atoms_down_energy
int molgroup_move_atoms_down_energy(Bmolgroup *molgroup, double max_angle, double max_shift)
Move atoms random distances down the energy gradient.
Definition: mol_monte.cpp:891
rwmolecule.h
Header file for reading reflection files.
mcm_molecule_groups
int mcm_molecule_groups(Bmolgroup *molgroup, Bmodel *model, Bmd *md, Bimage *map, double beta, double max_angle, double max_shift, long max_iter, int rigid)
Monte Carlo fit of a set of molecule groups.
Definition: mol_monte.cpp:543
Bmolgroup
Definition: rwmolecule.h:170
molgroup_atom_overlap
double molgroup_atom_overlap(Bmolgroup *molgroup, Bmd *md)
Calculates an energy term based on atom overlap.
Definition: mol_monte.cpp:759
model
Bmodel * model
Definition: bshow.cpp:32
Bstring
Definition: Bstring.h:29
beta
double beta(double volt)
Calculates the relative electron velocity.
Definition: ctf.cpp:447
monte_rigid_body_fit_energy
double monte_rigid_body_fit_energy(Bmolgroup *molgroup, Bimage *map, Bmd *md)
Calculates the potential energy for rigid body fitting.
Definition: mol_monte.cpp:661
rwmodel.h
Header file for reading and writing atomic model files.
molgroup_rigid_body_transform
int molgroup_rigid_body_transform(Bmolgroup *molgroup, double max_angle, double shift_std)
Randomly transforms a molecule or molecule group.
Definition: mol_monte.cpp:847
Vector3< double >
Bmodel
Definition: rwmodel.h:119
rwmd.h
Header to read and write molecular dynamics parameters in STAR format.
rwimg.h
Header file for 2D and 3D image I/O.
molgroup_generate_masked_grid_list
Bmolgroup * molgroup_generate_masked_grid_list(Bmolgroup *molgroup, Bimage *pmask, Vector3< double > grid_sampling, Bstring filename)
Generates multiple versions of a molecule at different locations.
Definition: mol_monte.cpp:260