mol_monte.h File Reference

Headers of functions using a monte carlo metroplis algorithm to energy minimize molecular positions. More...

#include "rwmolecule.h"
#include "rwimg.h"
#include "rwmodel.h"
#include "rwmd.h"

Functions
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))
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. More...
Bmodel *	molgroup_generate_masked_grid_list (Bmolgroup *molgroup, Vector3< double > grid_sampling, Bimage *pmask)
Bmolgroup *	molgroup_generate_orientation_list (Bmolgroup *molgroup, double angle_step, Bstring filename, int whole)
	Generates multiple versions of a molecule at different locations. More...
Bmodel *	molgroup_generate_orientation_list (Bmolgroup *molgroup, double angle_step)
Bmolgroup *	mcm_molecule_list (Bmolgroup *molgroup, Bmd *md, Bimage *map, double beta, double max_angle, double max_shift, long max_iter, int rigid)
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. More...
int	mcm_molecule_list (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 molecule to a list of locations and orientations. More...
int	molgroup_set_box_to_map_boundaries (Bmolgroup *molgroup, Bimage *map)
	Sets the box in a molgroup to that defined by the map boundaries. More...
long	molgroup_test_if_within_box (Bmolgroup *molgroup, Vector3< double > min, Vector3< double > max)
	Tests if a molecule overlaps with a defined box. More...
double	monte_rigid_body_fit_energy (Bmolgroup *molgroup, Bimage *map, Bmd *md)
	Calculates the potential energy for rigid body fitting. More...
double	monte_atom_fit_energy (Bmolgroup *molgroup, Bimage *map, Bmd *md)
	Calculates the potential energy for fitting atoms to a map. More...
double	monte_bond_fit_energy (Bmolgroup *molgroup, Bimage *map, Bmd *md)
	Calculates the potential energy for fitting bonds to a map. More...
double	molgroup_atom_overlap (Bmolgroup *molgroup, Bmd *md)
	Calculates an energy term based on atom overlap. More...
int	molgroup_rigid_body_transform (Bmolgroup *molgroup, double max_angle, double shift_std)
	Randomly transforms a molecule or molecule group. More...
int	molgroup_move_atoms_down_energy (Bmolgroup *molgroup, double max_angle, double max_shift)
	Move atoms random distances down the energy gradient. More...

Detailed Description

Headers of functions using a monte carlo metroplis algorithm to energy minimize molecular positions.

Author

Bernard Heymann

Date

Created: 20041230

Modified: 20071223

Function Documentation

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.

Parameters

*molgroup	molecule group.
*model	model parameters (modified).
*md	molecular dynamics structure.
*map	map.
beta	equivalent of 1/kT.
max_angle	maximum allowed angular step size.
max_shift	maximum allowed shift.
max_iter	maximum number of iterations.
rigid	selection of mode.

Returns

Bmolgroup* new molecule group list.

For each model, the molecule group is first transformed to the model 
location and orientation. The whole ensemble is then refined with the 
Monte Carlo Metropolis algorithm and the model parameters updated.

mcm_molecule_list() [1/2]

Bmolgroup * mcm_molecule_list	(	Bmolgroup *	molgroup,
		Bmd *	md,
		Bimage *	map,
		double	beta,
		double	max_angle,
		double	max_shift,
		long	max_iter,
		int	rigid
	)

mcm_molecule_list() [2/2]

int mcm_molecule_list	(	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 molecule to a list of locations and orientations.

Parameters

*molgroup	molecule group.
*model	model parameters (modified).
*md	molecular dynamics structure.
*map	map.
beta	equivalent of 1/kT.
max_angle	maximum allowed angular step size.
max_shift	maximum allowed shift.
max_iter	maximum number of iterations.
rigid	selection of mode.

Returns

Bmolgroup* new molecule group list.

For each model, the molecule group is first transformed to the model 
location and orientation. This is then refined with the Monte Carlo
Metropolis algorithm and the model parameters updated.

molgroup_atom_overlap()

double molgroup_atom_overlap	(	Bmolgroup *	molgroup,
		Bmd *	md
	)

Calculates an energy term based on atom overlap.

Parameters

*molgroup	molecular structure.
*md	molecular dynamics structure.

Returns

double total overlap energy.

The energy is defined as linear decay to the reference separation distance
and zero beyond:
    Esep = Ksep * (1 - d/dsep)  for  d < dsep, zero otherwise

molgroup_generate_masked_grid_list() [1/2]

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.

Parameters

*molgroup	molecule group.
*pmask	mask to get limit grid positions.
grid_sampling	sampling for grid search.
filename	output base file name.

Returns

Bmolgroup* linked list of molecule groups.

The locations of the molecules are defined on the intersection of a 
grid and a user-defined mask.
The numbered output filename is also set.
Note: the molecule group minima and maxima should be set to the 
volume to be searched before calling this function.

molgroup_generate_masked_grid_list() [2/2]

Bmodel * molgroup_generate_masked_grid_list	(	Bmolgroup *	molgroup,
		Vector3< double >	grid_sampling,
		Bimage *	pmask
	)

molgroup_generate_orientation_list() [1/2]

Bmodel * molgroup_generate_orientation_list	(	Bmolgroup *	molgroup,
		double	angle_step
	)

molgroup_generate_orientation_list() [2/2]

Bmolgroup * molgroup_generate_orientation_list	(	Bmolgroup *	molgroup,
		double	angle_step,
		Bstring	filename,
		int	whole
	)

Generates multiple versions of a molecule at different locations.

Parameters

*molgroup	molecule group.
angle_step	angular step size in radians.
filename	output base file name.
whole	treat the whole ensemble as a rigid body.

Returns

Bmolgroup* linked list of molecule groups.

The molecule group is rotated in place to give all orientations
with a given angle step size between the views.
The numbered output filename is also set.

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.

Parameters

*molgroup	molecular structure.
max_angle	(not used).
max_shift	maximum shift for each atom.

Returns

double 0.

The distance of movement is limited to the maximum shift.

molgroup_rigid_body_transform()

int molgroup_rigid_body_transform	(	Bmolgroup *	molgroup,
		double	max_angle,
		double	shift_std
	)

Randomly transforms a molecule or molecule group.

Parameters

*molgroup	molecular structure.
max_angle	maximum rotation angle.
shift_std	gaussian length for shift vector.

Returns

int 0.

The transformation is calculted as a random angular rotation and a
random shift. The shift is sampled from a random vector with a
gaussian length distribution.

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.

Parameters

*molgroup	molecule group.
*map	map to get boundaries from.

Returns

int 0.

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.

Parameters

*molgroup	molecule group.
min	start of box.
max	end of box.

Returns

long 0.

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.

Parameters

*molgroup	molecular structure.
*map	density map.
*md	molecular dynamics structure.

Returns

double potential energy.

The energy is the sum of the bond, angle, and map energies.

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.

Parameters

*molgroup	molecular structure.
*map	density map.
*md	molecular dynamics structure.

Returns

double potential energy.

The energy is the sum of the bond, angle, and map energies.

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)
	)

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.

Parameters

*molgroup	molecular structure.
*map	density map.
*md	molecular dynamics structure.

Returns

double potential energy.

The energy is the sum of the overlap, map, and point force energies.