Library routines used for model processing. More...

#include "model_util.h"
#include "model_transform.h"
#include "model_select.h"
#include "model_links.h"
#include "mol_transform.h"
#include "mol_compare.h"
#include "mol_util.h"
#include "symmetry.h"
#include "matrix_linear.h"
#include "matrix_util.h"
#include "Matrix3.h"
#include "random_numbers.h"
#include "linked_list.h"
#include "utilities.h"

Functions
long	models_process (Bmodel model, long(modfunc)(Bmodel ))
	Process a list of models using the specified function. More...

long	models_process (Bmodel model, long i, long(modfunc)(Bmodel , long))

long	models_process (Bmodel model, double d, long(modfunc)(Bmodel , double))

long	models_process (Bmodel model, Bstring &str, long(modfunc)(Bmodel , Bstring &str))

long	models_process (Bmodel model, string &str, long(modfunc)(Bmodel , string &str))

long	model_list (Bmodel *model)
	Lists models in table form. More...

long	model_list_comp (Bmodel *model)
	Lists models with component counts in table form. More...

long	model_replace_components (Bmodel model, Bmodel modref)
	Replaces all components in a model with reference components. More...

long	model_merge (Bmodel *model)
	Merges components from all models into one. More...

long	model_number_ids (Bmodel *model)
	Add a number to each model id. More...

long	model_rename (Bmodel *model, char first_name)
	Rename models with alphabetical letters. More...

long	model_rename_components (Bmodel *model)
	Rename components. More...

double	model_mass (Bmodel *model)
	Calculates the mass of a model from component masses. More...

long	model_mass_all (Bmodel *model)
	Calculates the masses of all the models in the list. More...

Vector3< double >	model_center_of_mass (Bmodel *model)
	Calculates the center-of-mass of a model. More...

Vector3< double >	models_center_of_coordinates (Bmodel *model)
	Calculates the center-of-mass of a list of models. More...

double	model_distance_sum (Bmodel *model, Vector3< double > loc)
	Calculates the sum of distances of model components to a location. More...

Vector3< double >	model_geometric_median_estimate (Bmodel *model, Vector3< double > pgm)
	Calculates the geometric median estimate of model components. More...

Vector3< double >	model_geometric_median (Bmodel *model)
	Calculates the geometric median of model components. More...

double	model_gyration_radius (Bmodel *model)
	Calculates the radius of gyration for a model. More...

Vector3< double >	model_principal_axes (Bmodel model, Vector3< double > eigenvec)
	Calculates the principal axes of a model. More...

Vector3< double >	model_principal_axes (Bmodel *model, Matrix &eigenvec)

long	model_principal_axes (Bmodel *model)

long	model_radial_distribution (Bmodel *model, double interval)
	Calculates the radial distribution function of a model. More...

long	molgroup_write_into_grid (Bmolgroup molgroup, Vector3< int > size, Vector3< double > min, double sampling, int grid)

Bmolgroup *	model_assemble (Bmodel *model, Bstring &paramfile, int separate)
	Concatenates selected molecules into one group. More...

Bmodel *	model_generate_com (Bmolgroup *molgroup)
	Calculates the centers-of-mass of molecule group components and generates a new model. More...

long	model_update_centers_of_mass (Bmodel model, Bmolgroup molgroup)
	Updates the centers-of-mass of molecule group components. More...

long	model_average_components (Bmodel *model, int number)
	Averages sequential components. More...

Bcomponent **	component_get_array (Bmodel *model, long &n)
	Generates an array of pointers to component structures. More...

Vector3< double >	component_plane (vector< Bcomponent * > &comparray, double &offset)
	Calculates a plane through an array of components. More...

vector< Vector3< double > >	models_calculate_bounds (Bmodel *model)
	Calculates the bounds of a list of models. More...

vector< vector< Bcomponent * > >	model_component_grid (Bmodel *model, Vector3< long > &size, Vector3< double > &origin, Vector3< double > &sampling)
	Generates lists of atoms based on a grid. More...

vector< Bcomponent * >	models_get_component_array (Bmodel *model)
	Generates an array of pointers to model components. More...

vector< vector< Bcomponent * > >	model_split_into_slices (Bmodel *model, double bottom, double top, double thickness)
	Splits the components of models into slices. More...

Variables
int	verbose

Detailed Description

Library routines used for model processing.

Author: Bernard Heymann

Date: Created: 20060908; Modified: 20230120

Function Documentation

◆ component_get_array()

Bcomponent ** component_get_array	(	Bmodel *	model,
		long &	n
	)

Generates an array of pointers to component structures.

Parameters

*model	model structure.
&n	pointer to number of comps found.

Returns: Bcomponent** array of pointers to components.

◆ component_plane()

Vector3< double > component_plane	(	vector< Bcomponent * > &	comparray,
		double &	offset
	)

Calculates a plane through an array of components.

Parameters

**comparray	array of components.
&offset	offset from plane.

Returns

Vector3<double> plane normal.

A plane is fit through the polygon vertices and the normal calculated from:
    n•p = d
where n is the normal vector, p is a point in the plane, and d is the offset.
The polygon planarity is defined as the root-mean-square-deviation from 
the fitted plane.

◆ model_assemble()

Bmolgroup * model_assemble	(	Bmodel *	model,
		Bstring &	paramfile,
		int	separate
	)

Concatenates selected molecules into one group.

Parameters

*model	model parameters.
&paramfile	atomic parameter file.
separate	flag to generate separate molecule groups.

Returns

Bmolgroup* list of molecule groups.

Only the first model in the linked list is processed.

◆ model_average_components()

long model_average_components	(	Bmodel *	model,
		int	number
	)

Averages sequential components.

Parameters

*model	model structure to be modified.
number	number of components to average.

Returns

long number of remaining components.

Only the first component in each set with modified coordinates is kept.

◆ model_center_of_mass()

Vector3< double > model_center_of_mass ( Bmodel * model )

Calculates the center-of-mass of a model.

Parameters

*model model parameters.

Returns

Vector3<double> center-of-mass.

Only the first model in the list is processed.

◆ model_component_grid()

vector< vector< Bcomponent * > > model_component_grid	(	Bmodel *	model,
		Vector3< long > &	size,
		Vector3< double > &	origin,
		Vector3< double > &	sampling
	)

Generates lists of atoms based on a grid.

Parameters

*model	model list.
size	size of grid.
origin	origin of grid.
sampling	spacing in each dimension.

Returns

vector<vector<Bcomponent*>> array of component arrays.

The goal is to fit all the components within the grid boundaries.
Components located outside the grid will be added to the edges.

◆ model_distance_sum()

double model_distance_sum	(	Bmodel *	model,
		Vector3< double >	loc
	)

Calculates the sum of distances of model components to a location.

Parameters

*model	model parameters.
loc	reference location.

Returns

double sum of distances.

Only the first model in the list is processed.

◆ model_generate_com()

Bmodel * model_generate_com ( Bmolgroup * molgroup )

Calculates the centers-of-mass of molecule group components and generates a new model.

Parameters

*molgroup list of molecule groups.

Returns

Bmodel* new model.

Each molecule is assumed to be a component.

◆ model_geometric_median()

Vector3< double > model_geometric_median ( Bmodel * model )

Calculates the geometric median of model components.

Parameters

*model model parameters.

Returns

Vector3<double> geometric median.

Only the first model in the list is processed.
Based on Weiszfeld’s method.

◆ model_geometric_median_estimate()

Vector3< double > model_geometric_median_estimate	(	Bmodel *	model,
		Vector3< double >	pgm
	)

Calculates the geometric median estimate of model components.

Parameters

*model	model parameters.
pgm	previous geometric median estimate.

Returns

Vector3<double> new geomtric median estimate.

Only the first model in the list is processed.

◆ model_gyration_radius()

double model_gyration_radius ( Bmodel * model )

Calculates the radius of gyration for a model.

Parameters

*model model parameters.

Returns

double radius of gyration.

Only the first model in the list is processed.

◆ model_list()

long model_list ( Bmodel * model )

Lists models in table form.

Parameters

*model model parameters.

Returns: long number of models.

◆ model_list_comp()

long model_list_comp ( Bmodel * model )

Lists models with component counts in table form.

Parameters

*model model parameters.

Returns: long number of models.

◆ model_mass()

double model_mass ( Bmodel * model )

Calculates the mass of a model from component masses.

Parameters

*model model parameters.

Returns

double model mass.

The component type masses must be provided.
Only the first model in the list is processed.

◆ model_mass_all()

long model_mass_all ( Bmodel * model )

Calculates the masses of all the models in the list.

Parameters

*model linked list of model parameters.

Returns

long number of selected models.

The component type masses must be provided.

◆ model_merge()

long model_merge ( Bmodel * model )

Merges components from all models into one.

Parameters

*model model parameters.

Returns: long number of components.

◆ model_number_ids()

long model_number_ids ( Bmodel * model )

Add a number to each model id.

Parameters

*model model parameters.

Returns

long number of models.

The intention is to give unique id's to models.

◆ model_principal_axes() [1/3]

long model_principal_axes ( Bmodel * model )

◆ model_principal_axes() [2/3]

Vector3< double > model_principal_axes	(	Bmodel *	model,
		Matrix &	eigenvec
	)

◆ model_principal_axes() [3/3]

Vector3< double > model_principal_axes	(	Bmodel *	model,
		Vector3< double > *	eigenvec
	)

Calculates the principal axes of a model.

Parameters

*model	model structure.
*eigenvec	eigen vectors (can be NULL).

Returns

Vector3<double> 3-valued vector of principal axes.

Only the first model in the list is processed.

◆ model_radial_distribution()

long model_radial_distribution	(	Bmodel *	model,
		double	interval
	)

Calculates the radial distribution function of a model.

Parameters

*model	model structure.
interval	interval between bins.

Returns

long 0.

Only the first model in the list is processed.

◆ model_rename()

long model_rename	(	Bmodel *	model,
		char	first_name
	)

Rename models with alphabetical letters.

Parameters

*model	model parameters.
first_name	letter of first model.

Returns: long number of models.

◆ model_rename_components()

long model_rename_components ( Bmodel * model )

Rename components.

Parameters

*model model parameters.

Returns

long number of components.

The number of links to a component determines its new name.
Only the first model is processed.

◆ model_replace_components()

long model_replace_components	(	Bmodel *	model,
		Bmodel *	modref
	)

Replaces all components in a model with reference components.

Parameters

*model	model structure to be modified.
*modref	reference model.

Returns

long number of components used in reference.

Only the first model in the reference is used.
All models will have identical sets of components.

◆ model_split_into_slices()

vector< vector< Bcomponent * > > model_split_into_slices	(	Bmodel *	model,
		double	bottom,
		double	top,
		double	thickness
	)

Splits the components of models into slices.

Parameters

*model	model.
bottom	minimum coordinate in z.
top	maximum coordinate in z.
thickness	slice thickness.

Returns: vector<vector<Bcomponent*>> sets of arrays of pointers to components.

◆ model_update_centers_of_mass()

long model_update_centers_of_mass	(	Bmodel *	model,
		Bmolgroup *	molgroup
	)

Updates the centers-of-mass of molecule group components.

Parameters

*model	model parameters.
*molgroup	list of molecule groups.

Returns

long number of selected components.

The identifiers of the molecule groups must correspond to the component identifiers.

◆ models_calculate_bounds()

vector< Vector3< double > > models_calculate_bounds ( Bmodel * model )

Calculates the bounds of a list of models.

Parameters

*model model list.

Returns: vector<Vector3<double>> minimum and maximum bounds.

◆ models_center_of_coordinates()

Vector3< double > models_center_of_coordinates ( Bmodel * model )

Calculates the center-of-mass of a list of models.

Parameters

*model model parameters.

Returns: Vector3<double> center-of-mass.

◆ models_get_component_array()

vector< Bcomponent * > models_get_component_array ( Bmodel * model )

Generates an array of pointers to model components.

Parameters

*model model.

Returns: vector<Bcomponent*> array of pointers to components.

◆ models_process() [1/5]

long models_process	(	Bmodel *	model,
		Bstring &	str,
		long(modfunc)(Bmodel *, Bstring &str)
	)

◆ models_process() [2/5]

long models_process	(	Bmodel *	model,
		double	d,
		long(modfunc)(Bmodel *, double)
	)

◆ models_process() [3/5]

long models_process	(	Bmodel *	model,
		long	i,
		long(modfunc)(Bmodel *, long)
	)

◆ models_process() [4/5]

long models_process	(	Bmodel *	model,
		long(modfunc)(Bmodel *)
	)

Process a list of models using the specified function.

Parameters

*model	list of models.
modfunc	function to be called.

Returns: long aggregate number returned by function.

◆ models_process() [5/5]

long models_process	(	Bmodel *	model,
		string &	str,
		long(modfunc)(Bmodel *, string &str)
	)

◆ molgroup_write_into_grid()

long molgroup_write_into_grid	(	Bmolgroup *	molgroup,
		Vector3< int >	size,
		Vector3< double >	min,
		double	sampling,
		int *	grid
	)

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ component_get_array()

◆ component_plane()

◆ model_assemble()

◆ model_average_components()

◆ model_center_of_mass()

◆ model_component_grid()

◆ model_distance_sum()

◆ model_generate_com()

◆ model_geometric_median()

◆ model_geometric_median_estimate()

◆ model_gyration_radius()

◆ model_list()

◆ model_list_comp()

◆ model_mass()

◆ model_mass_all()

◆ model_merge()

◆ model_number_ids()

◆ model_principal_axes() [1/3]

◆ model_principal_axes() [2/3]

◆ model_principal_axes() [3/3]

◆ model_radial_distribution()

◆ model_rename()

◆ model_rename_components()

◆ model_replace_components()

◆ model_split_into_slices()

◆ model_update_centers_of_mass()

◆ models_calculate_bounds()

◆ models_center_of_coordinates()

◆ models_get_component_array()

◆ models_process() [1/5]

◆ models_process() [2/5]

◆ models_process() [3/5]

◆ models_process() [4/5]

◆ models_process() [5/5]

◆ molgroup_write_into_grid()

Variable Documentation

◆ verbose