model_util.h File Reference

Library routines used for model processing. More...

#include "rwmodel.h"
#include "rwmolecule.h"
#include "Bstring.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...
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...
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 &ncomp)
	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...

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_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_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)
	)