model_select.h File Reference

Header file for reading and writing atomic model files. More...

#include "rwmodel.h"
#include "Bimage.h"
#include "Bstring.h"

Functions
long	model_selection_stats (Bmodel *model)
	Calculates selection statistics. More...
long	model_show_selection (Bmodel *model)
	Shows the distrubution of selections. More...
long	model_select (Bmodel *model, Bstring &comptype)
	Selects models, components and component types. More...
long	model_select (Bmodel *model, long number)
	Resets the selection to all models. More...
long	model_select_all (Bmodel *model)
	Resets the selection to all models. More...
long	model_select_unknowns (Bmodel *model)
	Resets the selection to all unknown models. More...
long	model_reset_selection (Bmodel *model)
	Resets the selection to all components. More...
long	model_unset_selection (Bmodel *model)
	Unsets the selection to all components but not models. More...
long	model_invert_selection (Bmodel *model)
	Inverts the selection of all components. More...
long	model_select_sets (Bmodel *model, int size, int flag)
	Selects sets of components, each set with the same size. More...
long	models_select_within_bounds (Bmodel *model, Vector3< double > &start, Vector3< double > &end)
	Selects components within bounds for a list of models. More...
long	model_select_number_of_components (Bmodel *model, int ncomp_min, int ncomp_max)
	Selects models within a range of the number of components. More...
int	model_select_random (Bmodel *model, long number)
	Selects a random number of components. More...
long	model_select_closed (Bmodel *model, int closure_rule, int val_order)
	Determines if a polyhedron is closed given a rule. More...
long	model_select_fullerene (Bmodel *model)
	Selects fullerene type models. More...
long	model_select_non_fullerene (Bmodel *model)
	Selects non-fullerene type models. More...
long	model_select_valence (Bmodel *model, int valence)
	Selects fullerene type models. More...
long	model_select_polygons (Bmodel *model, int order)
	Selects model polygons with a given order. More...
long	model_select_first (Bmodel *model, int first)
	Selects the first number of components. More...
long	model_select_within_shell (Bmodel *model, Vector3< double > center, double minrad, double maxrad)
	Selects components within a shell. More...
long	model_select_in_mask (Bmodel *model, Bimage *pmask)
	Selects components within a mask. More...
long	model_delete (Bmodel **model)
	Deletes tagged models, components and links. More...
long	model_delete_comp_type (Bmodel *model, Bstring &comptype)
	Deletes components based on their types. More...
long	model_delete_non_selected (Bmodel **model)
	Deletes selected components and associated links from the model. More...
long	model_type_from_selection (Bmodel *model, Bstring *comp_type, Bstring &filename)
	Converts selection numbers to different types. More...
long	model_fom_deselect (Bmodel *model, double fom_cutoff)
	Deselects components based on the FOM. More...
long	model_fom_max_fraction_deselect (Bmodel *model, double fom_fraction)
	Deselects components based on the FOM relative to the maximum FOM. More...
long	model_fom_histogram (Bmodel *model, double fom_step)
	Selects components based on the FOM. More...
long	model_fom_ranking (Bmodel *model, int nrank)
	Ranks components based on the FOM. More...
long	model_delete_overlapped_components (Bmodel **model, double distance)
	Deletes components that are too close to others. More...
long	model_average_overlapped_components (Bmodel *model, double distance)
	Averages components within a distance. More...
long	model_prune_simple (Bmodel *model, double mindist)
	Prunes overlapping components based on a distance criterion. More...
long	model_prune_fom (Bmodel *model, double distance)
long	model_prune_similar (Bmodel *model)
	Averages similar components and reduces redundancy. More...
long	model_prune_fit (Bmodel *model, double distance)
	Deselects components based on overlap distance and the FOM. More...
long	model_prune_large (Bmodel *model, double sampling)
	Deselects components based on overlap distance and the FOM. More...
long	model_find_overlap (Bmodel *model, Bstring &reffile, double distance)
	Finds the components that overlap with the reference. More...

Detailed Description

Header file for reading and writing atomic model files.

Author

Bernard Heymann

Date

Created: 20060908

Modified: 20220323

Function Documentation

model_average_overlapped_components()

long model_average_overlapped_components	(	Bmodel *	model,
		double	distance
	)

Averages components within a distance.

Parameters

*model	model.
distance	overlap distance.

Returns

long 0.

Components within the given distance are averaged and the first
instance is retained while the others are deleted.

model_delete()

long model_delete

(

Bmodel **

model

)

Deletes tagged models, components and links.

Parameters

**model

pointer to model parameters.

Returns

long remaining number of components.

A model, component or link is tagged for deletion by a negative selection flag.

model_delete_comp_type()

long model_delete_comp_type	(	Bmodel *	model,
		Bstring &	comptype
	)

Deletes components based on their types.

Parameters

*model	model parameters.
&comptype	component type.

Returns

long number of components remaining.

model_delete_non_selected()

long model_delete_non_selected

(

Bmodel **

model

)

Deletes selected components and associated links from the model.

Parameters

**model

pointer to model parameters.

Returns

long remaining number of components.

model_delete_overlapped_components()

long model_delete_overlapped_components	(	Bmodel **	model,
		double	distance
	)

Deletes components that are too close to others.

Parameters

**model	model handle.
distance	distance to test for.

Returns

long 0.

If a component is too close to another, the component further down
in the list is deleted.

model_find_overlap()

long model_find_overlap	(	Bmodel *	model,
		Bstring &	reffile,
		double	distance
	)

Finds the components that overlap with the reference.

Parameters

*model	model parameters.
&reffile	reference molecule file name.
distance	distance for overlap.

Returns

long number of components selected.

All components that are within the distance criterion of the components
in the reference model are deselected.

model_fom_deselect()

long model_fom_deselect	(	Bmodel *	model,
		double	fom_cutoff
	)

Deselects components based on the FOM.

Parameters

*model	model parameters.
fom_cutoff	FOM threshold.

Returns

long number of components selected.

The FOM is assumed to be a value from 0 to 1 and components with
FOM's below the given cutoff are deselected.

model_fom_histogram()

long model_fom_histogram	(	Bmodel *	model,
		double	fom_step
	)

Selects components based on the FOM.

Parameters

*model	model parameters.
fom_step	FOM step size.

Returns

long number of components.

The FOM is assumed to represent energy and therefore values below
the given cutoff are selected.

model_fom_max_fraction_deselect()

long model_fom_max_fraction_deselect	(	Bmodel *	model,
		double	fom_fraction
	)

Deselects components based on the FOM relative to the maximum FOM.

Parameters

*model	model parameters.
fom_fraction	FOM threshold.

Returns

long number of components selected.

The FOM/FOMmax ratio is calculated and components with ratios below
the given fraction are deselected.

model_fom_ranking()

long model_fom_ranking	(	Bmodel *	model,
		int	nrank
	)

Ranks components based on the FOM.

Parameters

*model	model parameters.
nrank	number of levels.

Returns

long number of selected components.

Each selected component is ranked into one of a number of levels.

model_invert_selection()

long model_invert_selection

(

Bmodel *

model

)

Inverts the selection of all components.

Parameters

*model

model parameters.

Returns

long number of components selected.

model_prune_fit()

long model_prune_fit	(	Bmodel *	model,
		double	distance
	)

Deselects components based on overlap distance and the FOM.

Parameters

*model	model parameters.
distance	overlap distance.

Returns

long number of components selected.

The selected component with the highest FOM is chosen as the first 
component in the solution set and all components within the distance 
criterion from it are deselected. The selected component with the next 
highest FOM is then chosen and again, all components within the distance 
criterion from it are deselected.
This is repeated until there are no more selected components to choose.
Only the first model is processed.

model_prune_fom()

long model_prune_fom	(	Bmodel *	model,
		double	distance
	)

model_prune_large()

long model_prune_large	(	Bmodel *	model,
		double	sampling
	)

Deselects components based on overlap distance and the FOM.

Parameters

*model	model parameters.
sampling	grid sampling.

Returns

long number of components selected.

Each component location is mapped to a grid point and the component FOM
is assigned to the grid point if it is larger.
Peaks are determined within each 3x3x3 kernel: a peak is defined as
having a higher value than any of its 26 neigbors.
The component associated with the value at a peak is selected.
Only the first model is processed.

model_prune_similar()

long model_prune_similar

(

Bmodel *

model

)

Averages similar components and reduces redundancy.

Parameters

*model

model parameters.

Returns

lon number of clusters.

A view distance matrix is calculated for all the components.
All components within a small distance (~10% of model radius) are averaged
into the first component and the rest are deselected.
Only the first model is processed.

model_prune_simple()

long model_prune_simple	(	Bmodel *	model,
		double	mindist
	)

Prunes overlapping components based on a distance criterion.

Parameters

*model	model structure to be modified.
mindist	distance criterion.

Returns

long number of remaining components.

The first component in any pair of overlapping components is kept.

model_reset_selection()

long model_reset_selection

(

Bmodel *

model

)

Resets the selection to all components.

Parameters

*model

model parameters.

Returns

long number of components selected.

Only one model is modified.

model_select() [1/2]

long model_select	(	Bmodel *	model,
		Bstring &	selstr
	)

Selects models, components and component types.

Parameters

*model	model parameters.
&selstr	selection string.

Returns

long number of selections made.

The selection string can have one of the following formats:
    #model@component
    #model%comp_type
    ^model_type@component
    ^model_type%comp_type
Only elements originally selected is considered, except where the "." is used.

model_select() [2/2]

long model_select	(	Bmodel *	model,
		long	number
	)

Resets the selection to all models.

Parameters

*model	model parameters.
number	selection number to select.

Returns

long number of components selected.

model_select_all()

long model_select_all

(

Bmodel *

model

)

Resets the selection to all models.

Parameters

*model

model parameters.

Returns

long number of models selected.

model_select_closed()

long model_select_closed	(	Bmodel *	model,
		int	closure_rule,
		int	val_order
	)

Determines if a polyhedron is closed given a rule.

Parameters

*model	model parameters.
closure_rule	1=valency, 2=order.
val_order	magnitude of valency or order.

Returns

long number of models selected.

Polyhedron closure is arbitrarily decided by a rule:
1.  Fixed valency.
3.  Fixed polygon order.
Models that fail the given rule are deselected.
If the given valency or order is zero, it is set to the value for
the first component or polygon.

model_select_first()

long model_select_first	(	Bmodel *	model,
		int	first
	)

Selects the first number of components.

Parameters

*model	model parameters.
first	first number of components to select.

Returns

long number of components selected.

model_select_fullerene()

long model_select_fullerene

(

Bmodel *

model

)

Selects fullerene type models.

Parameters

*model

model structure.

Returns

long number of models selected.

Each model is tested for the presence of polygons that have orders
only of five or six.

model_select_in_mask()

long model_select_in_mask	(	Bmodel *	model,
		Bimage *	pmask
	)

Selects components within a mask.

Parameters

*model	model parameters.
pmask	first number of components to select.

Returns

long number of components selected.

model_select_non_fullerene()

long model_select_non_fullerene

(

Bmodel *

model

)

Selects non-fullerene type models.

Parameters

*model

model structure.

Returns

long number of models selected.

Each model is tested for the presence of polygons that have orders
different from five or six.

model_select_number_of_components()

long model_select_number_of_components	(	Bmodel *	model,
		int	ncomp_min,
		int	ncomp_max
	)

Selects models within a range of the number of components.

Parameters

*model	model parameters.
ncomp_min	minimum number of components.
ncomp_max	maximum number of components.

Returns

long number of models selected.

model_select_polygons()

long model_select_polygons	(	Bmodel *	model,
		int	order
	)

Selects model polygons with a given order.

Parameters

*model	model to color.
order	polygon order.

Returns

long 0.

model_select_random()

int model_select_random	(	Bmodel *	model,
		long	number
	)

Selects a random number of components.

Parameters

*model	model parameters.
number	number of components.

Returns

int 0.

model_select_sets()

long model_select_sets	(	Bmodel *	model,
		int	size,
		int	flag
	)

Selects sets of components, each set with the same size.

Parameters

*model	parameter structure with all parameters.
size	number of components in each set.
flag	flag to not count across model boundaries.

Returns

long number of components selected.

Sets up sets of components, each set identified as a number in the
selection array.

model_select_unknowns()

long model_select_unknowns

(

Bmodel *

model

)

Resets the selection to all unknown models.

Parameters

*model

model parameters.

Returns

long number of models selected.

model_select_valence()

long model_select_valence	(	Bmodel *	model,
		int	valence
	)

Selects fullerene type models.

Parameters

*model	model structure.
valence	component valence

Returns

long number of models selected.

Each model is tested for the presence of polygons that have orders
only of five or six.

model_select_within_shell()

long model_select_within_shell	(	Bmodel *	model,
		Vector3< double >	center,
		double	minrad,
		double	maxrad
	)

Selects components within a shell.

Parameters

*model	model parameters.
center	center of the shell.
minrad	minimum radius of the sphere.
maxrad	radius of the sphere.

Returns

long number of components selected.

model_selection_stats()

long model_selection_stats

(

Bmodel *

model

)

Calculates selection statistics.

Parameters

*model

model parameters.

Returns

long number of components selected.

The FOM is assumed to be a value from 0 to 1.

model_show_selection()

long model_show_selection

(

Bmodel *

model

)

Shows the distrubution of selections.

Parameters

*model

model parameters.

Returns

long number of selection levels.

model_type_from_selection()

long model_type_from_selection	(	Bmodel *	model,
		Bstring *	comp_type,
		Bstring &	filename
	)

Converts selection numbers to different types.

Parameters

*model	model parameters.
*comp_type	linked list of strings.
&filename	component type file name.

Returns

long number of component types assigned.

model_unset_selection()

long model_unset_selection

(

Bmodel *

model

)

Unsets the selection to all components but not models.

Parameters

*model

model parameters.

Returns

long number of components deselected.

models_select_within_bounds()

long models_select_within_bounds	(	Bmodel *	model,
		Vector3< double > &	start,
		Vector3< double > &	end
	)

Selects components within bounds for a list of models.

Parameters

*model	list of models.
&start	minimum coordinates.
&end	maximum coordinates.

Returns

long number of components selected.