model_views.cpp File Reference

Library routines used for analyzing the views of components in models. More...

#include "rwimg.h"
#include "model_views.h"
#include "model_util.h"
#include "model_neighbors.h"
#include "mol_compare.h"
#include "Matrix3.h"
#include "linked_list.h"
#include "utilities.h"

Functions
list< View2< float > >	views_from_model (Bmodel *model)
	Returns a list of component views. More...
list< View2< float > >	views_from_models (Bmodel *model)
	Returns a list of component views. More...
long	model_set_views (Bmodel *model, View2< float > view)
	Sets views. More...
long	model_invert_views (Bmodel *model)
	Invert views. More...
long	model_find_views (Bmodel *model, Bstring &reffile, Bstring &paramfile)
	Finds the molecule views with respect to a reference. More...
Vector3< double >	component_normal (Bcomponent *comp)
View2< float >	component_view (Bcomponent *comp)
long	model_calculate_views (Bmodel *model, Bstring &mode)
	Calculates the views associated with each component. More...
long	model_calculate_local_views (Bmodel *model)
	Calculates the views associated with each component based on neighbors. More...
long	model_view_directions (Bmodel *model, int bin_width, int ref_flag)
	Analyzes view directions in a model. More...
int	component_hand (Bstring s)
	Determines the hand of a component. More...

Variables
int	verbose

Detailed Description

Library routines used for analyzing the views of components in models.

Author

Bernard Heymann

Date

Created: 20081120

Modified: 20210205

Function Documentation

component_hand()

int component_hand

(

Bstring

s

)

Determines the hand of a component.

Parameters

&s	string with encoded order.

Returns

int the hand.

Requirement: The string must be either a 3 or 6-digit code.
The reverse of the string is generated and the canonical version 
compared to the canonical version of the original string.
The handedness is then returned as the sign of the comparison.
The reverse of the 6-digit code is defined as reversing the
first and last 3 digits separately.

component_normal()

Vector3< double > component_normal

(

Bcomponent *

comp

)

component_view()

View2< float > component_view

(

Bcomponent *

comp

)

model_calculate_local_views()

long model_calculate_local_views

(

Bmodel *

model

)

Calculates the views associated with each component based on neighbors.

Parameters

*model

model structure (views modified).

Returns

long number of selected components.

The view for a vertex is calculated from the vertex vector and the first link.
The vertex vector points away from the origin and is calculated as follows:
Angles defined for the vertex:
    vv = normalized sum of the cross products for each pair of links
        constituting an angle
Angles not defined:
    vv = component coordinates - origin
The origin is defined as the current zero coordinates, the center-of-mass,
or from the map.

model_calculate_views()

long model_calculate_views	(	Bmodel *	model,
		Bstring &	mode
	)

Calculates the views associated with each component.

Parameters

*model	model structure (views modified).
&mode	none=current, com, map, local.

Returns

long number of selected components.

The view for a vertex is calculated from the vertex vector and the first link.
The vertex vector points away from the origin and is calculated as follows:
Angles defined for the vertex:
    vv = normalized sum of the cross products for each pair of links
        constituting an angle
Angles not defined:
    vv = component coordinates - origin
The origin is defined as the current zero coordinates, the center-of-mass,
or from the map.

model_find_views()

long model_find_views	(	Bmodel *	model,
		Bstring &	reffile,
		Bstring &	paramfile
	)

Finds the molecule views with respect to a reference.

Parameters

*model	model parameters.
&reffile	reference molecule file name.
&paramfile	atomic parameter file.

Returns

long number of molecules selected.

The positioning of each molecule is based on the center of mass of the reference.

model_invert_views()

long model_invert_views

(

Bmodel *

model

)

Invert views.

Parameters

*model

model parameters.

Returns

long number of selected components.

It calculates the inverse of each component view.
Only the first model is processed.

model_set_views()

long model_set_views	(	Bmodel *	model,
		View2< float >	view
	)

Sets views.

Parameters

*model	model parameters.
view	set view.

Returns

long number of selected components.

Each component view is set tot the given view.

model_view_directions()

long model_view_directions	(	Bmodel *	model,
		int	bin_width,
		int	ref_flag
	)

Analyzes view directions in a model.

Parameters

*model	model parameters.
bin_width	bin width in degrees.
ref_flag	flag to select the reference vector (0=z-axis, 1=component location)

Returns

long number of molecules selected.

The angle between the component view and a reference vector is calculated.
A histogram of the angles is constructed and reported.
The reference vector can be the z-axis, or the component location.

views_from_model()

list< View2< float > > views_from_model

(

Bmodel *

model

)

Returns a list of component views.

Parameters

*model

model parameters.

Returns

list<View2<float>> list of views.

Only the first model is processed.

views_from_models()

list< View2< float > > views_from_models

(

Bmodel *

model

)

Returns a list of component views.

Parameters

*model

model parameters.

Returns

View* list of views.

All models are processed.

Variable Documentation

verbose

int verbose

extern