mol_alpha.cpp File Reference

Functions to make and analyze alpha helices. More...

#include "rwmolecule.h"
#include "mol_alpha.h"
#include "mol_transform.h"
#include "mol_util.h"
#include "Bimage.h"
#include "linked_list.h"
#include "random_numbers.h"
#include "Matrix3.h"
#include "utilities.h"

Classes
struct	AlphaTemplate

Macros
#define	NTEMPATOM   6
#define	DAXIS   2.303
#define	HRISE   1.5
#define	HANGLE   100

Functions
Bmolgroup *	molgroup_generate_alpha_helix (int length)
	Generates an alpha helix of the desired length. More...
Bmolecule *	mol_generate_alpha_helix (int length)
	Generates an alpha helix of the desired length. More...
int	molgroup_set_alpha_helix (Bmolgroup *molgroup, int helix_start, int helix_end)
	Sets a residue range to an alpha helix in all molecules. More...
int	molgroup_find_helical_axes (Bmolgroup *molgroup)
	Calculates the centers and orientations of all alpha helices. More...
Vector3< double >	alpha_find_center (Bresidue *resfirst, Bresidue *reslast)
	Calculates the center of an alpha helix. More...
Vector3< double >	alpha_find_orientation (Bresidue *resfirst, Bresidue *reslast)
	Calculates the orientation of an alpha helix. More...
Vector3< double >	mol_find_alpha_orientation (Bmolecule *mol, int set_std)
	Calculates the orientation of an alpha helix. More...
Vector3< double >	point_on_helix_axis (Vector3< double > ca1, Vector3< double > ca2, Vector3< double > ca3)
	Calculates a point on an alpha helix corresponding to a Ca atom. More...
long	find_closest_mean (long k, Vector3< double > *mc, Vector3< double > *ma, Vector3< double > c, Vector3< double > a, double afac)
Bmolgroup *	molgroup_consolidate_alpha (Bmolgroup *molgroup)
	Cluster a set of alpha helices to consolidate helices. More...

Variables
int	verbose
struct AlphaTemplate	alpha_template []

Detailed Description

Functions to make and analyze alpha helices.

Author

Bernard Heymann

Date

Created: 20050315

Modified: 20111030

Macro Definition Documentation

DAXIS

#define DAXIS   2.303

HANGLE

#define HANGLE   100

HRISE

#define HRISE   1.5

NTEMPATOM

#define NTEMPATOM   6

Function Documentation

alpha_find_center()

Vector3< double > alpha_find_center	(	Bresidue *	resfirst,
		Bresidue *	reslast
	)

Calculates the center of an alpha helix.

Parameters

*resfirst	first residue in helix.
*reslast	last residue in helix.

Returns

Vector3<double> center.

alpha_find_orientation()

Vector3< double > alpha_find_orientation	(	Bresidue *	resfirst,
		Bresidue *	reslast
	)

Calculates the orientation of an alpha helix.

Parameters

*resfirst	first residue in helix.
*reslast	last residue in helix.

Returns

Vector3<double> axis.

find_closest_mean()

long find_closest_mean	(	long	k,
		Vector3< double > *	mc,
		Vector3< double > *	ma,
		Vector3< double >	c,
		Vector3< double >	a,
		double	afac
	)

mol_find_alpha_orientation()

Vector3< double > mol_find_alpha_orientation	(	Bmolecule *	mol,
		int	set_std
	)

Calculates the orientation of an alpha helix.

Parameters

*mol	molecule.
set_std	rotate and shift to a standard orientation.

Returns

Vector3<double> axis.

mol_generate_alpha_helix()

Bmolecule * mol_generate_alpha_helix

(

int

length

)

Generates an alpha helix of the desired length.

Parameters

length

number of alanines to generate.

Returns

int 0.

molgroup_consolidate_alpha()

Bmolgroup * molgroup_consolidate_alpha

(

Bmolgroup *

molgroup

)

Cluster a set of alpha helices to consolidate helices.

Parameters

*molgroup

molecule group with alpha helices (deallocated).

Returns

Bmolgroup* new molecule group.

molgroup_find_helical_axes()

int molgroup_find_helical_axes

(

Bmolgroup *

molgroup

)

Calculates the centers and orientations of all alpha helices.

Parameters

*molgroup

molecule group.

Returns

int 0.

molgroup_generate_alpha_helix()

Bmolgroup * molgroup_generate_alpha_helix

(

int

length

)

Generates an alpha helix of the desired length.

Parameters

length

number of alanines to generate.

Returns

int 0.

molgroup_set_alpha_helix()

int molgroup_set_alpha_helix	(	Bmolgroup *	molgroup,
		int	helix_start,
		int	helix_end
	)

Sets a residue range to an alpha helix in all molecules.

Parameters

*molgroup	molecule group.
helix_start	first residue in helix.
helix_end	last residue in helix.

Returns

int 0.

point_on_helix_axis()

Vector3< double > point_on_helix_axis	(	Vector3< double >	ca1,
		Vector3< double >	ca2,
		Vector3< double >	ca3
	)

Calculates a point on an alpha helix corresponding to a Ca atom.

The point on the alpha helix corresponding to the second Ca atom is returned.

Parameters

ca1	first Ca atom.
ca2	second Ca atom.
ca3	third Ca atom.

Returns

Vector3<double> point on alpha helix.

Variable Documentation

alpha_template

struct AlphaTemplate alpha_template[]

Initial value:

= {
    {"N",  {1.378, -0.646, -0.926}},
    {"CA", {2.303,  0.000,  0.000}},
    {"C",  {1.599,  0.860,  1.028}},
    {"O",  {2.020,  1.002,  2.171}},
    {"CB", {3.260,  0.864, -0.824}},
    {"H",  {1.279, -0.316, -1.865}}
}

verbose

int verbose

extern