mol_alpha.h File Reference

Header for functions to make and analyze alpha helices. More...

#include "rwmolecule.h"

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...
Bmolgroup *	molgroup_consolidate_alpha (Bmolgroup *molgroup)
	Cluster a set of alpha helices to consolidate helices. More...

Detailed Description

Header for functions to make and analyze alpha helices.

Author

Bernard Heymann

Date

Created: 20050315

Modified: 20060121

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.

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.