Library routines used for atomic coordinate transformations. More...

#include "rwmolecule.h"
#include "mol_transform.h"
#include "mol_util.h"
#include "linked_list.h"
#include "utilities.h"

Functions
Bmolgroup *	molgroup_rotate (Bmolgroup *molgroup, Matrix3 mat, Vector3< double > origin, Vector3< double > trans)

Bmolecule *	mol_rotate (Bmolecule *mol, Matrix3 mat, Vector3< double > origin, Vector3< double > trans)

int	molgroup_coor_shift (Bmolgroup *molgroup, Vector3< double > shift)
	Translates a molecule group. More...

int	mol_coor_shift (Bmolecule *mol, Vector3< double > shift)
	Translates a molecule. More...

int	molgroup_coor_rotate (Bmolgroup *molgroup, Transform t)
	Rotates and translates a molecule group. More...

int	mol_coor_rotate (Bmolecule *mol, Transform t)
	Rotates and translates a molecule. More...

Bmolgroup *	molgroup_rotate_to_view (Bmolgroup *molgroup, View view, Vector3< double > origin, Vector3< double > trans)
	Rotates a molecule group to a specified view and translates it afterwards. More...

Bmolgroup *	molgroup_rotate_from_view (Bmolgroup *molgroup, View view, Vector3< double > origin, Vector3< double > trans)
	Rotates a molecule group from a specified view and translates it afterwards. More...

Bmolecule *	mol_rotate_to_view (Bmolecule *mol, View view, Vector3< double > origin, Vector3< double > trans)
	Rotates a molecule to a specified view and translates it afterwards. More...

Bmolecule *	mol_rotate_from_view (Bmolecule *mol, View view, Vector3< double > origin, Vector3< double > trans)
	Rotates a molecule from a specified view and translates it afterwards. More...

int	molgroup_coor_transform (Bmolgroup *molgroup, Transform t)
	Rotates and translates a molecule group. More...

int	mol_coor_transform (Bmolecule *mol, Transform t)
	Rotates and translates a molecule. More...

int	molgroup_coor_invert (Bmolgroup *molgroup, Vector3< double > point)
	Inverts the coordinates of a molecule through a given point. More...

int	molgroup_resolve_pbc (Bmolgroup *molgroup)
	Recombines coordinates split across periodic box boundaries. More...

int	molgroup_pack_in_periodic_box (Bmolgroup *molgroup)
	Distributes coordinates across periodic box boundaries. More...

int	molgroup_coor_shift_PBC (Bmolgroup *molgroup, Vector3< double > shift)
	Translates a molecule within a periodic box. More...

int	molgroup_coor_shift_rotate_PBC (Bmolgroup *molgroup, Vector3< double > origin, Matrix3 mat, Vector3< double > shift)
	Translates and rotates a molecule within a periodic box. More...

int	molgroup_shift_to_center_of_mass (Bmolgroup *molgroup)
	Translates a set of coordinates to the center of mass. More...

int	mol_shift_to_center_of_mass (Bmolecule *mol)
	Translates a set of coordinates to the center of mass. More...

int	molgroup_place_at_coordinates (Bmolgroup *molgroup, Vector3< double > location)
	Translates a set of coordinates to a defined center-of-mass. More...

Variables
int	verbose

Detailed Description

Library routines used for atomic coordinate transformations.

Author: Bernard Heymann

Date: Created: 19980214; Modified: 20070614

Function Documentation

◆ mol_coor_rotate()

int mol_coor_rotate	(	Bmolecule *	mol,
		Transform	t
	)

Rotates and translates a molecule.

The new coordinates are:
    coord_new = (coord - origin)*rot_mat + origin + shift.

Parameters

*mol	molecule structure.
t	transform structure.

Returns: int 0.

◆ mol_coor_shift()

int mol_coor_shift	(	Bmolecule *	mol,
		Vector3< double >	shift
	)

Translates a molecule.

Parameters

*mol	molecule structure.
shift	three-valued translation vector.

Returns: int 0.

◆ mol_coor_transform()

int mol_coor_transform	(	Bmolecule *	mol,
		Transform	t
	)

Rotates and translates a molecule.

The new coordinates are:
    coord_new = (coord - origin)*rot_mat + origin + shift.

Parameters

*mol	molecule structure.
t	transform structure.

Returns: int 0.

◆ mol_rotate()

Bmolecule * mol_rotate	(	Bmolecule *	mol,
		Matrix3	mat,
		Vector3< double >	origin,
		Vector3< double >	trans
	)

◆ mol_rotate_from_view()

Bmolecule * mol_rotate_from_view	(	Bmolecule *	mol,
		View	view,
		Vector3< double >	origin,
		Vector3< double >	trans
	)

Rotates a molecule from a specified view and translates it afterwards.

A new rotated and translated molecule is generated.

Parameters

*mol	molecule structure (unmodified).
view	view to rotate from.
origin	origin of rotation.
trans	3-valued translation vector.

Returns: Bmolecule* new molecule group.

◆ mol_rotate_to_view()

Bmolecule * mol_rotate_to_view	(	Bmolecule *	mol,
		View	view,
		Vector3< double >	origin,
		Vector3< double >	trans
	)

Rotates a molecule to a specified view and translates it afterwards.

A new rotated and translated molecule is generated.

Parameters

*mol	molecule structure (unmodified).
view	view to rotate to.
origin	origin of rotation.
trans	3-valued translation vector.

Returns: Bmolecule* new molecule group.

◆ mol_shift_to_center_of_mass()

int mol_shift_to_center_of_mass ( Bmolecule * mol )

Translates a set of coordinates to the center of mass.

The function mol_center_of_mass is used to calculate the center of mass.
The function mol_coor_shift is used to shift the coordinates.

Parameters

*mol	molecule structure.

Returns: int 0.

◆ molgroup_coor_invert()

int molgroup_coor_invert	(	Bmolgroup *	molgroup,
		Vector3< double >	point
	)

Inverts the coordinates of a molecule through a given point.

Parameters

*molgroup	molecule group structure.
point	3-valued inversion point.

Returns: int 0.

◆ molgroup_coor_rotate()

int molgroup_coor_rotate	(	Bmolgroup *	molgroup,
		Transform	t
	)

Rotates and translates a molecule group.

The new coordinates are:
    coord_new = (coord - origin)*rot_mat + origin + shift.

Parameters

*molgroup	molecule group structure.
t	transform structure.

Returns: int 0.

◆ molgroup_coor_shift()

int molgroup_coor_shift	(	Bmolgroup *	molgroup,
		Vector3< double >	shift
	)

Translates a molecule group.

Parameters

*molgroup	molecule group structure.
shift	three-valued translation vector.

Returns: int 0.

◆ molgroup_coor_shift_PBC()

int molgroup_coor_shift_PBC	(	Bmolgroup *	molgroup,
		Vector3< double >	shift
	)

Translates a molecule within a periodic box.

The periodic box is defined in the molecule group structure.

Parameters

*molgroup	molecule group structure.
shift	three-valued translation vector.

Returns: int 0.

◆ molgroup_coor_shift_rotate_PBC()

int molgroup_coor_shift_rotate_PBC	(	Bmolgroup *	molgroup,
		Vector3< double >	origin,
		Matrix3	mat,
		Vector3< double >	shift
	)

Translates and rotates a molecule within a periodic box.

The molecule group is first rotated around the origin and then shifted.
The periodic box is defined in the molecule group structure.

Parameters

*molgroup	molecule group structure.
origin	3-valued origin for rotation.
mat	3x3 rotation matrix.
shift	3-valued translation vector.

Returns: int 0.

◆ molgroup_coor_transform()

int molgroup_coor_transform	(	Bmolgroup *	molgroup,
		Transform	t
	)

Rotates and translates a molecule group.

The new coordinates are:
    coord_new = (coord - origin)*rot_mat + origin + shift.

Parameters

*molgroup	molecule group structure.
t	transform structure.

Returns: int 0.

◆ molgroup_pack_in_periodic_box()

int molgroup_pack_in_periodic_box ( Bmolgroup * molgroup )

Distributes coordinates across periodic box boundaries.

Parameters

*molgroup molecule group structure.

Returns: int 0.

◆ molgroup_place_at_coordinates()

int molgroup_place_at_coordinates	(	Bmolgroup *	molgroup,
		Vector3< double >	location
	)

Translates a set of coordinates to a defined center-of-mass.

The function molgroup_center_of_mass is used to calculate the center of mass.
The function molgroup_coor_shift is used to shift the coordinates.

Parameters

*molgroup	molecule group structure.
location	desired center-of-mass coordinates.

Returns: int 0.

◆ molgroup_resolve_pbc()

int molgroup_resolve_pbc ( Bmolgroup * molgroup )

Recombines coordinates split across periodic box boundaries.

Parameters

*molgroup molecule group structure.

Returns

int 0.

The center of mass of each molecule is calculated to determine the
shift needed to be applied to get the center of mass within the box.

◆ molgroup_rotate()

Bmolgroup * molgroup_rotate	(	Bmolgroup *	molgroup,
		Matrix3	mat,
		Vector3< double >	origin,
		Vector3< double >	trans
	)

◆ molgroup_rotate_from_view()

Bmolgroup * molgroup_rotate_from_view	(	Bmolgroup *	molgroup,
		View	view,
		Vector3< double >	origin,
		Vector3< double >	trans
	)

Rotates a molecule group from a specified view and translates it afterwards.

A new rotated and translated molecule group is generated.

Parameters

*molgroup	molecule group structure (unmodified).
view	view to rotate from.
origin	origin of rotation.
trans	3-valued translation vector.

Returns: Bmolgroup* new molecule group.

◆ molgroup_rotate_to_view()

Bmolgroup * molgroup_rotate_to_view	(	Bmolgroup *	molgroup,
		View	view,
		Vector3< double >	origin,
		Vector3< double >	trans
	)

Rotates a molecule group to a specified view and translates it afterwards.

A new rotated and translated molecule group is generated.

Parameters

*molgroup	molecule group structure (unmodified).
view	view to rotate to.
origin	origin of rotation.
trans	3-valued translation vector.

Returns: Bmolgroup* new molecule group.

◆ molgroup_shift_to_center_of_mass()

int molgroup_shift_to_center_of_mass ( Bmolgroup * molgroup )

Translates a set of coordinates to the center of mass.

The function molgroup_center_of_mass is used to calculate the center of mass.
The function molgroup_coor_shift is used to shift the coordinates.

Parameters

*molgroup molecule group structure.

Returns: int 0.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ mol_coor_rotate()

◆ mol_coor_shift()

◆ mol_coor_transform()

◆ mol_rotate()

◆ mol_rotate_from_view()

◆ mol_rotate_to_view()

◆ mol_shift_to_center_of_mass()

◆ molgroup_coor_invert()

◆ molgroup_coor_rotate()

◆ molgroup_coor_shift()

◆ molgroup_coor_shift_PBC()

◆ molgroup_coor_shift_rotate_PBC()

◆ molgroup_coor_transform()

◆ molgroup_pack_in_periodic_box()

◆ molgroup_place_at_coordinates()

◆ molgroup_resolve_pbc()

◆ molgroup_rotate()

◆ molgroup_rotate_from_view()

◆ molgroup_rotate_to_view()

◆ molgroup_shift_to_center_of_mass()

Variable Documentation

◆ verbose