mol_compare.cpp File Reference

Library routines used to compare sets of atomic coordinates. More...

#include "rwmolecule.h"
#include "rwatomprop.h"
#include "mol_symmetry.h"
#include "mol_compare.h"
#include "mol_transform.h"
#include "mol_util.h"
#include "seq_align.h"
#include "Matrix3.h"
#include "matrix_linear.h"
#include "Matrix.h"
#include "symmetry.h"
#include "utilities.h"

Functions
double	molgroup_rotate_and_compare (Bmolgroup *molgroup, Transform t)
	Copies and rotates the molecule group and compares it with the original. More...
Transform	molgroup_find_transformation (Bmolgroup *molgroup1, Bmolgroup *molgroup2)
	Determines the transformation between two groups of identical molecules. More...
Transform	mol_find_transformation (Bmolecule *mol1, Bmolecule *mol2, int offset)
	Determines the transformation between two identical molecules. More...
double	molgroup_calculate_rmsd (Bmolgroup *molgroup1, Bmolgroup *molgroup2)
	Calculates the root-mean-square-deviation between two molecule groups. More...
double	mol_calculate_rmsd (Bmolecule *mol1, Bmolecule *mol2)
	Calculates the RMSD between two molecules. More...
double	molgroup_calc_brute_rmsd (Bmolgroup *molgroup1, Bmolgroup *molgroup2)
	Calculates the RMSD based on nearest atoms. More...
Matrix	mol_distance_matrix (Bmolecule *m1, Bmolecule *m2)
	Calculates the distance matrix between the residues in two molecules. More...

Variables
int	verbose

Detailed Description

Library routines used to compare sets of atomic coordinates.

Author

Bernard Heymann

Date

Created: 20021020

Modified: 20150209

Function Documentation

mol_calculate_rmsd()

double mol_calculate_rmsd	(	Bmolecule *	mol1,
		Bmolecule *	mol2
	)

Calculates the RMSD between two molecules.

Parameters

*mol1	first molecule.
*mol2	second molecule.

Returns

double RMSD.

The root-mean-square-deviation between two sets of corrdinates is given by:
    R = sqrt(sum(length(coord1-coord2))/number).

mol_distance_matrix()

Matrix mol_distance_matrix	(	Bmolecule *	m1,
		Bmolecule *	m2
	)

Calculates the distance matrix between the residues in two molecules.

Parameters

*m1	first molecules structure.
*m2	second molecules structure.

Returns

Matrix distance matrix.

The matrix is calculated from the pairwise distances between residues. 

mol_find_transformation()

Transform mol_find_transformation	(	Bmolecule *	mol1,
		Bmolecule *	mol2,
		int	offset
	)

Determines the transformation between two identical molecules.

Parameters

*mol1	first molecule.
*mol2	second molecule.
offset	offset of second sequence with respect to first.

Returns

Transform transform structure.

The transformation:
    coord2 = rot_mat * (coord1 - origin) + origin + shift
is solved.
The algorithm is set up in parts, solving first for:
    coord2 = rot_mat * coord1 + shift_temp
The last term is given by:
    shift_temp = shift + origin - rot_mat * origin
The shift vector must be parallel to the rotation axis, and is
determined as:
    shift = axis * |shift_temp| * cos(alpha)
where alpha is the angle between shift_temp and the rotation axis.
The origin is then calculated from:
    origin = (shift_temp - shift) * inverse(id_mat - rot_mat)
Note that the origin still has one degree of freedom: It can be
anywhere along the rotation axis.

molgroup_calc_brute_rmsd()

double molgroup_calc_brute_rmsd	(	Bmolgroup *	molgroup1,
		Bmolgroup *	molgroup2
	)

Calculates the RMSD based on nearest atoms.

Parameters

*molgroup1	first molecule group.
*molgroup2	second molecule group.

Returns

double RMSD.

molgroup_calculate_rmsd()

double molgroup_calculate_rmsd	(	Bmolgroup *	molgroup1,
		Bmolgroup *	molgroup2
	)

Calculates the root-mean-square-deviation between two molecule groups.

Parameters

*molgroup1	first molecule group.
*molgroup2	second molecule group.

Returns

double root-mean-square-deviation.

The two molecule groups must have identical structures.

molgroup_find_transformation()

Transform molgroup_find_transformation	(	Bmolgroup *	molgroup1,
		Bmolgroup *	molgroup2
	)

Determines the transformation between two groups of identical molecules.

Parameters

*molgroup1	first molecule group.
*molgroup2	second molecule group.

Returns

Transform transform structure.

molgroup_rotate_and_compare()

double molgroup_rotate_and_compare	(	Bmolgroup *	molgroup,
		Transform	t
	)

Copies and rotates the molecule group and compares it with the original.

Parameters

*molgroup	molecule group.
t	rotation operation.

Returns

double RMSD.

Variable Documentation

verbose

int verbose

extern