mol_symmetry.cpp File Reference

Library routines used for symmetry operations on atomic coordinates. More...

#include "rwmolecule.h"
#include "rwatomprop.h"
#include "rwresprop.h"
#include "mol_compare.h"
#include "mol_symmetry.h"
#include "mol_transform.h"
#include "mol_util.h"
#include "seq_align.h"
#include "Matrix3.h"
#include "matrix_linear.h"
#include "symmetry.h"
#include "random_numbers.h"
#include "utilities.h"
#include <fstream>

Classes
struct	MassCOM

Functions
int	molgroup_apply_point_group (Bmolgroup *molgroup, Bsymmetry &sym, View ref_view)
	Generates all symmetry-related coordinates. More...
int	molgroup_generate_helix (Bmolgroup *molgroup, View ref_view, double helix_rise, double helix_angle, int gen_down, int gen_up)
	Generates a helix from the given parameters. More...
int	molgroup_apply_symmetry_from_pdb (Bmolgroup *molgroup, Bstring &filename)
	Generates all symmetry-related coordinates using PDB file matrices. More...
int	molgroup_apply_matrices_from_pdb (Bmolgroup *molgroup, Bstring &filename)
	Generates all symmetry-related coordinates using PDB file matrices. More...
int	molgroup_find_standard_view (Bmolgroup *molgroup, Bsymmetry &sym, View ref_view)
	Searches for the standard view based on point group symmetry. More...
int	molgroup_orient_to_standard_view (Bmolgroup *molgroup, Bsymmetry &sym, View ref_view, Bresidue_matrix *simat)
	Searches for the standard view based on point group symmetry. More...
double	molgroup_symmetry_RMSD (Bmolgroup *molgroup, Bsymmetry &sym)
	Calculates the RMSD for symmetry in the standard orientation. More...
double	molgroup_symmetry_B (Bmolgroup *molgroup, Bsymmetry &sym)
	Calculates the B factors from symmetry-related molecules. More...
int	molgroup_generate_crystal (Bmolgroup *molgroup, UnitCell uc, Vector3< int > number)
	Generates unit cells from a set of coordinates. More...

Variables
int	verbose

Detailed Description

Library routines used for symmetry operations on atomic coordinates.

Author

Bernard Heymann

Date

Created: 20021020

Modified: 20180226

Function Documentation

molgroup_apply_matrices_from_pdb()

int molgroup_apply_matrices_from_pdb	(	Bmolgroup *	molgroup,
		Bstring &	filename
	)

Generates all symmetry-related coordinates using PDB file matrices.

Parameters

*molgroup	molecule group structure.
&filename	PDB file with matrices.

Returns

int 0.

Uses the BIOMT records.

molgroup_apply_point_group()

int molgroup_apply_point_group	(	Bmolgroup *	molgroup,
		Bsymmetry &	sym,
		View	ref_view
	)

Generates all symmetry-related coordinates.

Parameters

*molgroup	molecule group structure.
*sym	symmetry structure.
ref_view	reference view.

Returns

int 0.

molgroup_apply_symmetry_from_pdb()

int molgroup_apply_symmetry_from_pdb	(	Bmolgroup *	molgroup,
		Bstring &	filename
	)

Generates all symmetry-related coordinates using PDB file matrices.

Parameters

*molgroup	molecule group structure.
&filename	PDB file with matrices.

Returns

int 0.

Uses the SMTRY records.

molgroup_find_standard_view()

int molgroup_find_standard_view	(	Bmolgroup *	molgroup,
		Bsymmetry &	sym,
		View	ref_view
	)

Searches for the standard view based on point group symmetry.

Parameters

*molgroup	molecule group structure.
*sym	point group symmetry.
ref_view	reference view.

Returns

int 0.

The molecule group is first analyzed to identify the different
chains and calculate their centers-of-mass and weights.
The overall center-of-mass defines a point on at least the
major symmetry axis (cyclic symmetries), or the likely intersection
of symmetry axes.
Note: This function does a reasonable job of orienting the molecule
group, but it may be off by up to an angstrom!!!

molgroup_generate_crystal()

int molgroup_generate_crystal	(	Bmolgroup *	molgroup,
		UnitCell	uc,
		Vector3< int >	number
	)

Generates unit cells from a set of coordinates.

Parameters

*molgroup	molecule group.
uc	unit cell dimensions.
number	number of unit cells in each lattice direction.

Returns

int 0, <0 if error.

The input molecule group is duplicated to generate the requested number
of copies in each lattice direction.

molgroup_generate_helix()

int molgroup_generate_helix	(	Bmolgroup *	molgroup,
		View	ref_view,
		double	helix_rise,
		double	helix_angle,
		int	gen_down,
		int	gen_up
	)

Generates a helix from the given parameters.

Parameters

*molgroup	molecule group structure.
ref_view	reference view.
helix_rise	helical rise.
helix_angle	helical rotation angle.
gen_down	number of asymmetric units generated upwards.
gen_up	number of asymmetric units generated downwards.

Returns

int 0.

molgroup_orient_to_standard_view()

int molgroup_orient_to_standard_view	(	Bmolgroup *	molgroup,
		Bsymmetry &	sym,
		View	ref_view,
		Bresidue_matrix *	simat
	)

Searches for the standard view based on point group symmetry.

Parameters

*molgroup	molecule group structure.
*sym	point group symmetry.
ref_view	reference view (default should be 0,0,1,0).
*simat	residue similarity matrix.

Returns

int 0.

Each pair of chains in the molecule groupis tested for sequence
identity to find symmetry-related molecules. For each pair of matched
molecules, the transformation to superimpose the one onto the other
is determined and the symmetry axis and translation calculated.
The collection of symmetry axes are clustered with a k-means 
algorithm and the predominant class assigned to the major 
symmetry axis. For dihedral point groups, a minor axis is also
assigned (randomly at this time). The molecule group is then
transformed to orient it with the major axis on {0,0,1} and
the minor axis on {1,0,0}, and the symmetry center at {0,0,0}.
Note: This function has not been extensively tested with all
point groups!!!

molgroup_symmetry_B()

double molgroup_symmetry_B	(	Bmolgroup *	molgroup,
		Bsymmetry &	sym
	)

Calculates the B factors from symmetry-related molecules.

Parameters

*molgroup	molecule group structure.
*sym	point group symmetry.

Returns

double RMSD.

The centers-of-mass for all the molecules are calculated as a reduced
representation of the molecule group. All symmetry operations are 
imposed on the centers, with the RMSD defined as minimum distance
between an original cneter and a transformed center.

molgroup_symmetry_RMSD()

double molgroup_symmetry_RMSD	(	Bmolgroup *	molgroup,
		Bsymmetry &	sym
	)

Calculates the RMSD for symmetry in the standard orientation.

Parameters

*molgroup	molecule group structure.
*sym	point group symmetry.

Returns

double RMSD.

The centers-of-mass for all the molecules are calculated as a reduced
representation of the molecule group. All symmetry operations are 
imposed on the centers, with the RMSD defined as minimum distance
between an original cneter and a transformed center.

Variable Documentation

verbose

int verbose

extern