Library routines used for atomic coordinates. More...

#include "rwmolecule.h"
#include "rwatomprop.h"
#include "rwresprop.h"
#include "mol_util.h"
#include "seq_util.h"
#include "linked_list.h"
#include "Matrix.h"
#include "utilities.h"
#include <map>

Functions
int	molgroup_Bfactors (Bmolgroup *molgroup)
	Calculates the average Bfactors for residues in molecules. More...

int	molgroup_print_sequence (Bmolgroup *molgroup)
	Prints the sequence of a molecule as a single letter code string. More...

int	molgroup_set_radius (Bmolgroup *molgroup, double radius)
	Shifts all coordinates to a given radius. More...

int	molgroup_rename (Bmolgroup *molgroup, char first_name)
	Renames molecules. More...

int	molgroup_residue_renumber (Bmolgroup *molgroup, int first)
	Renumbers residues. More...

int	molgroup_atom_renumber (Bmolgroup *molgroup, int first)
	Renumbers all atoms, disregarding molecule distinction. More...

int	molgroup_coor_reset_occupancy (Bmolgroup *molgroup, int range_first, int range_last, double occupancy)
	Sets occupancies to new values.. More...

double	molgroup_weight_from_atoms (Bmolgroup *molgroup)
	Calculates the weight of each molecule. More...

double	molgroup_weight_from_sequence (Bmolgroup *molgroup)
	Calculates the weight of each molecule. More...

Vector3< double >	molgroup_center_of_mass (Bmolgroup *molgroup)
	Calculates the center of mass of a molecule group. More...

Vector3< double >	molgroup_selected_center_of_mass (Bmolgroup *molgroup)
	Calculates the center of mass of a molecule group. More...

Vector3< double >	molgroup_show_center_of_mass (Bmolgroup *molgroup)
	Calculates the center of mass of a molecule group. More...

Vector3< double >	mol_center_of_mass (Bmolecule *mol)
	Calculates the center of mass of a molecule. More...

Vector3< double >	mol_show_center_of_mass (Bmolecule *mol)
	Calculates the center of mass of a molecule. More...

Vector3< double >	molgroup_principal_axes (Bmolgroup molgroup, Vector3< double > eigenvec)
	Calculates the principal axes of a molecule group. More...

Vector3< double >	mol_principal_axes (Bmolecule mol, Vector3< double > eigenvec)
	Calculates the principal axes of a molecule. More...

double	molgroup_sphericity (Bmolgroup *molgroup, double da)
	Calculates how close the coordinate set is to a spherical shape. More...

double	molgroup_density (Bmolgroup *molgroup)
	Calculates the number and mass density of a molecular system. More...

double	molgroup_volume (Bmolgroup *molgroup, Bstring &paramfile, int wrap)
	Calculates the volume of a molecular system. More...

int	molgroup_composition (Bmolgroup *molgroup, Bstring &paramfile)
	Calculates the elemental composition of a molecular system. More...

JSvalue	molgroup_elements (Bmolgroup *molgroup)
	Calculates the elemental composition. More...

JSvalue	molgroup_elements (Bmolgroup *molgroup, Bstring &paramfile)
	Calculates the elemental composition from residue compositions. More...

JSvalue	protein_composition_default (double mass)
	Default protein composition adjusted by mass. More...

int	molgroup_radial_density (Bmolgroup *molgroup, double interval, double cutoff, int wrap)
	Calculates a radial distribution function. More...

Latom **	molgroup_atom_mesh_lists (Bmolgroup *molgroup, Vector3< int > size, Vector3< double > sampling)
	Generates lists of atoms based on a grid. More...

vector< Batom * >	atom_get_array (Bmolgroup *molgroup)
	Generates an array of pointers to atom structures. More...

Variables
int	verbose

Detailed Description

Library routines used for atomic coordinates.

Author: Bernard Heymann

Date: Created: 19980214; Modified: 20220713

Function Documentation

◆ atom_get_array()

vector< Batom * > atom_get_array ( Bmolgroup * molgroup )

Generates an array of pointers to atom structures.

Parameters

*molgroup molecule group structure to be modified.

Returns: vector<Batom*> array of pointers to atoms.

◆ mol_center_of_mass()

Vector3< double > mol_center_of_mass ( Bmolecule * mol )

Calculates the center of mass of a molecule.

Parameters

*mol	molecule structure.

Returns: Vector3<double> 3-valued center of mass vector.

◆ mol_principal_axes()

Vector3< double > mol_principal_axes	(	Bmolecule *	mol,
		Vector3< double > *	eigenvec
	)

Calculates the principal axes of a molecule.

Parameters

*mol	molecule structure.
*eigenvec	eigen vectors (can be NULL).

Returns: Vector3<double> 3-valued vector of principal axes.

◆ mol_show_center_of_mass()

Vector3< double > mol_show_center_of_mass ( Bmolecule * mol )

Calculates the center of mass of a molecule.

Parameters

*mol	molecule structure.

Returns: Vector3<double> 3-valued center of mass vector.

◆ molgroup_atom_mesh_lists()

Latom ** molgroup_atom_mesh_lists	(	Bmolgroup *	molgroup,
		Vector3< int >	size,
		Vector3< double >	sampling
	)

Generates lists of atoms based on a grid.

The coordinates must be positive to fit into a grid starting at {0,0,0}.

Parameters

*molgroup	molecule group structure to be modified.
size	size of grid.
sampling	spacing in each dimension.

Returns: Latom** array of linked lists of atoms.

◆ molgroup_atom_renumber()

int molgroup_atom_renumber	(	Bmolgroup *	molgroup,
		int	first
	)

Renumbers all atoms, disregarding molecule distinction.

Parameters

*molgroup	molecule group structure.
first	number of first atom.

Returns: int 0.

◆ molgroup_Bfactors()

int molgroup_Bfactors ( Bmolgroup * molgroup )

Calculates the average Bfactors for residues in molecules.

Parameters

*molgroup molecule group structure.

Returns: int 0.

◆ molgroup_center_of_mass()

Vector3< double > molgroup_center_of_mass ( Bmolgroup * molgroup )

Calculates the center of mass of a molecule group.

Parameters

*molgroup molecule group structure.

Returns: Vector3<double> 3-valued center of mass vector.

◆ molgroup_composition()

int molgroup_composition	(	Bmolgroup *	molgroup,
		Bstring &	paramfile
	)

Calculates the elemental composition of a molecular system.

Parameters

*molgroup	molecule group structure.
&paramfile	atomic parameter file.

Returns: int 0.

◆ molgroup_coor_reset_occupancy()

int molgroup_coor_reset_occupancy	(	Bmolgroup *	molgroup,
		int	range_first,
		int	range_last,
		double	occupancy
	)

Sets occupancies to new values..

Parameters

*molgroup	molecule group structure.
range_first	first residue in range to change.
range_last	last residue in range to change.
occupancy	value to set occupancy to.

Returns: int 0.

◆ molgroup_density()

double molgroup_density ( Bmolgroup * molgroup )

Calculates the number and mass density of a molecular system.

Parameters

*molgroup molecule group structure.

Returns

double density: Da/A^3.

Requirement: The box size must be correctly specified in the
molecular group structure.
The number of molecules, residues and atoms are calculated and the
density for each number reported.
The total mass is calculated and the mass density reported as
Da/A^3 and g/ml.

◆ molgroup_elements() [1/2]

JSvalue molgroup_elements ( Bmolgroup * molgroup )

Calculates the elemental composition.

Parameters

*molgroup molecule group.

Returns: JSvalue composition.

◆ molgroup_elements() [2/2]

JSvalue molgroup_elements	(	Bmolgroup *	molgroup,
		Bstring &	paramfile
	)

Calculates the elemental composition from residue compositions.

Parameters

*molgroup	molecule group.
&paramfile	residue parameter file.

Returns: JSvalue composition.

◆ molgroup_principal_axes()

Vector3< double > molgroup_principal_axes	(	Bmolgroup *	molgroup,
		Vector3< double > *	eigenvec
	)

Calculates the principal axes of a molecule group.

Parameters

*molgroup	molecule group structure.
*eigenvec	eigen vectors (can be NULL).

Returns: Vector3<double> 3-valued vector of principal axes.

◆ molgroup_print_sequence()

int molgroup_print_sequence ( Bmolgroup * molgroup )

Prints the sequence of a molecule as a single letter code string.

Parameters

*molgroup molecule group structure.

Returns: int 0.

◆ molgroup_radial_density()

int molgroup_radial_density	(	Bmolgroup *	molgroup,
		double	interval,
		double	cutoff,
		int	wrap
	)

Calculates a radial distribution function.

Parameters

*molgroup	molecule group.
interval	interval between bins.
cutoff	distance cutoff.
wrap	flag to use periodic boundaries.

Returns

int 0.

The atoms are not distinguished by type or properties.

◆ molgroup_rename()

int molgroup_rename	(	Bmolgroup *	molgroup,
		char	first_name
	)

Renames molecules.

Parameters

*molgroup	molecule group structure.
first_name	letter of first molecule.

Returns

int 0.

Letters are assigned to the molecules in sequence starting from the
given first letter. If it extends beyond 'Z', it restarts at 'A'.

◆ molgroup_residue_renumber()

int molgroup_residue_renumber	(	Bmolgroup *	molgroup,
		int	first
	)

Renumbers residues.

Parameters

*molgroup	molecule group structure.
first	number of first residue.

Returns: int 0.

◆ molgroup_selected_center_of_mass()

Vector3< double > molgroup_selected_center_of_mass ( Bmolgroup * molgroup )

Calculates the center of mass of a molecule group.

Parameters

*molgroup molecule group structure.

Returns: Vector3<double> 3-valued center of mass vector.

◆ molgroup_set_radius()

int molgroup_set_radius	(	Bmolgroup *	molgroup,
		double	radius
	)

Shifts all coordinates to a given radius.

Parameters

*molgroup	molecule group structure.
radius	spherical radius.

Returns: int 0.

◆ molgroup_show_center_of_mass()

Vector3< double > molgroup_show_center_of_mass ( Bmolgroup * molgroup )

Calculates the center of mass of a molecule group.

Parameters

*molgroup molecule group structure.

Returns: Vector3<double> 3-valued center of mass vector.

◆ molgroup_sphericity()

double molgroup_sphericity	(	Bmolgroup *	molgroup,
		double	da
	)

Calculates how close the coordinate set is to a spherical shape.

Parameters

*molgroup	molecule group structure.
da	angular step size. (in radians)

Returns

double sphericity.

For each solid angle, the algorithm finds the coordinates with the
maximum distance from the center-of-mass.

◆ molgroup_volume()

double molgroup_volume	(	Bmolgroup *	molgroup,
		Bstring &	paramfile,
		int	wrap
	)

Calculates the volume of a molecular system.

Parameters

*molgroup	molecule group structure.
&paramfile	atomic parameter file.
wrap	flag to turn on wrapping.

Returns

double volume in angstrom^3.

The volume occupied by all the atoms is estimated from the footprint
under the Van der Waals volume of each atom.

◆ molgroup_weight_from_atoms()

double molgroup_weight_from_atoms ( Bmolgroup * molgroup )

Calculates the weight of each molecule.

Parameters

*molgroup molecule group structure.

Returns: double total mass of the molecule group.

◆ molgroup_weight_from_sequence()

double molgroup_weight_from_sequence ( Bmolgroup * molgroup )

Calculates the weight of each molecule.

Parameters

*molgroup molecule group structure.

Returns: double total mass of the molecule group.

◆ protein_composition_default()

JSvalue protein_composition_default ( double mass )

Default protein composition adjusted by mass.

Parameters

mass	molecular weight.

Returns: JSvalue composition.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ atom_get_array()

◆ mol_center_of_mass()

◆ mol_principal_axes()

◆ mol_show_center_of_mass()

◆ molgroup_atom_mesh_lists()

◆ molgroup_atom_renumber()

◆ molgroup_Bfactors()

◆ molgroup_center_of_mass()

◆ molgroup_composition()

◆ molgroup_coor_reset_occupancy()

◆ molgroup_density()

◆ molgroup_elements() [1/2]

◆ molgroup_elements() [2/2]

◆ molgroup_principal_axes()

◆ molgroup_print_sequence()

◆ molgroup_radial_density()

◆ molgroup_rename()

◆ molgroup_residue_renumber()

◆ molgroup_selected_center_of_mass()

◆ molgroup_set_radius()

◆ molgroup_show_center_of_mass()

◆ molgroup_sphericity()

◆ molgroup_volume()

◆ molgroup_weight_from_atoms()

◆ molgroup_weight_from_sequence()

◆ protein_composition_default()

Variable Documentation

◆ verbose