molecule_to_map.cpp File Reference

Functions to calculate a 3D map from atomic coordinates. More...

#include "molecule_to_map.h"
#include "scatter.h"
#include "Complex.h"
#include "UnitCell.h"
#include "linked_list.h"
#include "utilities.h"
#include <fstream>

Macros
#define	MAXSID   1024
#define	MAXSCAT   100
#define	MAXRAD   100

Functions
int	mol_to_image (Bmolgroup *molgroup, Bimage *p, Batomtype *atompar, double resolution, double Bfactor, int wrap, int gextype)
int	mol_to_structure_factors (Bmolgroup *molgroup, Bimage *p, Batomtype *atompar, double resolution, int wrap, double Bfactor)
Bimage *	img_from_molecule (Bmolgroup *molgroup, Vector3< double > origin, Vector3< long > size, Vector3< double > sampling, double resolution, double Bfactor, int wrap, int gextype, int spacegroup, UnitCell unit_cell)
	Calculates a 3D density map from a set of atomic coordinates. More...
int	compare_mol_map (Bmolgroup *molgroup, Bimage *pcalc, Bimage *p)
	Compares reference and calculated maps and calculates an occupancy for every atom in the molecule set. More...
Bimage *	img_sf_from_molecule (Bmolgroup *molgroup, Vector3< double > origin, Vector3< long > size, Vector3< double > sampling, double resolution, int spacegroup, UnitCell unit_cell, int wrap, double Bfactor, Bstring &paramfile)
	Calculates a 3D set of structure factors from a set of atomic coordinates. More...
double	one_sf (Bmolgroup *molgroup, Bimage *p, long i, double s, double scale, double *scat)
double *	get_potential_curves (Batomtype *atompar, double interval)
double *	get_scattering_curves (Batomtype *atompar, double Bfactor, double recip_interval, long &nscat)
map< string, vector< double > >	get_scattering_curves (map< string, Bcomptype > &types, double Bfactor, double recip_interval)

Variables
int	verbose

Detailed Description

Functions to calculate a 3D map from atomic coordinates.

Author

Bernard Heymann

Date

Created: 19970914

Modified: 20210216

Macro Definition Documentation

MAXRAD

#define MAXRAD   100

MAXSCAT

#define MAXSCAT   100

MAXSID

#define MAXSID   1024

Function Documentation

compare_mol_map()

int compare_mol_map	(	Bmolgroup *	molgroup,
		Bimage *	pcalc,
		Bimage *	p
	)

Compares reference and calculated maps and calculates an occupancy for every atom in the molecule set.

Parameters

*molgroup	set of molecules with atomic coordinates.
*pcalc	map calculated from the set of molecules.
*p	reference map.

Returns

int 0.

get_potential_curves()

double * get_potential_curves	(	Batomtype *	atompar,
		double	interval
	)

get_scattering_curves() [1/2]

double * get_scattering_curves	(	Batomtype *	atompar,
		double	Bfactor,
		double	recip_interval,
		long &	nscat
	)

get_scattering_curves() [2/2]

map< string, vector< double > > get_scattering_curves	(	map< string, Bcomptype > &	types,
		double	Bfactor,
		double	recip_interval
	)

img_from_molecule()

Bimage * img_from_molecule	(	Bmolgroup *	molgroup,
		Vector3< double >	origin,
		Vector3< long >	size,
		Vector3< double >	sampling,
		double	resolution,
		double	Bfactor,
		int	wrap,
		int	gextype,
		int	spacegroup,
		UnitCell	unit_cell
	)

Calculates a 3D density map from a set of atomic coordinates.

Parameters

*molgroup	set of molecules with atomic coordinates.
origin	3-valued origin vector (angstrom).
size	3-valued size vector (voxels).
sampling	sampling/voxel size (angstrom/voxel).
resolution	resolution (angstrom).
Bfactor	global B-factor to use, if 0, use individual atom B-factors
wrap	wrapping flag.
gextype	type of gaussian used: 0 = single, 1 = atomic potential
spacegroup	crystal space group.
unit_cell	6-valued vector of unit cell parameters.

Returns

Bimage* the new map.

A 3D map is calculated from atomic coordinates by placing a gaussian
sphere at each set of atomic coordinates. The resolution is set as
twice the sigma coefficient of the gaussian function. The amplitude
of the gaussian function is set so that the total density calculated
equals the atomic mass. The resultant map therefore has the density
units of Dalton/voxel.
The statistics of the new image is calculated.

img_sf_from_molecule()

Bimage * img_sf_from_molecule	(	Bmolgroup *	molgroup,
		Vector3< double >	origin,
		Vector3< long >	size,
		Vector3< double >	sampling,
		double	resolution,
		int	spacegroup,
		UnitCell	unit_cell,
		int	wrap,
		double	Bfactor,
		Bstring &	paramfile
	)

Calculates a 3D set of structure factors from a set of atomic coordinates.

Parameters

*molgroup	set of molecules with atomic coordinates.
origin	3-valued origin vector (voxels).
size	3-valued size vector (voxels).
sampling	sampling/voxel size (angstrom/voxel).
resolution	resolution (angstrom).
spacegroup	crystal space group.
unit_cell	6-valued vector of unit cell parameters.
wrap	0=cut atoms outside box, 1=wrap coordinates within unit cell.
Bfactor	constant for decay curve.
&paramfile	parameter file with scattering coefficients.

Returns

Bimage* the new structure factors.

All structure factors within a given resolution are calculated from
all the selected atomic coordinates. The coordinates are fractionalized
to fit into the given size box. If the size of the box is not given,
it defaults to:
    x_size = (max(x_coor) - min(x_coor)) / x_sampling
The atomic scattering profiles are read from the STAR database as the
amplitudes and B-factors of reciprocal space gaussians. For each profile,
a lookup table is calculated to speed up further calculations.
The statistics of the new image is calculated.

mol_to_image()

int mol_to_image	(	Bmolgroup *	molgroup,
		Bimage *	p,
		Batomtype *	atompar,
		double	resolution,
		double	Bfactor,
		int	wrap,
		int	gextype
	)

mol_to_structure_factors()

int mol_to_structure_factors	(	Bmolgroup *	molgroup,
		Bimage *	p,
		Batomtype *	atompar,
		double	resolution,
		int	wrap,
		double	Bfactor
	)

one_sf()

double one_sf	(	Bmolgroup *	molgroup,
		Bimage *	p,
		long	i,
		double	s,
		double	scale,
		double *	scat
	)

Variable Documentation

verbose

int verbose

extern