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Voltool.C File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <float.h>
#include "Inform.h"
#include "utilities.h"
#include "AtomSel.h"
#include "VMDApp.h"
#include "MoleculeList.h"
#include "VolumetricData.h"
#include "VolMapCreate.h"
#include "CUDAMDFF.h"
#include "MDFF.h"
#include <math.h>
#include <tcl.h>
#include "TclCommands.h"
#include "Measure.h"
#include "MolFilePlugin.h"
#include <iostream>
#include <string>
#include <sstream>
#include "Voltool.h"

Go to the source code of this file.

Functions
void	init_from_intersection (VolumetricData *mapA, const VolumetricData *mapB, VolumetricData *newvol)
	creates axes, bounding box and allocates data based on geometrical intersection of A and B. More...
void	init_from_intersection (VolumetricData *mapA, VolumetricData *mapB, VolumetricData *newvol)
	creates axes, bounding box and allocates data based on geometrical intersection of A and B. More...
void	init_from_union (VolumetricData *mapA, const VolumetricData *mapB, VolumetricData *newvol)
	creates axes, bounding box and allocates data based on geometrical union of A and B. More...
void	init_from_identity (VolumetricData *mapA, VolumetricData *newvol)
void	init_from_union (VolumetricData *mapA, VolumetricData *mapB, VolumetricData *newvol)
	creates axes, bounding box and allocates data based on geometrical union of A and B. More...
VolumetricData *	init_new_volume ()
	create a new empty volume. More...
int	init_new_volume_molecule (VMDApp *app, VolumetricData *newvol, const char *name)
	create a new VMD molecule with VolumetricData. More...
void	vol_com (VolumetricData *vol, float *com)
	calculate the centor of mass of a VolumetricData object. More...
void	add (VolumetricData *mapA, VolumetricData *mapB, VolumetricData *newvol, bool interp, bool USE_UNION)
	add voxel values from mapA and mapB together elementwise. More...
void	subtract (VolumetricData *mapA, VolumetricData *mapB, VolumetricData *newvol, bool interp, bool USE_UNION)
	subtract voxel values of mapB from mapA. More...
void	multiply (VolumetricData *mapA, VolumetricData *mapB, VolumetricData *newvol, bool interp, bool USE_UNION)
	multiplies voxel values of two mapA and mapB together. More...
void	average (VolumetricData *mapA, VolumetricData *mapB, VolumetricData *newvol, bool interp, bool USE_UNION)
	create a new VolumetricData object whose values are the average mapA and mapB at each location. More...
void	vol_moveto (VolumetricData *vol, float *com, float *pos)
	translate the center of mass of a given VolumetricData object to a specific cartesian coordinate. More...
void	vol_move (VolumetricData *vol, float *mat)
	apply a matrix transformation to a volumetricdata. More...
void	histogram (VolumetricData *vol, int nbins, long *bins, float *midpts)
	Calculate histogram of map. bins and midpts are return arrays for the counts and midpoints of the bins, respectively and must be the size of nbins. More...
int	write_file (VMDApp *app, Molecule *volmol, int volid, const char *filename)
	write volumetric data to a file using MoleFilePlugin. More...

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Function Documentation

void add (  VolumetricData *    mapA, VolumetricData *    mapB, VolumetricData *    newvol, bool    interp, bool    USE_UNION )

add voxel values from mapA and mapB together elementwise. Definition at line 249 of file Voltool.C. References VolumetricData::data, VolumetricData::gridsize, init_from_intersection, init_from_union, newvol, VolumetricData::voxel_coord, VolumetricData::voxel_value_from_coord_safe, VolumetricData::voxel_value_interpolate_from_coord_safe, and z.

void average (  VolumetricData *    mapA, VolumetricData *    mapB, VolumetricData *    newvol, bool    interp, bool    USE_UNION )

create a new VolumetricData object whose values are the average mapA and mapB at each location. Definition at line 352 of file Voltool.C. References VolumetricData::data, VolumetricData::gridsize, init_from_intersection, init_from_union, newvol, VolumetricData::voxel_coord, VolumetricData::voxel_value_from_coord_safe, VolumetricData::voxel_value_interpolate_from_coord_safe, and z.

void histogram (  VolumetricData *    vol, int    nbins, long *    bins, float *    midpts )

Calculate histogram of map. bins and midpts are return arrays for the counts and midpoints of the bins, respectively and must be the size of nbins. Definition at line 443 of file Voltool.C. References VolumetricData::data, VolumetricData::datarange, and VolumetricData::gridsize.

void init_from_identity (  VolumetricData *    mapA, VolumetricData *    newvol )

Definition at line 149 of file Voltool.C. References VolumetricData::data, VolumetricData::gridsize, newvol, VolumetricData::origin, vec_copy, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

void init_from_intersection (  VolumetricData *    mapA, VolumetricData *    mapB, VolumetricData *    newvol )

creates axes, bounding box and allocates data based on geometrical intersection of A and B. Definition at line 82 of file Voltool.C. References VolumetricData::data, dot_prod, VolumetricData::gridsize, MAX, MIN, newvol, VolumetricData::origin, vec_sub, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

void init_from_intersection (  VolumetricData *    mapA, const VolumetricData *    mapB, VolumetricData *    newvol )

creates axes, bounding box and allocates data based on geometrical intersection of A and B. Definition at line 51 of file Voltool.C. References VolumetricData::data, dot_prod, VolumetricData::gridsize, MAX, MIN, newvol, VolumetricData::origin, vec_sub, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

void init_from_union (  VolumetricData *    mapA, VolumetricData *    mapB, VolumetricData *    newvol )

creates axes, bounding box and allocates data based on geometrical union of A and B. Definition at line 167 of file Voltool.C. References VolumetricData::data, dot_prod, VolumetricData::gridsize, MAX, MIN, newvol, VolumetricData::origin, vec_zero, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

void init_from_union (  VolumetricData *    mapA, const VolumetricData *    mapB, VolumetricData *    newvol )

creates axes, bounding box and allocates data based on geometrical union of A and B. Definition at line 114 of file Voltool.C. References VolumetricData::data, dot_prod, VolumetricData::gridsize, MAX, MIN, newvol, VolumetricData::origin, vec_zero, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

VolumetricData* init_new_volume (    )

create a new empty volume. Definition at line 202 of file Voltool.C. References data, newvol, and NULL. Referenced by density_add, density_average, density_multiply, density_subtract, and mask.

int init_new_volume_molecule (  VMDApp *    app, VolumetricData *    newvol, const char *    name )

create a new VMD molecule with VolumetricData. Definition at line 216 of file Voltool.C. References VolumetricData::data, VMDApp::molecule_add_volumetric, VMDApp::molecule_addrep, VMDApp::molecule_new, VMDApp::molecule_set_style, newvol, VolumetricData::origin, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

void multiply (  VolumetricData *    mapA, VolumetricData *    mapB, VolumetricData *    newvol, bool    interp, bool    USE_UNION )

multiplies voxel values of two mapA and mapB together. Definition at line 303 of file Voltool.C. References VolumetricData::data, VolumetricData::gridsize, init_from_intersection, init_from_union, myisnan, newvol, VolumetricData::voxel_coord, VolumetricData::voxel_value_from_coord, VolumetricData::voxel_value_interpolate_from_coord, and z.

void subtract (  VolumetricData *    mapA, VolumetricData *    mapB, VolumetricData *    newvol, bool    interp, bool    USE_UNION )

subtract voxel values of mapB from mapA. Definition at line 276 of file Voltool.C. References VolumetricData::data, VolumetricData::gridsize, init_from_intersection, init_from_union, newvol, VolumetricData::voxel_coord, VolumetricData::voxel_value_from_coord_safe, VolumetricData::voxel_value_interpolate_from_coord_safe, and z.

void vol_com (  VolumetricData *    vol, float *    com )

calculate the centor of mass of a VolumetricData object. Definition at line 229 of file Voltool.C. References VolumetricData::data, VolumetricData::gridsize, vec_add, vec_scale, vec_zero, and VolumetricData::voxel_coord.

void vol_move (  VolumetricData *    vol, float *    mat )

apply a matrix transformation to a volumetricdata. Definition at line 399 of file Voltool.C. References mat, VolumetricData::origin, vec_add, vectrans, VolumetricData::xaxis, VolumetricData::yaxis, and VolumetricData::zaxis.

void vol_moveto (  VolumetricData *    vol, float *    com, float *    pos )

translate the center of mass of a given VolumetricData object to a specific cartesian coordinate. Definition at line 379 of file Voltool.C. References VolumetricData::origin, vec_add, and vec_sub.

int write_file (  VMDApp *    app, Molecule *    volmol, int    volid, const char *    filename )

write volumetric data to a file using MoleFilePlugin. Definition at line 464 of file Voltool.C. References VMDApp::get_plugin, MolFilePlugin::init_write, NULL, and MolFilePlugin::write_volumetric.

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