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cubeplugin.C File Reference

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "molfile_plugin.h"
#include "periodic_table.h"

Go to the source code of this file.

Compounds
struct	cube_box
struct	cube_t
Defines
#define	M_PI_2   1.57079632679489661922
Functions
int	cube_readbox (cube_box *box, float *x, float *y, float *z)
void	cube_buildrotmat (cube_t *cube, float *o, float *a, float *b)
void	eatline (FILE *fd)
void	close_cube_read (void *v)
void *	open_cube_read (const char *filepath, const char *filetype, int *natoms)
int	read_cube_structure (void *v, int *optflags, molfile_atom_t *atoms)
int	read_cube_timestep (void *v, int natoms, molfile_timestep_t *ts)
int	read_cube_metadata (void *v, int *nsets, molfile_volumetric_t **metadata)
int	read_cube_data (void *v, int set, float *datablock, float *colorblock)
int	VMDPLUGIN_init (void)
int	VMDPLUGIN_fini (void)
int	VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
Variables
const float	bohr = 0.529177249
molfile_plugin_t	plugin

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Define Documentation

#define M_PI_2   1.57079632679489661922

Definition at line 33 of file cubeplugin.C. Referenced by cube_readbox.

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Function Documentation

void close_cube_read (  void *    v )  [static]

Definition at line 559 of file cubeplugin.C. References cube_t::datacache, cube_t::fd, cube_t::file_name, and cube_t::vol. Referenced by open_cube_read.

void cube_buildrotmat (  cube_t *    cube, float *    o, float *    a, float *    b )  [static]

Definition at line 98 of file cubeplugin.C. References cube_t::origin, and cube_t::rotmat. Referenced by open_cube_read.

int cube_readbox (  cube_box *    box, float *    x, float *    y, float *    z )  [static]

Definition at line 62 of file cubeplugin.C. References cube_box::A, cube_box::alpha, cube_box::B, cube_box::beta, cube_box::C, cube_box::gamma, and M_PI_2. Referenced by open_cube_read.

void eatline (  FILE *    fd )  [static]

Definition at line 130 of file cubeplugin.C.

void* open_cube_read (  const char *    filepath, const char *    filetype, int *    natoms )  [static]

Definition at line 138 of file cubeplugin.C. References bohr, cube_t::box, close_cube_read, cube_t::coord, cube_t::crdpos, cube_buildrotmat, cube_readbox, cube_t::datacache, molfile_volumetric_t::dataname, cube_t::datapos, eatline, cube_t::fd, cube_t::file_name, molfile_volumetric_t::has_color, cube_t::nsets, cube_t::numatoms, molfile_volumetric_t::origin, cube_t::origin, cube_t::rotmat, cube_t::vol, molfile_volumetric_t::xaxis, molfile_volumetric_t::xsize, molfile_volumetric_t::yaxis, molfile_volumetric_t::ysize, molfile_volumetric_t::zaxis, and molfile_volumetric_t::zsize.

int read_cube_data (  void *    v, int    set, float *    datablock, float *    colorblock )  [static]

Definition at line 486 of file cubeplugin.C. References cube_t::datacache, cube_t::datapos, cube_t::fd, MOLFILE_ERROR, MOLFILE_SUCCESS, cube_t::nsets, cube_t::vol, molfile_volumetric_t::xsize, molfile_volumetric_t::ysize, and molfile_volumetric_t::zsize.

int read_cube_metadata (  void *    v, int *    nsets, molfile_volumetric_t **    metadata )  [static]

Definition at line 477 of file cubeplugin.C. References MOLFILE_SUCCESS, cube_t::nsets, and cube_t::vol.

int read_cube_structure (  void *    v, int *    optflags, molfile_atom_t *    atoms )  [static]

Definition at line 360 of file cubeplugin.C. References molfile_atom_t::atomicnumber, molfile_atom_t::chain, cube_t::crdpos, cube_t::fd, cube_t::file_name, get_pte_mass, get_pte_vdw_radius, molfile_atom_t::mass, MOLFILE_ATOMICNUMBER, MOLFILE_ERROR, MOLFILE_MASS, MOLFILE_RADIUS, MOLFILE_SUCCESS, molfile_atom_t::name, cube_t::numatoms, molfile_atom_t::radius, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type.

int read_cube_timestep (  void *    v, int    natoms, molfile_timestep_t *    ts )  [static]

Definition at line 413 of file cubeplugin.C. References cube_box::A, molfile_timestep_t::A, cube_box::alpha, molfile_timestep_t::alpha, cube_box::B, molfile_timestep_t::B, cube_box::beta, molfile_timestep_t::beta, bohr, cube_t::box, cube_box::C, molfile_timestep_t::C, cube_t::coord, molfile_timestep_t::coords, cube_t::crdpos, cube_t::fd, cube_t::file_name, cube_box::gamma, molfile_timestep_t::gamma, MOLFILE_EOF, MOLFILE_ERROR, MOLFILE_SUCCESS, cube_t::numatoms, cube_t::origin, and cube_t::rotmat.

int VMDPLUGIN_fini (  void    )

Definition at line 603 of file cubeplugin.C. References VMDPLUGIN_SUCCESS.

int VMDPLUGIN_init (  void    )

Definition at line 602 of file cubeplugin.C. References VMDPLUGIN_SUCCESS.

int VMDPLUGIN_register (  void *    v, vmdplugin_register_cb    cb )

Definition at line 604 of file cubeplugin.C. References vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

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Variable Documentation

const float bohr = 0.529177249 [static]

Definition at line 38 of file cubeplugin.C. Referenced by open_cube_read, and read_cube_timestep.

molfile_plugin_t plugin [static]

Initial value: { vmdplugin_ABIVERSION, MOLFILE_PLUGIN_TYPE, "cube", "Gaussian Cube", "Axel Kohlmeyer, John E. Stone", 0, 8, VMDPLUGIN_THREADSAFE, "cube", open_cube_read, read_cube_structure, 0, read_cube_timestep, close_cube_read, 0, 0, 0, 0, read_cube_metadata, read_cube_data, 0 } Definition at line 578 of file cubeplugin.C.

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