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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


Define Documentation

#define M_PI_2   1.57079632679489661922
 

Definition at line 33 of file cubeplugin.C.

Referenced by cube_readbox.


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.


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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