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cdfplugin.c File Reference

#include <netcdf.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "molfile_plugin.h"

Go to the source code of this file.

Compounds
struct	amberdata
struct	cdfdata
struct	mmtkdata
Defines
#define	CDF_TYPE_UNKNOWN   0
#define	CDF_TYPE_AMBER   1
#define	CDF_TYPE_MMTK   2
Functions
void	close_cdf_read (void *mydata)
int	open_amber_cdf_read (cdfdata *cdf)
int	open_mmtk_cdf_read (cdfdata *cdf)
void *	open_cdf_read (const char *filename, const char *filetype, int *natoms)
char *	find_closing_bracket (char *s)
void	atom_name_replace (char *name, char *substring, char letter)
void	atom_name_remove_underscores (char *name)
void	set_atom_attributes (molfile_atom_t *atoms, int natoms, char **atom_pointers, char chain_id, char *resname, int resnum, char *start, char *end, int name_correction_type)
int	read_mmtk_cdf_structure (void *mydata, int *optflags, molfile_atom_t *atoms)
int	read_cdf_structure (void *mydata, int *optflags, molfile_atom_t *atoms)
int	read_amber_cdf_timestep (void *mydata, int natoms, molfile_timestep_t *ts)
int	read_mmtk_cdf_timestep (void *mydata, int natoms, molfile_timestep_t *ts)
int	read_cdf_timestep (void *mydata, int natoms, molfile_timestep_t *ts)
VMDPLUGIN_API int	VMDPLUGIN_init (void)
VMDPLUGIN_API int	VMDPLUGIN_fini (void)
VMDPLUGIN_API int	VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
Variables
molfile_plugin_t	cdfplugin

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Define Documentation

#define CDF_TYPE_AMBER   1

Definition at line 30 of file cdfplugin.c. Referenced by open_amber_cdf_read, read_cdf_structure, and read_cdf_timestep.

#define CDF_TYPE_MMTK   2

Definition at line 31 of file cdfplugin.c. Referenced by open_mmtk_cdf_read, read_cdf_structure, and read_cdf_timestep.

#define CDF_TYPE_UNKNOWN   0

Definition at line 29 of file cdfplugin.c. Referenced by open_cdf_read.

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Function Documentation

void atom_name_remove_underscores (  char *    name )  [static]

Definition at line 454 of file cdfplugin.c. References name. Referenced by set_atom_attributes.

void atom_name_replace (  char *    name, char *    substring, char    letter )  [static]

Definition at line 446 of file cdfplugin.c. References name. Referenced by set_atom_attributes.

void close_cdf_read (  void *    mydata )  [static]

Definition at line 95 of file cdfplugin.c. References cdfdata::amber, amberdata::application, mmtkdata::comment, cdfdata::conventions, amberdata::conventionversion, cdfdata::mmtk, cdfdata::ncid, amberdata::program, amberdata::programversion, and amberdata::title. Referenced by open_cdf_read.

char* find_closing_bracket (  char *    s )  [static]

Definition at line 433 of file cdfplugin.c. Referenced by read_mmtk_cdf_structure.

int open_amber_cdf_read (  cdfdata *    cdf )  [static]

Definition at line 129 of file cdfplugin.c. References cdfdata::amber, amberdata::application, amberdata::atomdim, amberdata::atomdimid, CDF_TYPE_AMBER, amberdata::cell_angles_id, amberdata::cell_lengths_id, amberdata::conventionversion, amberdata::coordinates_id, amberdata::framedim, amberdata::framedimid, amberdata::has_box, cdfdata::natoms, cdfdata::ncid, amberdata::program, amberdata::programversion, amberdata::spatial_id, amberdata::spatialdim, amberdata::spatialdimid, amberdata::title, cdfdata::type, and amberdata::velocities_id. Referenced by open_cdf_read.

void* open_cdf_read (  const char *    filename, const char *    filetype, int *    natoms )  [static]

Definition at line 383 of file cdfplugin.c. References CDF_TYPE_UNKNOWN, close_cdf_read, cdfdata::conventions, cdfdata::natoms, cdfdata::ncid, open_amber_cdf_read, open_mmtk_cdf_read, and cdfdata::type.

int open_mmtk_cdf_read (  cdfdata *    cdf )  [static]

Definition at line 269 of file cdfplugin.c. References mmtkdata::atom_numberdim, mmtkdata::atom_numberdimid, mmtkdata::box_size_id, CDF_TYPE_MMTK, mmtkdata::comment, mmtkdata::configuration_id, mmtkdata::description_id, mmtkdata::description_lengthdim, mmtkdata::description_lengthdimid, mmtkdata::has_box, mmtkdata::minor_step_numberdim, mmtkdata::minor_step_numberdimid, cdfdata::mmtk, cdfdata::natoms, cdfdata::ncid, mmtkdata::step_numberdim, mmtkdata::step_numberdimid, cdfdata::type, mmtkdata::xyzdim, and mmtkdata::xyzdimid. Referenced by open_cdf_read.

int read_amber_cdf_timestep (  void *    mydata, int    natoms, molfile_timestep_t *    ts )  [static]

Definition at line 798 of file cdfplugin.c. References molfile_timestep_t::A, molfile_timestep_t::alpha, cdfdata::amber, amberdata::atomdim, molfile_timestep_t::B, molfile_timestep_t::beta, molfile_timestep_t::C, amberdata::cell_angles_id, amberdata::cell_lengths_id, amberdata::coordinates_id, molfile_timestep_t::coords, cdfdata::curframe, molfile_timestep_t::gamma, amberdata::has_box, MOLFILE_ERROR, MOLFILE_SUCCESS, cdfdata::ncid, and amberdata::spatialdim. Referenced by read_cdf_timestep.

int read_cdf_structure (  void *    mydata, int *    optflags, molfile_atom_t *    atoms )  [static]

Definition at line 782 of file cdfplugin.c. References CDF_TYPE_AMBER, CDF_TYPE_MMTK, MOLFILE_ERROR, MOLFILE_NOSTRUCTUREDATA, read_mmtk_cdf_structure, and cdfdata::type.

int read_cdf_timestep (  void *    mydata, int    natoms, molfile_timestep_t *    ts )  [static]

Definition at line 942 of file cdfplugin.c. References CDF_TYPE_AMBER, CDF_TYPE_MMTK, MOLFILE_ERROR, read_amber_cdf_timestep, read_mmtk_cdf_timestep, and cdfdata::type.

int read_mmtk_cdf_structure (  void *    mydata, int *    optflags, molfile_atom_t *    atoms )  [static]

Definition at line 515 of file cdfplugin.c. References molfile_atom_t::chain, cdfdata::curframe, mmtkdata::description, mmtkdata::description_id, mmtkdata::description_lengthdim, find_closing_bracket, cdfdata::mmtk, MOLFILE_ERROR, MOLFILE_NOOPTIONS, MOLFILE_SUCCESS, name, molfile_atom_t::name, cdfdata::natoms, cdfdata::ncid, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, set_atom_attributes, and molfile_atom_t::type. Referenced by read_cdf_structure.

int read_mmtk_cdf_timestep (  void *    mydata, int    natoms, molfile_timestep_t *    ts )  [static]

Definition at line 858 of file cdfplugin.c. References molfile_timestep_t::A, molfile_timestep_t::alpha, mmtkdata::atom_numberdim, molfile_timestep_t::B, molfile_timestep_t::beta, mmtkdata::box_size_id, molfile_timestep_t::C, mmtkdata::configuration_id, molfile_timestep_t::coords, cdfdata::curframe, molfile_timestep_t::gamma, mmtkdata::has_box, mmtkdata::minor_step_numberdim, cdfdata::mmtk, MOLFILE_ERROR, MOLFILE_SUCCESS, cdfdata::ncid, and mmtkdata::xyzdim. Referenced by read_cdf_timestep.

void set_atom_attributes (  molfile_atom_t *    atoms, int    natoms, char **    atom_pointers, char    chain_id, char *    resname, int    resnum, char *    start, char *    end, int    name_correction_type )  [static]

Definition at line 466 of file cdfplugin.c. References atom_name_remove_underscores, atom_name_replace, molfile_atom_t::chain, molfile_atom_t::name, molfile_atom_t::resid, and molfile_atom_t::resname. Referenced by read_mmtk_cdf_structure.

VMDPLUGIN_API int VMDPLUGIN_fini (  void    )

Definition at line 979 of file cdfplugin.c. References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init (  void    )

Definition at line 978 of file cdfplugin.c. References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_register (  void *    v, vmdplugin_register_cb    cb )

Definition at line 980 of file cdfplugin.c. References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

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Variable Documentation

molfile_plugin_t cdfplugin [static]

Initial value: { vmdplugin_ABIVERSION, MOLFILE_PLUGIN_TYPE, "netcdf", "NetCDF (AMBER, MMTK)", "John E. Stone", 0, 5, VMDPLUGIN_THREADSAFE, "nc", open_cdf_read, read_cdf_structure, 0, read_cdf_timestep, close_cdf_read, 0, 0, 0, 0, } Definition at line 957 of file cdfplugin.c.

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