#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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Definition at line 30 of file cdfplugin.c. Referenced by open_amber_cdf_read, read_cdf_structure, and read_cdf_timestep. |
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Definition at line 31 of file cdfplugin.c. Referenced by open_mmtk_cdf_read, read_cdf_structure, and read_cdf_timestep. |
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Definition at line 29 of file cdfplugin.c. Referenced by open_cdf_read. |
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Definition at line 454 of file cdfplugin.c. References name. Referenced by set_atom_attributes. |
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Definition at line 446 of file cdfplugin.c. References name. Referenced by set_atom_attributes. |
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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. |
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Definition at line 433 of file cdfplugin.c. Referenced by read_mmtk_cdf_structure. |
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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. |
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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. |
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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. |
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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. |
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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. |
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Definition at line 979 of file cdfplugin.c. References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS. |
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Definition at line 978 of file cdfplugin.c. References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS. |
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Definition at line 980 of file cdfplugin.c. References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS. |
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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. |