#include "largefiles.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "Gromacs.h"
#include "molfile_plugin.h"
Go to the source code of this file.
Compounds | |
struct | gmxdata |
Defines | |
#define | M_PI 3.14159265358979323846 |
#define | GROMACS_PLUGIN_MAJOR_VERSION 0 |
#define | GROMACS_PLUGIN_MINOR_VERSION 8 |
Functions | |
void * | open_gro_read (const char *filename, const char *, int *natoms) |
int | read_gro_structure (void *mydata, int *optflags, molfile_atom_t *atoms) |
int | read_gro_timestep (void *v, int natoms, molfile_timestep_t *ts) |
void | close_gro_read (void *v) |
void * | open_g96_read (const char *filename, const char *, int *natoms) |
int | read_g96_structure (void *mydata, int *optflags, molfile_atom_t *atoms) |
int | read_g96_timestep (void *v, int natoms, molfile_timestep_t *ts) |
void | close_g96_read (void *v) |
void * | open_trr_read (const char *filename, const char *filetype, int *natoms) |
int | read_trr_timestep (void *v, int natoms, molfile_timestep_t *ts) |
void | close_trr_read (void *v) |
void * | open_trr_write (const char *filename, const char *filetype, int natoms) |
int | write_trr_timestep (void *mydata, const molfile_timestep_t *ts) |
void | close_trr_write (void *v) |
VMDPLUGIN_API int | VMDPLUGIN_init () |
VMDPLUGIN_API int | VMDPLUGIN_register (void *v, vmdplugin_register_cb cb) |
VMDPLUGIN_API int | VMDPLUGIN_fini () |
Variables | |
molfile_plugin_t | gro_plugin |
molfile_plugin_t | g96_plugin |
molfile_plugin_t | trr_plugin |
molfile_plugin_t | xtc_plugin |
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Definition at line 491 of file gromacsplugin.C. |
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Definition at line 492 of file gromacsplugin.C. |
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Definition at line 33 of file gromacsplugin.C. Referenced by write_trr_timestep. |
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Definition at line 296 of file gromacsplugin.C. References mdio_close, and gmxdata::mf. |
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Definition at line 132 of file gromacsplugin.C. References mdio_close, and gmxdata::mf. |
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Definition at line 377 of file gromacsplugin.C. References mdio_close, and gmxdata::mf. |
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Definition at line 485 of file gromacsplugin.C. References mdio_close, and gmxdata::mf. |
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Definition at line 138 of file gromacsplugin.C. References g96_countatoms, g96_header, MAX_G96_LINE, MAX_MDIO_TITLE, MDFMT_G96, mdio_errmsg, mdio_errno, mdio_open, mdio_readline, gmxdata::mf, gmxdata::natoms, md_header::timeval, and md_header::title. |
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Definition at line 46 of file gromacsplugin.C. References gro_header, MAX_MDIO_TITLE, MDFMT_GRO, mdio_errmsg, mdio_errno, mdio_open, gmxdata::mf, gmxdata::natoms, md_header::natoms, md_header::timeval, and md_header::title. |
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Definition at line 307 of file gromacsplugin.C. References MDFMT_TRR, MDFMT_XTC, mdio_close, mdio_errmsg, mdio_errno, mdio_header, mdio_open, gmxdata::mf, gmxdata::natoms, and md_header::natoms. |
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Definition at line 384 of file gromacsplugin.C. References host_is_little_endian, MDFMT_TRR, MDFMT_XTC, mdio_errmsg, mdio_errno, mdio_open, MDIO_WRITE, gmxdata::mf, gmxdata::natoms, md_file::prec, md_file::rev, and gmxdata::step. |
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Definition at line 187 of file gromacsplugin.C. References md_atom::atomname, molfile_atom_t::chain, md_file::f, g96_rec, MAX_G96_LINE, mdio_errmsg, mdio_errno, mdio_readline, gmxdata::mf, MOLFILE_ERROR, MOLFILE_NOOPTIONS, MOLFILE_SUCCESS, molfile_atom_t::name, gmxdata::natoms, md_atom::resid, molfile_atom_t::resid, md_atom::resname, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type. |
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Definition at line 75 of file gromacsplugin.C. References md_atom::atomname, molfile_atom_t::chain, md_file::f, gro_rec, MAX_GRO_LINE, mdio_errmsg, mdio_errno, mdio_readline, gmxdata::mf, MOLFILE_ERROR, MOLFILE_NOOPTIONS, MOLFILE_SUCCESS, molfile_atom_t::name, gmxdata::natoms, md_atom::resid, molfile_atom_t::resid, md_atom::resname, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type. |
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Definition at line 605 of file gromacsplugin.C. References VMDPLUGIN_API. |
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Definition at line 593 of file gromacsplugin.C. References VMDPLUGIN_API. |
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Definition at line 597 of file gromacsplugin.C. References VMDPLUGIN_API, and vmdplugin_register_cb. |
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Definition at line 416 of file gromacsplugin.C. References molfile_timestep_t::A, molfile_timestep_t::alpha, molfile_timestep_t::B, molfile_timestep_t::beta, molfile_timestep_t::C, molfile_timestep_t::coords, md_file::fmt, molfile_timestep_t::gamma, M_PI, MDFMT_TRR, gmxdata::mf, MOLFILE_ERROR, MOLFILE_SUCCESS, gmxdata::natoms, put_trx_int, put_trx_real, put_trx_string, gmxdata::step, and TRX_MAGIC. |
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Initial value: { vmdplugin_ABIVERSION, MOLFILE_PLUGIN_TYPE, "g96", "Gromacs g96", "David Norris, Justin Gullingsrud", GROMACS_PLUGIN_MAJOR_VERSION, GROMACS_PLUGIN_MINOR_VERSION, VMDPLUGIN_THREADUNSAFE, "g96", open_g96_read, read_g96_structure, 0, read_g96_timestep, close_g96_read, 0, 0, 0, 0, 0, 0, 0 } Definition at line 521 of file gromacsplugin.C. |
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Initial value: { vmdplugin_ABIVERSION, MOLFILE_PLUGIN_TYPE, "gro", "Gromacs GRO", "David Norris, Justin Gullingsrud", GROMACS_PLUGIN_MAJOR_VERSION, GROMACS_PLUGIN_MINOR_VERSION, VMDPLUGIN_THREADUNSAFE, "gro", open_gro_read, read_gro_structure, 0, read_gro_timestep, close_gro_read, 0, 0, 0, 0, 0, 0, 0 } Definition at line 497 of file gromacsplugin.C. |
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Initial value: { vmdplugin_ABIVERSION, MOLFILE_PLUGIN_TYPE, "trr", "Gromacs TRR Trajectory", "David Norris, Justin Gullingsrud, Axel Kohlmeyer", GROMACS_PLUGIN_MAJOR_VERSION, GROMACS_PLUGIN_MINOR_VERSION, VMDPLUGIN_THREADUNSAFE, "trr", open_trr_read, 0, 0, read_trr_timestep, close_trr_read, open_trr_write, 0, write_trr_timestep, close_trr_write, 0, 0, 0 } Definition at line 545 of file gromacsplugin.C. |
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Initial value: { vmdplugin_ABIVERSION, MOLFILE_PLUGIN_TYPE, "xtc", "Gromacs XTC Compressed Trajectory", "David Norris, Justin Gullingsrud", GROMACS_PLUGIN_MAJOR_VERSION, GROMACS_PLUGIN_MINOR_VERSION, VMDPLUGIN_THREADUNSAFE, "xtc", open_trr_read, 0, 0, read_trr_timestep, close_trr_read, 0, 0, 0, 0, 0, 0, 0 } Definition at line 569 of file gromacsplugin.C. |