/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
*
- *
+ *
* This file is part of Gromacs Copyright (c) 1991-2008
* David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
*
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org
- *
+ *
* And Hey:
* Gnomes, ROck Monsters And Chili Sauce
*/
/* PluginMgr.C: Copyright: */
/***************************************************************************
- *cr
- *cr (C) Copyright 1995-2009 The Board of Trustees of the
- *cr University of Illinois
- *cr All Rights Reserved
- *cr
-Developed by: Theoretical and Computational Biophysics Group
+ * cr
+ * cr (C) Copyright 1995-2009 The Board of Trustees of the
+ * cr University of Illinois
+ * cr All Rights Reserved
+ * cr
+ Developed by: Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign
http://www.ks.uiuc.edu/
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the Software), to deal with
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
-of the Software, and to permit persons to whom the Software is furnished to
-do so, subject to the following conditions:
-
-Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimers.
-
-Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimers in the documentation
-and/or other materials provided with the distribution.
-
-Neither the names of Theoretical and Computational Biophysics Group,
-University of Illinois at Urbana-Champaign, nor the names of its contributors
-may be used to endorse or promote products derived from this Software without
-specific prior written permission.
-
-THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
-OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS WITH THE SOFTWARE.
+ Permission is hereby granted, free of charge, to any person obtaining a copy of
+ this software and associated documentation files (the Software), to deal with
+ the Software without restriction, including without limitation the rights to
+ use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+ of the Software, and to permit persons to whom the Software is furnished to
+ do so, subject to the following conditions:
+
+ Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimers.
+
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimers in the documentation
+ and/or other materials provided with the distribution.
+
+ Neither the names of Theoretical and Computational Biophysics Group,
+ University of Illinois at Urbana-Champaign, nor the names of its contributors
+ may be used to endorse or promote products derived from this Software without
+ specific prior written permission.
+
+ THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS WITH THE SOFTWARE.
***************************************************************************/
/* catdcd.c: Copyright: */
#include <string.h>
#include <assert.h>
-/*
+/*
* Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
*/
#include "external/vmd_molfile/molfile_plugin.h"
-static int register_cb(void *v, vmdplugin_t *p) {
- const char *key = p->name;
+static int register_cb(void *v, vmdplugin_t *p)
+{
+ const char *key = p->name;
t_gmxvmdplugin *vmdplugin = (t_gmxvmdplugin*)v;
- if (strcmp(key,vmdplugin->filetype)==0)
+ if (strcmp(key, vmdplugin->filetype) == 0)
{
vmdplugin->api = (molfile_plugin_t *)p;
}
return VMDPLUGIN_SUCCESS;
}
-static int load_sharedlibrary_plugins(const char *fullpath,t_gmxvmdplugin* vmdplugin) {
+static int load_sharedlibrary_plugins(const char *fullpath, t_gmxvmdplugin* vmdplugin)
+{
/* Open the dll; try to execute the init function. */
- void *handle, *ifunc, *registerfunc;
+ void *handle, *ifunc, *registerfunc;
handle = vmddlopen(fullpath);
- if (!handle) {
- if (debug) fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath, vmddlerror()); /*only to debug because of stdc++ erros */
+ if (!handle)
+ {
+ if (debug)
+ {
+ fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath, vmddlerror()); /*only to debug because of stdc++ erros */
+ }
return 0;
}
ifunc = vmddlsym(handle, "vmdplugin_init");
- if (!ifunc || ((initfunc)(ifunc))()) {
+ if (!ifunc || ((initfunc)(ifunc))())
+ {
printf("\nvmdplugin_init() for %s returned an error; plugin(s) not loaded.\n", fullpath);
vmddlclose(handle);
return 0;
}
registerfunc = vmddlsym(handle, "vmdplugin_register");
- if (!registerfunc) {
+ if (!registerfunc)
+ {
printf("\nDidn't find the register function in %s; plugin(s) not loaded.\n", fullpath);
vmddlclose(handle);
return 0;
- } else {
+ }
+ else
+ {
/* Load plugins from the library.*/
((regfunc)registerfunc)(vmdplugin, register_cb);
- }
-
+ }
+
/* in case this library does not support the filetype, close it */
if (vmdplugin->api == NULL)
{
}
/*return: 1: success, 0: last frame, -1: error*/
-gmx_bool read_next_vmd_frame(int status,t_trxframe *fr)
+gmx_bool read_next_vmd_frame(int status, t_trxframe *fr)
{
- int rc,i;
- rvec vec, angle;
+ int rc, i;
+ rvec vec, angle;
molfile_timestep_t ts;
fr->bV = fr->vmdplugin->bV;
-
+
#ifdef GMX_DOUBLE
snew(ts.coords, fr->natoms*3);
if (fr->bV)
rc = fr->vmdplugin->api->read_next_timestep(fr->vmdplugin->handle, fr->natoms, &ts);
- if (rc < -1) {
+ if (rc < -1)
+ {
fprintf(stderr, "\nError reading input file (error code %d)\n", rc);
}
if (rc < 0)
}
#ifdef GMX_DOUBLE
- for (i=0;i<fr->natoms;i++)
+ for (i = 0; i < fr->natoms; i++)
{
fr->x[i][0] = .1*ts.coords[i*3];
fr->x[i][1] = .1*ts.coords[i*3+1];
sfree(ts.velocities);
}
#else
- for (i=0;i<fr->natoms;i++)
+ for (i = 0; i < fr->natoms; i++)
{
- svmul(.1,fr->x[i],fr->x[i]);
+ svmul(.1, fr->x[i], fr->x[i]);
if (fr->bV)
{
- svmul(.1,fr->v[i],fr->v[i]);
+ svmul(.1, fr->v[i], fr->v[i]);
}
}
#endif
- fr->bX = 1;
+ fr->bX = 1;
fr->bBox = 1;
- vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
- angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
- matrix_convert(fr->box,vec,angle);
- if (fr->vmdplugin->api->abiversion>10)
+ vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
+ angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
+ matrix_convert(fr->box, vec, angle);
+ if (fr->vmdplugin->api->abiversion > 10)
{
fr->bTime = TRUE;
- fr->time = ts.physical_time;
+ fr->time = ts.physical_time;
}
else
{
static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
{
- char pathname[GMX_PATH_MAX],filename[GMX_PATH_MAX];
- const char *pathenv;
- const char *err;
- int i;
- int ret=0;
- char pathenv_buffer[GMX_PATH_MAX];
+ char pathname[GMX_PATH_MAX], filename[GMX_PATH_MAX];
+ const char *pathenv;
+ const char *err;
+ int i;
+ int ret = 0;
+ char pathenv_buffer[GMX_PATH_MAX];
#ifndef GMX_NATIVE_WINDOWS
- glob_t globbuf;
- const char *defpath_suffix = "/plugins/*/molfile";
- const char *defpathenv = GMX_VMD_PLUGIN_PATH;
+ glob_t globbuf;
+ const char *defpath_suffix = "/plugins/*/molfile";
+ const char *defpathenv = GMX_VMD_PLUGIN_PATH;
#else
WIN32_FIND_DATA ffd;
- HANDLE hFind = INVALID_HANDLE_VALUE;
- char progfolder[GMX_PATH_MAX];
- char defpathenv[GMX_PATH_MAX];
- const char *defpath_suffix = "\\plugins\\WIN32\\molfile";
- SHGetFolderPath(NULL,CSIDL_PROGRAM_FILES,NULL,SHGFP_TYPE_CURRENT,progfolder);
- sprintf(defpathenv,"%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile",progfolder);
+ HANDLE hFind = INVALID_HANDLE_VALUE;
+ char progfolder[GMX_PATH_MAX];
+ char defpathenv[GMX_PATH_MAX];
+ const char *defpath_suffix = "\\plugins\\WIN32\\molfile";
+ SHGetFolderPath(NULL, CSIDL_PROGRAM_FILES, NULL, SHGFP_TYPE_CURRENT, progfolder);
+ sprintf(defpathenv, "%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile", progfolder);
#endif
- vmdplugin->api = NULL;
- vmdplugin->filetype = strrchr(fn,'.');
+ vmdplugin->api = NULL;
+ vmdplugin->filetype = strrchr(fn, '.');
if (!vmdplugin->filetype)
{
return 0;
* given at configure time. This last might be hard-coded to the
* default for VMD installs. */
pathenv = getenv("VMD_PLUGIN_PATH");
- if (pathenv==NULL)
+ if (pathenv == NULL)
{
pathenv = getenv("VMDDIR");
if (NULL == pathenv)
{
printf("\nNeither VMD_PLUGIN_PATH or VMDDIR set. ");
- printf("Using default location:\n%s\n",defpathenv);
- pathenv=defpathenv;
+ printf("Using default location:\n%s\n", defpathenv);
+ pathenv = defpathenv;
}
else
{
#else
snprintf(pathenv_buffer, sizeof(pathenv_buffer), "%s%s", pathenv, defpath_suffix);
#endif
- printf("Using semi-default location:\n%s\n",pathenv_buffer);
+ printf("Using semi-default location:\n%s\n", pathenv_buffer);
pathenv = pathenv_buffer;
}
}
- strncpy(pathname,pathenv,sizeof(pathname));
+ strncpy(pathname, pathenv, sizeof(pathname));
#ifndef GMX_NATIVE_WINDOWS
- strcat(pathname,"/*.so");
+ strcat(pathname, "/*.so");
glob(pathname, 0, NULL, &globbuf);
if (globbuf.gl_pathc == 0)
{
printf("\nNo VMD Plugins found\n"
- "Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the\n"
- "VMD installation.\n"
- "The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.\n");
+ "Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the\n"
+ "VMD installation.\n"
+ "The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.\n");
return 0;
}
- for (i=0; i<globbuf.gl_pathc && vmdplugin->api == NULL; i++)
+ for (i = 0; i < globbuf.gl_pathc && vmdplugin->api == NULL; i++)
{
/* FIXME: Undefined which plugin is chosen if more than one plugin
can read a certain file ending. Requires some additional command
line option or enviroment variable to specify which plugin should
be picked.
- */
- ret|=load_sharedlibrary_plugins(globbuf.gl_pathv[i],vmdplugin);
+ */
+ ret |= load_sharedlibrary_plugins(globbuf.gl_pathv[i], vmdplugin);
}
globfree(&globbuf);
#else
- strcat(pathname,"\\*.so");
+ strcat(pathname, "\\*.so");
hFind = FindFirstFile(pathname, &ffd);
- if (INVALID_HANDLE_VALUE == hFind)
+ if (INVALID_HANDLE_VALUE == hFind)
{
printf("\nNo VMD Plugins found\n");
return 0;
- }
+ }
do
{
- sprintf(filename,"%s\\%s",pathenv,ffd.cFileName);
- ret|=load_sharedlibrary_plugins(filename,vmdplugin);
+ sprintf(filename, "%s\\%s", pathenv, ffd.cFileName);
+ ret |= load_sharedlibrary_plugins(filename, vmdplugin);
}
- while (FindNextFile(hFind, &ffd ) != 0 && vmdplugin->api == NULL );
+ while (FindNextFile(hFind, &ffd ) != 0 && vmdplugin->api == NULL);
FindClose(hFind);
#endif
{
printf("\nCould not open any VMD library.\n");
err = vmddlerror();
- if (!err)
+ if (!err)
{
printf("Compiled with dlopen?\n");
}
else
{
- printf("Last error:\n%s\n",err);
+ printf("Last error:\n%s\n", err);
}
return 0;
}
if (vmdplugin->api == NULL)
{
- printf("\nNo plugin for %s found\n",vmdplugin->filetype);
+ printf("\nNo plugin for %s found\n", vmdplugin->filetype);
return 0;
}
return 0;
}
- printf("\nUsing VMD plugin: %s (%s)\n",vmdplugin->api->name,vmdplugin->api->prettyname);
+ printf("\nUsing VMD plugin: %s (%s)\n", vmdplugin->api->name, vmdplugin->api->prettyname);
return 1;
}
-int read_first_vmd_frame(int *status,const char *fn,t_trxframe *fr,int flags)
+int read_first_vmd_frame(int *status, const char *fn, t_trxframe *fr, int flags)
{
- molfile_timestep_metadata_t *metadata=NULL;
-
- snew(fr->vmdplugin,1);
- if (!load_vmd_library(fn,fr->vmdplugin))
+ molfile_timestep_metadata_t *metadata = NULL;
+
+ snew(fr->vmdplugin, 1);
+ if (!load_vmd_library(fn, fr->vmdplugin))
{
return 0;
}
fr->vmdplugin->handle = fr->vmdplugin->api->open_file_read(fn, fr->vmdplugin->filetype, &fr->natoms);
- if (!fr->vmdplugin->handle) {
+ if (!fr->vmdplugin->handle)
+ {
fprintf(stderr, "\nError: could not open file '%s' for reading.\n",
fn);
return 0;
}
- if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN) {
+ if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN)
+ {
fprintf(stderr, "\nFormat of file %s does not record number of atoms.\n", fn);
return 0;
- } else if (fr->natoms == MOLFILE_NUMATOMS_NONE) {
+ }
+ else if (fr->natoms == MOLFILE_NUMATOMS_NONE)
+ {
fprintf(stderr, "\nNo atoms found by VMD plugin in file %s.\n", fn );
return 0;
- } else if (fr->natoms < 1) { /*should not be reached*/
+ }
+ else if (fr->natoms < 1) /*should not be reached*/
+ {
fprintf(stderr, "\nUnknown number of atoms %d for VMD plugin opening file %s.\n",
fr->natoms, fn );
return 0;
}
-
- snew(fr->x,fr->natoms);
+
+ snew(fr->x, fr->natoms);
fr->vmdplugin->bV = 0;
if (fr->vmdplugin->api->abiversion > 10 && fr->vmdplugin->api->read_timestep_metadata)
fr->vmdplugin->bV = metadata->has_velocities;
if (fr->vmdplugin->bV)
{
- snew(fr->v,fr->natoms);
+ snew(fr->v, fr->natoms);
}
}
else
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff