From b42c1f45c0593958d3d75add785342712d684dbb Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 14 Apr 2015 09:34:16 +0200
Subject: [PATCH] Added crd plugin
This allows reading crd files without linking external plugins
---
regtest/basic/rt-molfile-4/config | 1 -
regtest/basic/rt-molfile-5/config | 1 -
src/molfile/crdplugin.cpp | 259 ++++++++++++++++++++++++++++++
src/molfile/libmolfile_plugin.h | 6 +
4 files changed, 265 insertions(+), 2 deletions(-)
create mode 100644 src/molfile/crdplugin.cpp
diff --git a/regtest/basic/rt-molfile-4/config b/regtest/basic/rt-molfile-4/config
index b2e719f1e..1906c7544 100644
--- a/regtest/basic/rt-molfile-4/config
+++ b/regtest/basic/rt-molfile-4/config
@@ -1,3 +1,2 @@
type=driver
-plumed_needs=external-molfile
arg="--plumed plumed.dat --mf_crd test.crd --natoms 2257"
diff --git a/regtest/basic/rt-molfile-5/config b/regtest/basic/rt-molfile-5/config
index 23bc4f0b1..32ed95d5b 100644
--- a/regtest/basic/rt-molfile-5/config
+++ b/regtest/basic/rt-molfile-5/config
@@ -1,3 +1,2 @@
type=driver
-plumed_needs=external-molfile
arg="--plumed plumed.dat --mf_crdbox test.crd --natoms 9560"
diff --git a/src/molfile/crdplugin.cpp b/src/molfile/crdplugin.cpp
new file mode 100644
index 000000000..14eb5e218
--- /dev/null
+++ b/src/molfile/crdplugin.cpp
@@ -0,0 +1,259 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+University of Illinois Open Source License
+Copyright 2003 Theoretical and Computational Biophysics Group,
+All rights reserved.
+
+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.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+/***************************************************************************
+ *cr
+ *cr (C) Copyright 1995-2009 The Board of Trustees of the
+ *cr University of Illinois
+ *cr All Rights Reserved
+ *cr
+ ***************************************************************************/
+
+/***************************************************************************
+ * RCS INFORMATION:
+ *
+ * $RCSfile: crdplugin.c,v $
+ * $Author: johns $ $Locker: $ $State: Exp $
+ * $Revision: 1.39 $ $Date: 2013/04/13 03:29:48 $
+ *
+ ***************************************************************************/
+
+/*
+ * TODO: This plugin should probably be merged with the 'rst7' plugin, since
+ * the differences between them are minor, and there's no logical reason
+ * for them to be implemented completely independently as they are now.
+ * The major differences in formatting are in regard to the 6F12.7 (rst7)
+ * versus 10F8.3 (crd) ascii floating point conversion modes.
+ */
+
+#include "largefiles.h" /* platform dependent 64-bit file I/O defines */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "molfile_plugin.h"
+
+namespace PLMD{
+namespace molfile{
+
+typedef struct {
+ FILE *file;
+ int has_box;
+ int numatoms;
+} crddata;
+
+static void *open_crd_read(const char *filename, const char *filetype,
+ int *natoms) {
+
+ FILE *fd;
+ crddata *data;
+
+ fd = fopen(filename, "rb");
+ if (!fd) return NULL;
+
+ /* first line is title, so skip past it */
+ while (getc(fd) != '\n');
+
+ /*
+ * CRD's don't store the number of atoms in the timestep, so we assume that
+ * the application will determine this for us.
+ */
+ data = (crddata *)malloc(sizeof(crddata));
+ data->file = fd;
+ *natoms = MOLFILE_NUMATOMS_UNKNOWN;
+ /* filetype "crd" has no box; filetype "crdbox" does. */
+ data->has_box = strcmp(filetype, "crd");
+ return data;
+}
+
+/*
+ * CRD files with box info are indistinguishable from regular CRD's.
+ * We regard CRD's with box info as a different file format.
+ * CRD's don't tell how many atoms there are in each frame. We therefore
+ * rely on the numatoms field in the molfile_timestep_t parameter.
+ */
+static int read_crd_timestep(void *mydata, int natoms, molfile_timestep_t *ts) {
+ crddata *crd = (crddata *)mydata;
+ int i, j;
+ float x, y, z;
+ float a, b, c;
+
+ /* Read in the atom coordinates */
+ for (i=0; i<natoms; i++) {
+ j = fscanf(crd->file, "%f %f %f", &x, &y, &z);
+ if (j == EOF) {
+ return MOLFILE_ERROR;
+ } else if (j <= 0) {
+ fprintf(stderr, "Problem reading CRD file\n");
+ return MOLFILE_ERROR;
+ }
+
+ /* only save coords if we're given a valid ts pointer */
+ /* otherwise assume that VMD wants us to skip it. */
+ if (ts != NULL) {
+ ts->coords[3*i ] = x;
+ ts->coords[3*i+1] = y;
+ ts->coords[3*i+2] = z;
+ }
+ }
+
+
+ /* Read the PBC box info. */
+ if (crd->has_box) {
+ j = fscanf(crd->file, "%f %f %f", &a, &b, &c);
+ if (j == EOF) {
+ printf("EOF in box\n");
+ return MOLFILE_ERROR;
+ } else if (j <= 0) {
+ printf("Problem reading box part of CRD file, scanf returned %d\n",j);
+ return MOLFILE_ERROR;
+ }
+
+ /* only save coords if we're given a valid ts pointer */
+ /* otherwise assume that VMD wants us to skip it. */
+ if (ts != NULL) {
+ ts->A = a;
+ ts->B = b;
+ ts->C = c;
+
+ /* XXX periodic cell angles are only stored in the PARM file */
+ /* we should probably retrieve these from the already-loaded */
+ /* molecule when possible. */
+ ts->alpha = 90.0;
+ ts->beta = 90.0;
+ ts->gamma = 90.0;
+ }
+ }
+
+ return MOLFILE_SUCCESS;
+}
+
+static void close_crd_read(void *mydata) {
+ crddata *crd = (crddata *)mydata;
+ fclose(crd->file);
+ free(crd);
+}
+
+static void *open_crd_write(const char *path, const char *filetype,
+ int natoms) {
+ crddata *crd;
+ FILE *fd;
+
+ fd = fopen(path, "wb");
+ if (!fd) {
+ fprintf(stderr, "Could not open file %s for writing\n", path);
+ return NULL;
+ }
+ fprintf(fd, "TITLE : Created by VMD with %d atoms\n", natoms);
+
+ crd = (crddata *)malloc(sizeof(crddata));
+ crd->file = fd;
+ crd->numatoms = natoms;
+ crd->has_box = strcmp(filetype, "crd");
+ return crd;
+}
+
+static int write_crd_timestep(void *v, const molfile_timestep_t *ts) {
+ crddata *crd = (crddata *)v;
+ int i;
+ int lfdone=0;
+ const int ndata = crd->numatoms * 3;
+
+ for (i=0; i<ndata; i++) {
+ lfdone = 0;
+ fprintf(crd->file, "%8.3f", ts->coords[i]);
+ if ((i+1) % 10 == 0) {
+ fprintf(crd->file, "\n");
+ lfdone = 1;
+ }
+ }
+ if (!lfdone)
+ fprintf(crd->file, "\n");
+
+ if (crd->has_box) {
+ fprintf (crd->file, "%8.3f%8.3f%8.3f\n", ts->A, ts->B, ts->C);
+ }
+
+ return MOLFILE_SUCCESS;
+}
+
+static void close_crd_write(void *v) {
+ crddata *crd = (crddata *)v;
+ fclose(crd->file);
+ free(crd);
+}
+
+/* registration stuff */
+
+static molfile_plugin_t plugin;
+static molfile_plugin_t crdboxplugin;
+
+VMDPLUGIN_API int VMDPLUGIN_init(void) {
+ memset(&plugin, 0, sizeof(molfile_plugin_t));
+ plugin.abiversion = vmdplugin_ABIVERSION;
+ plugin.type = MOLFILE_PLUGIN_TYPE;
+ plugin.name = "crd";
+ plugin.prettyname = "AMBER Coordinates";
+ plugin.author = "Justin Gullingsrud, John Stone";
+ plugin.majorv = 0;
+ plugin.minorv = 9;
+ plugin.is_reentrant = VMDPLUGIN_THREADSAFE;
+ plugin.filename_extension = "mdcrd,crd";
+ plugin.open_file_read = open_crd_read;
+ plugin.read_next_timestep = read_crd_timestep;
+ plugin.close_file_read = close_crd_read;
+ plugin.open_file_write = open_crd_write;
+ plugin.write_timestep = write_crd_timestep;
+ plugin.close_file_write = close_crd_write;
+
+ memcpy(&crdboxplugin, &plugin, sizeof(molfile_plugin_t));
+ crdboxplugin.name = "crdbox";
+ crdboxplugin.prettyname = "AMBER Coordinates with Periodic Box";
+
+ return VMDPLUGIN_SUCCESS;
+}
+
+VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {
+ (*cb)(v, (vmdplugin_t *)&plugin);
+ (*cb)(v, (vmdplugin_t *)&crdboxplugin);
+ return VMDPLUGIN_SUCCESS;
+}
+
+VMDPLUGIN_API int VMDPLUGIN_fini(void) { return VMDPLUGIN_SUCCESS; }
+
+}
+}
+
diff --git a/src/molfile/libmolfile_plugin.h b/src/molfile/libmolfile_plugin.h
index decef25e1..cf78a7f4e 100644
--- a/src/molfile/libmolfile_plugin.h
+++ b/src/molfile/libmolfile_plugin.h
@@ -44,6 +44,9 @@ namespace molfile{
int molfile_dcdplugin_init(void);
int molfile_dcdplugin_register(void *, vmdplugin_register_cb);
int molfile_dcdplugin_fini(void);
+ int molfile_crdplugin_init(void);
+ int molfile_crdplugin_register(void *, vmdplugin_register_cb);
+ int molfile_crdplugin_fini(void);
int molfile_gromacsplugin_init(void);
int molfile_gromacsplugin_register(void *, vmdplugin_register_cb);
int molfile_gromacsplugin_fini(void);
@@ -53,16 +56,19 @@ namespace molfile{
#define MOLFILE_INIT_ALL \
molfile_dcdplugin_init(); \
+ molfile_crdplugin_init(); \
molfile_gromacsplugin_init(); \
molfile_pdbplugin_init(); \
#define MOLFILE_REGISTER_ALL(v, cb) \
molfile_dcdplugin_register(v, cb); \
+ molfile_crdplugin_register(v, cb); \
molfile_gromacsplugin_register(v, cb); \
molfile_pdbplugin_register(v, cb); \
#define MOLFILE_FINI_ALL \
molfile_dcdplugin_fini(); \
+ molfile_crdplugin_fini(); \
molfile_gromacsplugin_fini(); \
molfile_pdbplugin_fini(); \
--
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