[svn-r3487] Purpose:

    Code Movement
Description:
    Moved the tools into their own separate directories (except for these
    small tools which are REALLY small, not tested, or documented,
    really...They just get put into the misc/ directory).
Platforms tested:
    Linux and Kelgia

1 files changed, 503 insertions, 0 deletions

diff --git a/tools/misc/pdb2hdf.c b/tools/misc/pdb2hdf.c
new file mode 100644
index 0000000..7ecd28e
--- /dev/null
+++ b/tools/misc/pdb2hdf.c
@@ -0,0 +1,503 @@
+/*
+ * Copyright ©  1999 NCSA
+ *              All rights reserved.
+ *
+ * Programmer:  Robb Matzke <matzke@llnl.gov>
+ *              Tuesday, October 12, 1999
+ *
+ * Purpose:	Creates an HDF5 file from a PDB file.  The raw data can be
+ *		left in the PDB file, creating an HDF5 file that contains
+ *		meta data that points into the PDB file.
+ */
+#include <assert.h>
+#include <hdf5.h>
+#include <pdb.h>
+#include <score.h>
+#include <stdio.h>
+#include <string.h>
+
+/*
+ * libsilo renames all the PDB functions. However, this source files uses
+ * their documented names, so we have #define's to translate them to Silo
+ * terminology.
+ */
+#ifdef H5_HAVE_LIBSILO
+#   define PD_open			lite_PD_open
+#   define PD_close			lite_PD_close
+#   define PD_ls			lite_PD_ls
+#   define PD_cd			lite_PD_cd
+#   define PD_inquire_entry		lite_PD_inquire_entry
+#   define PD_read			lite_PD_read
+#   define _PD_fixname			_lite_PD_fixname
+#   define _PD_rl_defstr		_lite_PD_rl_defstr
+#   define SC_free			lite_SC_free
+#endif
+
+static int verbose_g = 0;		/*verbose output?		*/
+static int cached_g = 0;		/*use core file driver?		*/
+
+
+/*-------------------------------------------------------------------------
+ * Function:	usage
+ *
+ * Purpose:	Print a usage message.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage(const char *arg0)
+{
+    char	*progname;
+
+    if ((progname=strrchr(arg0, '/')) && progname[1]) progname++;
+    else progname = arg0;
+
+    fprintf(stderr, "\
+usage: %s [OPTIONS] [PDBFILE ...]\n\
+   OPTIONS\n\
+      -h, -?, --help   Print a usage message and exit\n\
+      -c, --cached     Cache all data in memory before writing the output\n\
+      -v, --verbose    Print the name of each object processed\n\
+      -V, --version    Show the version number of this program\n\
+\n\
+   The options and PDB file names may be interspersed and are processed from\n\
+   left to right.\n\
+\n\
+   The name of the HDF5 file is generated by taking the basename of the PDB\n\
+   file and replacing the last extension (or appending if no extension) with\n\
+   the characters \".h5\". For example, \"/tmp/test/eos.data\" would result\n\
+   in an HDF5 file called \"eos.h5\" in the current directory.\n",
+	    progname);
+    
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	version
+ *
+ * Purpose:	Print the version number.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Friday, October 15, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+version(const char *arg0)
+{
+    const char	*progname;
+
+    if ((progname=strrchr(arg0, '/')) && progname[1]) progname++;
+    else progname = arg0;
+    print_version(progname);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_name
+ *
+ * Purpose:	Given a PDB file name create the corresponding HDF5 file
+ *		name. This is done by taking the base name of the PDB file
+ *		and replacing (or appending) the last extension with ".h5".
+ *
+ * Return:	Success:	HDF_NAME
+ *
+ *		Failure:	NULL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static char *
+fix_name(const char *pdb_name, char *hdf_name, size_t size)
+{
+    char	*s;
+    const char	*ext;
+    
+    if (!pdb_name || !hdf_name) return NULL;
+    if ((s=strrchr(pdb_name, '/'))) pdb_name = s;
+    if (NULL==(ext=strrchr(pdb_name, '.'))) ext = pdb_name + strlen(pdb_name);
+    if ((size_t)((ext-pdb_name)+4) > size) return NULL; /*overflow*/
+    memcpy(hdf_name, pdb_name, ext-pdb_name);
+    strcpy(hdf_name+(ext-pdb_name), ".h5");
+    return hdf_name;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_type
+ *
+ * Purpose:	Given a PDB datatype return a corresponding hdf5 datatype.
+ *		The hdf5 datatype should be closed when the caller is
+ *		finished using it.
+ *
+ * Return:	Success:	HDF5 datatype
+ *
+ *		Failure:	negative
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static hid_t
+fix_type(PDBfile *pdb, const char *s)
+{
+    hid_t	type = -1;
+    defstr 	*d = _lite_PD_lookup_type((char*)s, pdb->chart);
+
+    /* PDB checking */
+    assert(d);
+    assert(d->size>0);
+    if (d->onescmp) return -1;
+    
+    
+    if (!strcmp(s, "char")) {
+	/*
+	 * Character datatypes. Use whatever sign the native system uses by
+	 * default.
+	 */
+	type = H5Tcopy(H5T_NATIVE_CHAR);
+	
+    } else if (!strcmp(s, "integer")) {
+	/*
+	 * Integer datatypes. PDB supports various sizes of signed or
+	 * unsigned integers.
+	 */
+	type = H5Tcopy(d->unsgned?H5T_NATIVE_UINT:H5T_NATIVE_INT);
+	H5Tset_size(type, d->size);
+	H5Tset_precision(type, 8*d->size);
+	assert(NORMAL_ORDER==d->order_flag || REVERSE_ORDER==d->order_flag);
+	H5Tset_order(type,
+		     NORMAL_ORDER==d->order_flag?H5T_ORDER_BE:H5T_ORDER_LE);
+	
+    } else if (!strcmp(s, "float") || !strcmp(s, "double")) {
+	/*
+	 * Floating-point datatypes
+	 */
+	size_t	nbits, spos, epos, esize, mpos, msize;
+
+	type = H5Tcopy(H5T_NATIVE_FLOAT);
+	H5Tset_size(type, d->size);
+	H5Tset_precision(type, 8*d->size);
+	assert(d->order);
+	H5Tset_order(type, 1==d->order[0]?H5T_ORDER_BE:H5T_ORDER_LE);
+	
+	/*
+	 * format[0] = # of bits per number                     
+	 * format[1] = # of bits in exponent                    
+	 * format[2] = # of bits in mantissa                    
+	 * format[3] = start bit of sign                        
+	 * format[4] = start bit of exponent                    
+	 * format[5] = start bit of mantissa                    
+	 * format[6] = high order mantissa bit (CRAY needs this)
+	 * format[7] = bias of exponent
+	 */
+	assert(d->format && d->format[0] == 8*d->size);
+	nbits = d->format[0];
+	spos = nbits - (d->format[3]+1);
+	esize = d->format[1];
+	epos = nbits - (d->format[4]+esize);
+	msize = d->format[2];
+	mpos = nbits - (d->format[5]+msize);
+	H5Tset_fields(type, spos, epos, esize, mpos, msize);
+	H5Tset_ebias(type, d->format[7]);
+    }
+    return type;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_space
+ *
+ * Purpose:	Convert a PDB dimension list into an HDF5 data space.
+ *
+ * Return:	Success:	HDF5 data space
+ *
+ *		Failure:	negative
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static hid_t
+fix_space(const dimdes *dim)
+{
+    hsize_t	size[H5S_MAX_RANK];
+    int		rank;
+
+    for (rank=0; rank<H5S_MAX_RANK && dim; rank++, dim=dim->next) {
+	size[rank] = dim->number;
+    }
+    if (rank>=H5S_MAX_RANK) return -1;
+    return H5Screate_simple(rank, size, NULL);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_external
+ *
+ * Purpose:	Sets the external file information for a dataset creation
+ *		property list based on information from PDB.
+ *
+ * Return:	Success:	non-negative
+ *
+ *		Failure:	negative
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+fix_external(hid_t dcpl, const char *pdb_file_name, long nelmts,
+	     hsize_t elmt_size, symblock *block)
+{
+    int		i;
+    
+    for (i=0; nelmts>0; i++) {
+	hsize_t nbytes = block[i].number * elmt_size;
+	H5Pset_external(dcpl, pdb_file_name, block[i].diskaddr, nbytes);
+	nelmts -= block[i].number;
+    }
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	traverse
+ *
+ * Purpose:	Traverse the current working directory of the PDB file.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+traverse(PDBfile *pdb, const char *pdb_file_name, hid_t hdf)
+{
+    int			nitems, i, in_subdir=FALSE;
+    char		**list=NULL;
+    hid_t		group=-1, h_type=-1, h_space=-1, dset=-1, dcpl=-1;
+    hsize_t		elmt_size;
+    const syment	*ep=NULL;
+
+    if (NULL==(list=PD_ls(pdb, ".", NULL, &nitems))) {
+	fprintf(stderr, "cannot obtain PDB directory contents\n");
+	goto error;
+    }
+
+    for (i=0; i<nitems; i++) {
+	ep = PD_inquire_entry(pdb, list[i], TRUE, NULL);
+	if (verbose_g) {
+	    printf("%s %s\n", _PD_fixname(pdb, list[i]), ep->type);
+	    fflush(stdout);
+	}
+	
+
+	if ('/'==list[i][strlen(list[i])-1]) {
+	    /*
+	     * This is a PDB directory. Make a corresponding HDF5 group and
+	     * traverse into that PDB directory and HDF5 group
+	     */
+	    if ((group=H5Gcreate(hdf, list[i], 0))<0) {
+		fprintf(stderr, "cannot create HDF group %s\n", list[i]);
+		goto error;
+	    }
+	    if (!PD_cd(pdb, list[i])) {
+		fprintf(stderr, "cannot cd into PDB directory %s\n", list[i]);
+		goto error;
+	    } else {
+		in_subdir = TRUE;
+	    }
+	    
+	    traverse(pdb, pdb_file_name, group);
+	    if (!PD_cd(pdb, "..")) {
+		fprintf(stderr, "cannot traverse out of PDB %s\n", list[i]);
+		goto error;
+	    }
+	    H5Gclose(group);
+	    
+	} else {
+	    /* This is some non-directory PDB object */
+
+	    /* Create an HDF5 datatype from the PDB type */
+	    if ((h_type=fix_type(pdb, ep->type))<0) {
+		fprintf(stderr, "cannot create datatype for %s (%s)\n",
+		       list[i], ep->type);
+		continue;
+	    }
+	    elmt_size = H5Tget_size(h_type);
+
+	    /* Create an HDF5 dataspace from the PDB dimensions */
+	    if ((h_space=fix_space(ep->dimensions))<0) {
+		fprintf(stderr, "cannot create datatype for %s\n", list[i]);
+		continue;
+	    }
+
+	    /* Create pointers to the external PDB data */
+	    dcpl = H5Pcreate(H5P_DATASET_CREATE);
+	    fix_external(dcpl, pdb_file_name, ep->number, elmt_size,
+			 ep->blocks);
+
+	    /* Create the dataset */
+	    if ((dset=H5Dcreate(hdf, list[i], h_type, h_space, dcpl))<0) {
+		fprintf(stderr, "cannot create dataset for %s\n", list[i]);
+	    }
+
+	    H5Pclose(dcpl);
+	    H5Dclose(dset);
+	    H5Sclose(h_space);
+	    H5Tclose(h_type);
+	}
+	
+    }
+
+    for (i=0; i<nitems; i++) {
+	SC_free(list[i]);
+    }
+    SC_free(list);
+    return 0;
+
+ error:
+    if (group>=0) H5Gclose(group);
+    if (in_subdir) PD_cd(pdb, "..");
+    if (list) {
+	for (i=0; i<nitems; i++) {
+	    SC_free(list[i]);
+	}
+	SC_free(list);
+    }
+    return -1;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	Create an HDF5 file from a PDB file.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	non-zero
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, char *argv[])
+{
+    int		argno;
+    char	_hdf_name[512], *hdf_name, *pdb_name, *s;
+    PDBfile	*pdb;
+    hid_t	hdf, fapl;
+
+    /* Print a help message if called with no arguments */
+    if (1==argc) {
+	usage(argv[0]);
+	exit(1);
+    }
+
+    /* Process arguments in order; switches interspersed with files */
+    for (argno=1; argno<argc; argno++) {
+	if (!strcmp("--help", argv[argno])) {
+	    usage(argv[0]);
+	    exit(1);
+	} else if (!strcmp("--verbose", argv[argno])) {
+	    verbose_g++;
+	} else if (!strcmp("--cached", argv[argno])) {
+	    cached_g++;
+	} else if (!strcmp("--version", argv[argno])) {
+	    version(argv[0]);
+	} else if ('-'==argv[argno][0] && '-'!=argv[argno][1]) {
+	    for (s=argv[argno]+1; *s; s++) {
+		switch (*s) {
+		case '?':
+		case 'h':		/*--help*/
+		    usage(argv[0]);
+		    exit(0);
+		case 'c':		/*--cached*/
+		    cached_g++;
+		    break;
+		case 'v':		/*--verbose*/
+		    verbose_g++;
+		    break;
+		case 'V':		/*--version*/
+		    version(argv[0]);
+		    break;
+		default:
+		    usage(argv[0]);
+		    exit(1);
+		}
+	    }
+	} else if ('-'==argv[argno][0]) {
+	    usage(argv[0]);
+	    exit(1);
+	} else {
+	    /* This must be a file name. Process it. */
+	    fapl = H5Pcreate(H5P_FILE_ACCESS);
+	    if (cached_g) H5Pset_fapl_core(fapl, 1024*1024, TRUE);
+
+	    pdb_name = argv[argno];
+	    hdf_name = fix_name(argv[argno], _hdf_name, sizeof _hdf_name);
+	    if (NULL==(pdb=PD_open(pdb_name, "r"))) {
+		fprintf(stderr, "%s: unable to open PDB file\n", pdb_name);
+		exit(1);
+	    }
+	    if ((hdf=H5Fcreate(hdf_name, H5F_ACC_TRUNC, H5P_DEFAULT,
+			       fapl))<0) {
+		fprintf(stderr, "%s: unable to open HDF file\n", hdf_name);
+		exit(1);
+	    }
+	    H5Pclose(fapl);
+	    
+	    /*
+	     * Traverse the PDB file to create the HDF5 file.
+	     */
+	    traverse(pdb, pdb_name, hdf);
+
+	    /* Close the files */
+	    if (!PD_close(pdb)) {
+		fprintf(stderr, "%s: problems closing PDB file\n", pdb_name);
+		exit(1);
+	    }
+	    if (H5Fclose(hdf)<0) {
+		fprintf(stderr, "%s: problems closing HDF file\n", hdf_name);
+		exit(1);
+	    }
+	}
+    }
+    return 0;
+}