/********************************************************************** * cif2cbf -- convert a cif to a cbf file * * Version 0.7.4 12 January 2004 * * * * Herbert J. Bernstein, Bernstein + Sons * * 5 Brewster Lane, Bellport, NY 11713-2803 * * yaya@bernstein-plus-sons.com * **********************************************************************/ /********************************************************************** * SYNOPSIS * * * * cif2cbf [-i input_cif] [-o output_cbf] \ * * [-c {p[acked]|c[annonical]|[n[one]}] \ * * [-m {h[eaders]|n[oheaders]}] [-d {d[igest]|n[odigest]}] \ * * [-e {b[ase64]|q[uoted-printable]| \ * * d[ecimal]|h[exadecimal]|o[ctal]|n[one]}] \ * * [-b {f[orward]|b[ackwards]}] \ * * [input_cif] [output_cbf] * * * * the options are: * * * * -i input_cif (default: stdin) * * the input file in CIF or CBF format. If input_cif is not * * specified or is given as "-", it is copied from stdin to a * * temporary file. * * * * -o output_cbf (default: stdout) * * the output cif (if base64 or quoted-printable encoding is used) * * or cbf (if no encoding is used). if no output_cif is specified * * or is given as "-", the output is written to stdout * * * * The remaining options specify the characteristics of the * * output cbf. The characteristics of the input cif are derived * * from context. * * * * -c compression_scheme (packed, canonical or none, * * default packed) * * * * -m [no]headers (default headers for cifs, noheaders for cbfs) * * selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996) * * headers within binary data value text fields. * * * * -d [no]digest (default md5 digest [R. Rivest, RFC 1321, April * * 1992 using"RSA Data Security, Inc. MD5 Message-Digest * * Algorithm"] when MIME headers are selected) * * * * -e encoding (base64, quoted-printable or none, default base64) * * specifies one of the standard MIME encodings for an ascii cif * * or "none" for a binary cbf * * * * * * * **********************************************************************/ /********************************************************************** * CREDITS * * * * This program is a Crystallographic Information File (CIF) * * application. Please see the IUCR Policy below. See the IUCR * * web page (http://www.iucr.org) or its mirrors for background * * and references on CIF. * * * * This program is a Crystallographic Binary File (CBF) application. * * Please see the ImgCIF/CBF web page at * * * * http://ndbserver.rutgers.edu/mmcif/cbf * * * * for background and references. The CBF definition is available * * on the web page created by Andy Hammersley at * * * * http://www.ersf.fr/computing/Forum/imgCIF/cbf_definition.html * * * * This program is a CBFlib application. See "CBFLIB, An ANSI-C * * API for Crystallographic Binary Files", Version 0.1, April 1998 * * by Paul J. Ellis, Stanford Synchrotron Radiation Laboratory, * * ellis@ssrl.slac.stanford.edu * * * * This program uses routines derived from mpack/munpack version * * 1.5, ftp://ftp.andrew.cmu.edu/pub/mpack by John G. Myers, * * jgm+@cmu.edu. "Mpack and munpack are utilties for encoding and * * decoding ... binary files in MIME ... format." Please see the * * copyright notices and disclaimers in the mpack/munpack routines * * * * This program uses routines derived from the "RSA Data Security, * * Inc. MD5 Message-Digest Algorithm." Please see the copyright * * notice and disclaimer in md5c.c * **********************************************************************/ /********************************************************************** * NOTICE * * Creative endeavors depend on the lively exchange of ideas. There * * are laws and customs which establish rights and responsibilities * * for authors and the users of what authors create. This notice * * is not intended to prevent you from using the software and * * documents in this package, but to ensure that there are no * * misunderstandings about terms and conditions of such use. * * * * Please read the following notice carefully. If you do not * * understand any portion of this notice, please seek appropriate * * professional legal advice before making use of the software and * * documents included in this software package. In addition to * * whatever other steps you may be obliged to take to respect the * * intellectual property rights of the various parties involved, if * * you do make use of the software and documents in this package, * * please give credit where credit is due by citing this package, * * its authors and the URL or other source from which you obtained * * it, or equivalent primary references in the literature with the * * same authors. * * * * Some of the software and documents included within this software * * package are the intellectual property of various parties, and * * placement in this package does not in any way imply that any * * such rights have in any way been waived or diminished. * * * * With respect to any software or documents for which a copyright * * exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. * * * * Even though the authors of the various documents and software * * found here have made a good faith effort to ensure that the * * documents are correct and that the software performs according * * to its documentation, and we would greatly appreciate hearing of * * any problems you may encounter, the programs and documents any * * files created by the programs are provided **AS IS** without any * * warranty as to correctness, merchantability or fitness for any * * particular or general use. * * * * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF * * PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE * * PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS * * OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE * * PROGRAMS OR DOCUMENTS. * **********************************************************************/ /********************************************************************** * * * The IUCr Policy * * for the Protection and the Promotion of the STAR File and * * CIF Standards for Exchanging and Archiving Electronic Data * * * * Overview * * * * The Crystallographic Information File (CIF)[1] is a standard for * * information interchange promulgated by the International Union of * * Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the * * recommended method for submitting publications to Acta * * Crystallographica Section C and reports of crystal structure * * determinations to other sections of Acta Crystallographica * * and many other journals. The syntax of a CIF is a subset of the * * more general STAR File[2] format. The CIF and STAR File approaches * * are used increasingly in the structural sciences for data exchange * * and archiving, and are having a significant influence on these * * activities in other fields. * * * * Statement of intent * * * * The IUCr's interest in the STAR File is as a general data * * interchange standard for science, and its interest in the CIF, * * a conformant derivative of the STAR File, is as a concise data * * exchange and archival standard for crystallography and structural * * science. * * * * Protection of the standards * * * * To protect the STAR File and the CIF as standards for * * interchanging and archiving electronic data, the IUCr, on behalf * * of the scientific community, * * * * * holds the copyrights on the standards themselves, * * * * * owns the associated trademarks and service marks, and * * * * * holds a patent on the STAR File. * * * * These intellectual property rights relate solely to the * * interchange formats, not to the data contained therein, nor to * * the software used in the generation, access or manipulation of * * the data. * * * * Promotion of the standards * * * * The sole requirement that the IUCr, in its protective role, * * imposes on software purporting to process STAR File or CIF data * * is that the following conditions be met prior to sale or * * distribution. * * * * * Software claiming to read files written to either the STAR * * File or the CIF standard must be able to extract the pertinent * * data from a file conformant to the STAR File syntax, or the CIF * * syntax, respectively. * * * * * Software claiming to write files in either the STAR File, or * * the CIF, standard must produce files that are conformant to the * * STAR File syntax, or the CIF syntax, respectively. * * * * * Software claiming to read definitions from a specific data * * dictionary approved by the IUCr must be able to extract any * * pertinent definition which is conformant to the dictionary * * definition language (DDL)[3] associated with that dictionary. * * * * The IUCr, through its Committee on CIF Standards, will assist * * any developer to verify that software meets these conformance * * conditions. * * * * Glossary of terms * * * * [1] CIF: is a data file conformant to the file syntax defined * * at http://www.iucr.org/iucr-top/cif/spec/index.html * * * * [2] STAR File: is a data file conformant to the file syntax * * defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html * * * * [3] DDL: is a language used in a data dictionary to define data * * items in terms of "attributes". Dictionaries currently approved * * by the IUCr, and the DDL versions used to construct these * * dictionaries, are listed at * * http://www.iucr.org/iucr-top/cif/spec/ddl/index.html * * * * Last modified: 30 September 2000 * * * * IUCr Policy Copyright (C) 2000 International Union of * * Crystallography * **********************************************************************/ #include "cbf.h" #include "img.h" #include #include #include #include #include #include #include #define BUFSIZ 8192 int local_exit (int status); #undef cbf_failnez #define cbf_failnez(x) \ {int err; \ err = (x); \ if (err) { \ fprintf(stderr,"CBFlib fatal error %d\n",err); \ local_exit (-1); \ } \ } void set_MP_terms(int crterm, int nlterm); int main (int argc, char *argv []) { FILE *in, *out, *file; clock_t a,b; cbf_handle cif; cbf_handle cbf; int c; int errflg = 0; char *cifin, *cbfout; char ciftmp[19]; int ciftmpfd; int ciftmpused; int nbytes; char buf[BUFSIZ]; unsigned int blocks, categories, blocknum, catnum; const char *datablock_name; const char *category_name; const char *column_name; const char *value; unsigned int colnum, rownum; unsigned int columns; unsigned int rows; int mime, digest, encoding, compression, bytedir, cbforcif, term; /* Extract options */ /********************************************************************** * cif2cbf [-i input_cif] [-o output_cbf] \ * * [-c {p[acked]|c[annonical]|[n[one]}] \ * * [-m {h[eaders]|n[oheaders]}] [-d {d[igest]|n[odigest]}] \ * * [-e {b[ase64]|q[uoted-printable]| \ * * d[ecimal]|h[exadecimal]|o[ctal]|n[one]}] \ * * [-b {f[orward]|b[ackwards]}] \ * * [input_cif] [output_cbf] * * * **********************************************************************/ mime = 0; digest = 0; encoding = 0; compression = 0; bytedir = 0; cifin = NULL; cbfout = NULL; ciftmpused = 0; while ((c = getopt(argc, argv, "i:o:c:m:d:e:b:")) != EOF) { switch (c) { case 'i': if (cifin) errflg++; else cifin = optarg; break; case 'o': if (cbfout) errflg++; else cbfout = optarg; break; case 'c': if (compression) errflg++; if (optarg[0] == 'p' || optarg[0] == 'P') { compression = CBF_PACKED; } else { if (optarg[0] == 'c' || optarg[0] == 'C') { compression = CBF_CANONICAL; } else { if (optarg[0] == 'n' || optarg[0] == 'N') { compression = CBF_NONE; } else { errflg++; } } } break; case 'm': if (mime) errflg++; if (optarg[0] == 'h' || optarg[0] == 'H' ) { mime = MIME_HEADERS; } else { if (optarg[0] == 'n' || optarg[0] == 'N' ) { mime = PLAIN_HEADERS; } else { errflg++; } } break; case 'd': if (digest) errflg++; if (optarg[0] == 'd' || optarg[0] == 'H' ) { digest = MSG_DIGEST; } else { if (optarg[0] == 'n' || optarg[0] == 'N' ) { digest = MSG_NODIGEST; } else { errflg++; } } break; case 'b': if (bytedir) errflg++; if (optarg[0] == 'f' || optarg[0] == 'F') { bytedir = ENC_FORWARD; } else { if (optarg[0] == 'b' || optarg[0] == 'B' ) { bytedir = ENC_BACKWARD; } else { errflg++; } } break; case 'e': if (encoding) errflg++; if (optarg[0] == 'b' || optarg[0] == 'B' ) { encoding = ENC_BASE64; } else { if (optarg[0] == 'q' || optarg[0] == 'Q' ) { encoding = ENC_QP; } else { if (optarg[0] == 'd' || optarg[0] == 'D' ) { encoding = ENC_BASE10; } else { if (optarg[0] == 'h' || optarg[0] == 'H' ) { encoding = ENC_BASE16; } else { if (optarg[0] == 'o' || optarg[0] == 'O' ) { encoding = ENC_BASE8; } else { if (optarg[0] == 'n' || optarg[0] == 'N' ) { encoding = ENC_NONE; } else { errflg++; } } } } } } break; default: errflg++; break; } } for (; optind < argc; optind++) { if (!cifin) { cifin = argv[optind]; } else { if (!cbfout) { cbfout = argv[optind]; } else { errflg++; } } } if (errflg) { fprintf(stderr,"cif2cbf: Usage: \n"); fprintf(stderr, " cif2cbf [-i input_cif] [-o output_cbf] \\\n"); fprintf(stderr, " [-c {p[acked]|c[annonical]|[n[one]}] \\\n"); fprintf(stderr, " [-m {h[eaders]|n[oheaders]}] [-d {d[igest]|n[odigest]}] \\\n"); fprintf(stderr, " [-e {b[ase64]|q[uoted-printable]|\\\n"); fprintf(stderr, " d[ecimal]|h[examdecimal|o[ctal]|n[one]}] \\\n"); fprintf(stderr, " [-w {2|3|4|6|8}] [-b {f[orward]|b[ackwards]}\\\n"); fprintf(stderr, " [input_cif] [output_cbf] \n\n"); exit(2); } /* Set up for CIF of CBF output */ if (!encoding) { encoding = ENC_BASE64; } cbforcif = CBF; term = ENC_CRTERM | ENC_LFTERM; if (encoding == ENC_BASE64 || \ encoding == ENC_QP || \ encoding == ENC_BASE10 || \ encoding == ENC_BASE16 || \ encoding == ENC_BASE8) { cbforcif = CIF; term = ENC_LFTERM; } /* Set up for headers */ if (!mime) { mime = MIME_HEADERS; } if (!digest) { if (mime == MIME_HEADERS) { digest = MSG_DIGEST; } else { digest = MSG_NODIGEST; } } /* Set up for decimal, hexadecimal or octal output */ if (!bytedir) bytedir = ENC_BACKWARD; /* Set up for Compression */ if (!compression) compression = CBF_PACKED; /* Read the cif */ if (!cifin || strcmp(cifin?cifin:"","-") == 0) { strcpy(ciftmp, "/tmp/cif2cbfXXXXXX"); if ((ciftmpfd = mkstemp(ciftmp)) == -1 ) { fprintf(stderr,"Can't create temporary file %s.\n", ciftmp); fprintf(stderr,"%s\n",strerror(errno)); exit(1); } if ( (file = fdopen(ciftmpfd, "w+")) == NULL) { fprintf(stderr,"Can't open temporary file %s.\n", ciftmp); fprintf(stderr,"%s\n",strerror(errno)); exit(1); } while ((nbytes = fread(buf, 1, BUFSIZ, stdin))) { if(nbytes != fwrite(buf, 1, nbytes, file)) { fprintf(stderr,"Failed to write %s.\n", ciftmp); exit(1); } } fclose(file); cifin = ciftmp; ciftmpused = 1; } if ( cbf_make_handle (&cif) ) { fprintf(stderr,"Failed to create handle for input_cif\n"); exit(1); } if ( cbf_make_handle (&cbf) ) { fprintf(stderr,"Failed to create handle for output_cbf\n"); exit(1); } a = clock (); /* Read the file */ if (!(in = fopen (cifin, "rb"))) { fprintf (stderr,"Couldn't open the input CIF file %s\n", cifin); exit (1); } if (ciftmpused) { if (unlink(ciftmp) != 0 ) { fprintf(stderr,"cif2cif: Can't unlink temporary file %s.\n", ciftmp); fprintf(stderr,"%s\n",strerror(errno)); exit(1); } } cbf_failnez (cbf_read_file (cif, in, MSG_DIGEST)) cbf_failnez (cbf_rewind_datablock(cif)) cbf_failnez (cbf_count_datablocks(cif, &blocks)) for (blocknum = 0; blocknum < blocks; blocknum++ ) { /* start of copy loop */ cbf_failnez (cbf_select_datablock(cif, blocknum)) cbf_failnez (cbf_datablock_name(cif, &datablock_name)) cbf_failnez (cbf_force_new_datablock(cbf, datablock_name)) if ( !cbf_rewind_category(cif) ) { cbf_failnez (cbf_count_categories(cif, &categories)) for (catnum = 0; catnum < categories; catnum++) { cbf_select_category(cif, catnum); cbf_category_name(cif,&category_name); cbf_force_new_category(cbf, category_name); cbf_count_rows(cif,&rows); cbf_count_columns(cif,&columns); /* Transfer the columns names from cif to cbf */ if ( ! cbf_rewind_column(cif) ) { do { cbf_failnez(cbf_column_name(cif, &column_name)) cbf_failnez(cbf_new_column(cbf, column_name)) } while ( ! cbf_next_column(cif) ); cbf_rewind_column(cif); cbf_rewind_row(cif); } /* Transfer the rows from cif to cbf */ for (rownum = 0; rownum < rows; rownum++ ) { cbf_failnez (cbf_select_row(cif, rownum)) cbf_failnez (cbf_new_row(cbf)) cbf_rewind_column(cif); for (colnum = 0; colnum < columns; colnum++ ) { const char *typeofvalue; cbf_failnez (cbf_select_column(cif, colnum)) if ( ! cbf_get_value(cif, &value) ) { cbf_failnez (cbf_get_typeofvalue(cif, &typeofvalue)) cbf_failnez (cbf_select_column(cbf, colnum)) cbf_failnez (cbf_set_value(cbf, value)) cbf_failnez (cbf_set_typeofvalue(cbf, typeofvalue)) } else { void * array; int binary_id, elsigned, elunsigned; size_t elements,elements_read, elsize; int minelement, maxelement; unsigned int cifcompression; cbf_failnez(cbf_get_integerarrayparameters( cif, &cifcompression, &binary_id, &elsize, &elsigned, &elunsigned, &elements, &minelement, &maxelement)) if ((array=malloc(elsize*elements))) { cbf_failnez (cbf_select_column(cbf,colnum)) cbf_failnez (cbf_get_integerarray( cif, &binary_id, array, elsize, elsigned, elements, &elements_read)) cbf_failnez(cbf_set_integerarray( cbf, compression, binary_id, array, elsize, elsigned, elements)) free(array); } else { fprintf(stderr, "\nFailed to allocate memory %ld bytes", (long) elsize*elements); exit(1); } } } } } } } b = clock (); fprintf (stderr, " Time to read input_cif: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC); a = clock (); if ( ! cbfout || strcmp(cbfout?cbfout:"","-") == 0 ) { out = stdout; } else { out = fopen (cbfout, "w+b"); } if ( ! out ) { if (encoding == ENC_NONE) { printf (" Couldn't open the CBF file %s\n", cbfout); } else { printf (" Couldn't open the CIF file %s\n", cbfout); } exit (1); } cbf_failnez (cbf_write_file (cbf, out, 1, cbforcif, mime | digest, encoding | bytedir | term)) cbf_failnez (cbf_free_handle (cbf)) b = clock (); if (encoding == ENC_NONE) { fprintf (stderr, " Time to write the CBF image: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC); } else { fprintf (stderr, " Time to write the CIF image: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC); } exit(0); } int local_exit (int status) { exit(status); return 1; /* avoid warnings */ }