/* FILE: maxit_main.C */ /* VERSION: 1.600 */ /* DATE: 2/3/2005 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. The user of this software shall indemnify, hold harmless and defend Rutgers, its governors, trustees, officers, employees, students, agents and the authors against any and all claims, suits, losses, liabilities, damages, costs, fees, and expenses including reasonable attorneys' fees resulting from or arising out of the use of this software. This indemnification shall include, but is not limited to, any and all claims alleging products liability. */ /* PDB SOFTWARE LICENSE AGREEMENT BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS BECOMING A PARTY TO THIS AGREEMENT. IF LICENSEE DOES NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE. 1. LICENSE AGREEMENT This is a license between you ("Licensee") and the Protein Data Bank (PDB) at Rutgers, The State University of New Jersey (hereafter referred to as "RUTGERS"). The software is owned by RUTGERS and protected by copyright laws, and some elements are protected by laws governing trademarks, trade dress and trade secrets, and may be protected by patent laws. 2. LICENSE GRANT RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, and distribute in binary and source code format, or any derivative work thereof, together with any associated media, printed materials, and on-line or electronic documentation (if any) provided by RUTGERS (collectively, the "SOFTWARE"), subject to the following terms and conditions: (i) any distribution of the SOFTWARE shall bind the receiver to the terms and conditions of this Agreement; (ii) any distribution of the SOFTWARE in modified form shall clearly state that the SOFTWARE has been modified from the version originally obtained from RUTGERS. 2. COPYRIGHT; RETENTION OF RIGHTS. The above license grant is conditioned on the following: (i) you must reproduce all copyright notices and other proprietary notices on any copies of the SOFTWARE and you must not remove such notices; (ii) in the event you compile the SOFTWARE, you will include the copyright notice with the binary in such a manner as to allow it to be easily viewable; (iii) if you incorporate the SOFTWARE into other code, you must provide notice that the code contains the SOFTWARE and include a copy of the copyright notices and other proprietary notices. All copies of the SOFTWARE shall be subject to the terms of this Agreement. 3. NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS RUTGERS is under no obligation whatsoever to: (i) provide maintenance or support for the SOFTWARE; or (ii) to notify you of bug fixes, patches, or upgrades to the features, functionality or performance of the SOFTWARE ("Enhancements") (if any), whether developed by RUTGERS or third parties. If, in its sole discretion, RUTGERS makes an Enhancement available to you and RUTGERS does not separately enter into a written license agreement with you relating to such bug fix, patch or upgrade, then it shall be deemed incorporated into the SOFTWARE and subject to this Agreement. You are under no obligation whatsoever to provide any Enhancements to RUTGERS or the public that you may develop over time; however, if you choose to provide your Enhancements to RUTGERS, or if you choose to otherwise publish or distribute your Enhancements, in source code form without contemporaneously requiring end users or RUTGERS to enter into a separate written license agreement for such Enhancements, then you hereby grant RUTGERS a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into the SOFTWARE or other computer software, distribute, and sublicense your Enhancements or derivative works thereof, in binary and source code form. 4. FEES. 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Title and related rights in the content accessed through the SOFTWARE is the property of the applicable content owner and is protected by applicable law. The license granted under this Agreement gives Licensee no rights to such content. 7. DISCLAIMER OF WARRANTY. THE SOFTWARE IS PROVIDED FREE OF CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE. SHOULD THE SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS AGREEMENT. NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER. 8. LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. */ #include #include #include #include #include #include #include #include #include "_maxit.h" #include "erf_category.h" #include "erf_util.h" #include "ndb_filterexitlib.h" #include "ndb_misclib.h" #include "util.h" #define MXSTRLEN 200 #define MAX_OPTION_PDB_TO_CIF 1 #define MAX_OPTION_CIF_TO_PDB 2 #define MAX_OPTION_PDB_TO_NDB 3 #define MAX_OPTION_NDB_TO_PDB 4 #define MAX_OPTION_NDB_TO_CIF 5 #define MAX_OPTION_CIF_TO_NDB 6 #define MAX_OPTION_PDB_TO_ENCIF 7 #define MAX_OPTION_CIF_TO_CIF 8 #define MAX_OPTION_VALIDATION_PDB 9 #define MAX_OPTION_VALIDATION_NDB 10 #define MAX_OPTION_VALIDATION_CIF 11 #define MAX_OPTION_SYMMETRY_NDB 12 #define MAX_OPTION_SYMMETRY_CIF 13 #define MAX_OPTION_NCS_NDB 14 #define MAX_OPTION_NCS_CIF 15 #define MAX_OPTION_CHIRALITY_NDB 16 #define MAX_OPTION_CHIRALITY_CIF 17 #define MAX_OPTION_CORRESPND_NDB 18 #define MAX_OPTION_CORRESPND_CIF 19 #define MAX_OPTION_HYDROGEN_NDB 20 #define MAX_OPTION_HYDROGEN_CIF 21 #define MAX_OPTION_DEL_ATOM_NDB 22 #define MAX_OPTION_DEL_ATOM_CIF 23 #define MAX_OPTION_ADD_ATOM_NDB 24 #define MAX_OPTION_ADD_ATOM_CIF 25 #define MAX_OPTION_DEL_RESIDUE_NDB 26 #define MAX_OPTION_DEL_RESIDUE_CIF 27 #define MAX_OPTION_ADD_RESIDUE_NDB 28 #define MAX_OPTION_ADD_RESIDUE_CIF 29 #define MAX_OPTION_MERGE_RMK_NDB 30 #define MAX_OPTION_MERGE_RMK_CIF 31 #define MAX_OPTION_MERGE_COR_NDB 32 #define MAX_OPTION_MERGE_COR_CIF 33 #define MAX_OPTION_MOVE_HOH_NDB 34 #define MAX_OPTION_MOVE_HOH_CIF 35 #define MAX_OPTION_RES_NAME_NDB 36 #define MAX_OPTION_RES_NAME_CIF 37 #define MAX_OPTION_REP_RESIDUE_NDB 38 #define MAX_OPTION_REP_RESIDUE_CIF 39 #define MAX_OPTION_CHANGE_SYMMETRY 40 #define MAX_OPTION_CHANGE_NON_SYMM 41 #define MAX_OPTION_UPDATE_NA_FEATURE 42 #define MAX_OPTION_ORTH_TO_FRAC 43 #define MAX_OPTION_FRAC_TO_ORTH 44 #define MAX_OPTION_FRAC_TO_ORTH_CIF 45 #define MAX_OPTION_NDB_TO_NDBCIF 46 #define MAX_OPTION_NDBCIF_TO_NDB 47 #define MAX_OPTION_LAYER1_TO_2 48 #define MAX_OPTION_Q_ATOM_CIF 49 #define MAX_OPTION_MERGE_WATER 50 #define MAX_OPTION_GET_MATRIX 51 #define MAX_OPTION_UPDATE_HYDROGEN 52 #define MAX_OPTION_CHECK_FILE 53 #define MAX_OPTION_CLASSIFICATION 54 #define MAX_OPTION_BIOL_UNIT 55 #define MAX_OPTION_EXCHANGE 56 #define MAX_OPTION_ONE_LETTER_CODE 57 #define MAX_OPTION_HPUB_LETTER 58 #define MAX_OPTION_COMPLEXITY 59 #define MAX_OPTION_PACKING 60 #define MAX_OPTION_RENUMBER_PDB 61 static int output_ndb_format = NDB_FILE_FORMAT_NDBCIF; static int is_prev_check = 0; static int is_separate = 0; static int is_short_cut = 0; static int short_version = 0; static int remark = 0; static int is_binary = 0; static int standardized = 0; static int is_iupac = 0; static int is_special = 0; static int delete_atom = 0; static int recover_asym = 0; static int id_option = 0; static int exchange_in = 0; static int exchange_out = 0; static int public_flag = 0; static int together = 0; static int no_deriv = 0; static int identical_flag = 0; static int symmetry_flag = 0; static int keep_contact_author = 0; static int no_pdbx_strand_id = 0; static int is_nmr_view = 0; static char File_ID[100]; static char object_name[MXSTRLEN]; static char defalut_dir[] = "/ndbapps"; static void maxit(const int choice, const int num_file, const char *infile_name, const char *support_file, FILE *summary, FILE *summary1); static void maxit_check_files(const int choice, const char *infile_name, char *outfile_name); static void maxit_usage(const char *prog_name); int main(int argc, char *argv[]) { root_dir = getenv("RCSBROOT"); if (root_dir == NULL) root_dir = defalut_dir; int i, answer, commandLine = 0, temp_c = 0, num_file = 0; char infile_name1[MXSTRLEN], reply[MXSTRLEN], errfile[MXSTRLEN]; char support_file[MXSTRLEN], logfile[100]; FILE *infile = NULL, *summary = NULL, *summary1 = NULL; struct stat stat1; memset(infile_name1, 0, MXSTRLEN); memset(support_file, 0, MXSTRLEN); memset(File_ID, 0, 100); memset(object_name, 0, MXSTRLEN); strcpy(logfile, "maxit.err"); for (i = 1; i < argc; i++) { if (argv[i][0] == '-' ) { if (!strcmp(argv[i], "-f")) { i++; commandLine = 1; strcpy(infile_name1, argv[i]); } else if (!strcmp(argv[i], "-i")) { i++; commandLine = 1; strcpy(infile_name1, argv[i]); num_file = 1; } else if (!strcmp(argv[i], "-ib")) { i++; commandLine = 1; strcpy(infile_name1, argv[i]); num_file = 1; is_binary = 1; } else if (!strcmp(argv[i], "-o")) { i++; temp_c = atoi(argv[i]); } else if (!strcmp(argv[i], "-NDB")) { output_ndb_format = NDB_FILE_FORMAT_NDB; } else if (!strcasecmp(argv[i], "-nmr")) { is_nmr_view = 1; } else if (!strcmp(argv[i], "-p")) { is_prev_check = 1; } else if (!strcmp(argv[i], "-adit")) { is_prev_check = 2; } else if (!strcmp(argv[i], "-path")) { i++; root_dir = argv[i]; } else if (!strcasecmp(argv[i], "-s")) { is_separate = 1; } else if (!strcasecmp(argv[i], "-l")) { is_short_cut = 1; } else if (!strcasecmp(argv[i], "-M")) { i++; strcpy(support_file, argv[i]); } else if (!strcasecmp(argv[i], "-filename")) { i++; strcpy(File_ID, argv[i]); } else if (!strcasecmp(argv[i], "-ob")) { i++; strcpy(object_name, argv[i]); is_binary = 2; } else if (!strcasecmp(argv[i], "-output")) { i++; strcpy(logfile, argv[i]); } else if (!strcasecmp(argv[i], "-x")) { } else if (!strcasecmp(argv[i], "-remark")) { remark = 1; } else if (!strcasecmp(argv[i], "-standard")) { standardized = 1; } else if (!strcasecmp(argv[i], "-iupac")) { is_iupac = 1; /* } else if (!strcasecmp(argv[i], "-special")) { i++; is_special = atoi(argv[i]); */ } else if (!strcasecmp(argv[i], "-replace")) { is_special = 2; } else if (!strcasecmp(argv[i], "-delete")) { delete_atom = 1; } else if (!strcasecmp(argv[i], "-asym")) { recover_asym = 1; } else if (!strcasecmp(argv[i], "-pdbids")) { id_option |= 1; } else if (!strcasecmp(argv[i], "-ndbids")) { id_option |= 2; /* } else if (!strcasecmp(argv[i], "-rcsbids")) { id_option |= 4; */ } else if (!strcasecmp(argv[i], "-exchange_in")) { exchange_in = 1; } else if (!strcasecmp(argv[i], "-exchange_out")) { exchange_out = 1; } else if (!strcasecmp(argv[i], "-public")) { public_flag = 1; } else if (!strcasecmp(argv[i], "-together")) { together = 1; } else if (!strcasecmp(argv[i], "-short")) { short_version = 1; } else if (!strcasecmp(argv[i], "-no_deriv")) { no_deriv = 1; } else if (!strcasecmp(argv[i], "-identical")) { identical_flag = 1; } else if (!strcasecmp(argv[i], "-get_biol_unit")) { symmetry_flag = 1; } else if (!strcasecmp(argv[i], "-keep_contact_author")) { keep_contact_author = 1; } else if (!strcasecmp(argv[i], "-no_pdbx_strand_id")) { no_pdbx_strand_id = 1; } else { maxit_usage("maxit"); exit(1); } } else { maxit_usage("maxit"); exit(1); } } // if (!id_option) id_option = 1; if (exchange_out) standardized = 1; ndb_set_debug_level(NDB_MSG_INFO); ndb_open_log("maxit", logfile); if (!ndb_filterlib_init(root_dir)) { printf("Initial filter libaray failed\n"); return -1; } if (!ndb_maxitlib_init()) { printf("Initial maxit libaray failed\n"); return -1; } for (i = 0; i < NUM_TOKEN; i++) { Check_Format[i].Token_ID = find_card_id(Check_Format[i].TokenName); } while (temp_c != 'Q' && temp_c != 'q') { if (!commandLine) { num_file = 0; system("clear"); printf("\n\nMaxIT\n\n"); printf("[1] Translate PDB format file(s) to CIF format file(s)\n"); printf("[2] Translate CIF format file(s) to PDB format file(s)\n"); printf("[3] Translate PDB format file(s) to NDB format file(s)\n"); printf("[4] Translate NDB format file(s) to PDB format file(s)\n"); printf("[5] Translate NDB format file(s) to mmCIF format file(s)\n"); printf("[6] Translate CIF format file(s) to NDB format file(s)\n"); printf("[7] Translate PDB format file(s) to encapsulated CIF file(s)\n"); printf("[8] Translate CIF format file(s) to mmCIF format file(s)\n"); printf("[9] Validation: PDB format file(s)\n"); printf("[10] Validation: NDB format file(s)\n"); printf("[11] Validation: CIF format file(s)\n"); printf("[12] Generate symmetry related strands to NDB files(s)\n"); printf("[13] Generate symmetry related strands to mmCIF files(s)\n"); printf("[14] Generate NCS related strands to NDB file(s)\n"); printf("[15] Generate NCS related strands to mmCIF file(s)\n"); printf("[16] Correct Chirality of O1P/O2P and H atoms to NDB file(s)\n"); printf("[17] Correct Chirality of O1P/O2P and H atoms to mmCIF file(s)\n"); printf("[18] Create Correspondences between deposited and standard hydrogen atoms\n"); printf(" to NDB file(s)\n"); printf("[19] Create Correspondences between deposited and standard hydrogen atoms\n"); printf(" to mmCIF file(s)\n"); printf("[20] Remove Hydrogen atom(s) to NDB file(s)\n"); printf("[21] Remove Hydrogen atom(s) to mmCIF file(s)\n"); printf("[22] Delete Atom(s) to NDB file(s)\n"); printf("[23] Delete Atom(s) to mmCIF file(s)\n"); printf("[24] Insert Atom(s) to NDB file(s)\n"); printf("[25] Insert Atom(s) to mmCIF file(s)\n"); printf("[26] Delete Residue(s) to NDB file(s)\n"); printf("[27] Delete Residue(s) to mmCIF file(s)\n"); printf("[28] Insert Residue(s) to NDB file(s)\n"); printf("[29] Insert Residue(s) to mmCIF file(s)\n"); printf("[30] Merge Remarks to NDB file\n"); printf("[31] Merge Remarks to mmCIF file\n"); printf("[32] Merge Coordinates to NDB file\n"); printf("[33] Merge Coordinates to mmCIF file\n"); printf("[34] Moving Water(s) to NDB file(s)\n"); printf("[35] Moving Water(s) to CIF file(s)\n"); printf("[36] Switch Residue Name(s) to NDB file(s)\n"); printf("[37] Switch Residue Name(s) to CIF file(s)\n"); printf("[38] Replace Residue(s) to NDB file(s)\n"); printf("[39] Replace Residue(s) to mmCIF file(s)\n"); printf("[40] Moving coordinates using symmetry operation to mmCIF file(s)\n"); printf("[41] Moving coordinates using non-symmetry operation to mmCIF file(s)\n"); printf("[42] Update NA features to mmCIF file(s)\n"); printf("[43] Convert orthogonal coordinates to fractional using NDB files(s)\n"); printf("[44] Convert fractional coordinates to orthogonal using NDB files(s)\n"); printf("[45] Convert fractional coordinates to orthogonal using mmCIF file(s)\n"); printf("[46] Translating NDB format file(s) to NDBCIF format file(s)\n"); printf("[47] Translating NDBCIF format file(s) to NDB format file(s)\n"); printf("[48] Adding REVDAT for Layer1 to Layer2 using CIF file(s)\n"); printf("[49] Remove Q atom(s) to mmCIF file(s)\n"); printf("[50] Reorder Het Group(s) and Waters to mmCIF file(s)\n"); printf("[51] Get Virus Matrices to mmCIF file(s)\n"); printf("[52] Update Hydrogen Nomenclature to PDB file(s)\n"); printf("[53] Check PDB file(s)\n"); printf("[54] Get Classification of PDB file(s)\n"); printf("[55] Get Biological Unit PDB file(s)\n"); printf("[56] Convert mmCIF from exchange to internal dictionary\n"); printf("[57] Get one letter sequence from coordinates\n"); printf("[58] Get letter for 'HOLD FOR PUBLICATION' structures\n"); printf("[Q] Quit\n"); printf("\nEnter selection -->"); fflush(stdout); fflush(stdin); fscanf(stdin, "%s", reply); if (reply[0] == 'Q' || reply[0] == 'q') temp_c = 'q'; else temp_c = atoi(reply); } if (temp_c == 'Q' || temp_c == 'q') break; else if (temp_c < 1 || temp_c > MAX_OPTION_RENUMBER_PDB) { if (!commandLine) continue; else break; } else { if (!strcmp(infile_name1, "")) { if (temp_c >= MAX_OPTION_DEL_ATOM_NDB && temp_c <= MAX_OPTION_MERGE_COR_CIF) { num_file = 1; printf("Please enter the name of a single file to be processed-> "); fflush(stdout); fflush(stdin); fscanf(stdin, "%s", infile_name1); ndb_clean_string(infile_name1); printf("Please enter the name of the support file-> "); fflush(stdout); fflush(stdin); fscanf(stdin, "%s", support_file); ndb_clean_string(support_file); } else { printf("Please enter the number of files to be translated\n\n"); printf(" [1] for one file \n"); printf(" [2] for more than one file\n"); printf("\n Enter selection (default: 1) -->"); fflush(stdin); answer = fgetc(stdin); if (answer == '2') num_file = 0; else num_file = 1; fflush(stdin); if (num_file == 1) printf("\n\nPlease enter the name of a single file to be processed-> "); else printf("\n\nPlease enter the name of the list of files to be processed-> "); fflush(stdout); fflush(stdin); fscanf(stdin, "%s", infile_name1); ndb_clean_string(infile_name1); } } if (strcmp(infile_name1, "") && strcmp(infile_name1, "\n") && strcmp(infile_name1, "\t")) { if (stat(infile_name1, &stat1) < 0) { fprintf(stdout, "File %s did not exist.\n", infile_name1); ndb_log_message(NDB_MSG_ERR, "File %s did not exist.\n", infile_name1); memset(infile_name1, 0, MXSTRLEN); if (commandLine) break; else continue; } infile = fopen(infile_name1, "r"); if (infile == (FILE *) NULL) { fprintf(stdout, "Can not read file %s!\n\n", infile_name1); ndb_log_message(NDB_MSG_ERR, "Can not read file %s!\n\n", infile_name1); memset(infile_name1, 0, MXSTRLEN); if (commandLine) break; else continue; } for (i = strlen(infile_name1) - 1; i >= 0; i--) if (infile_name1[i] == '/') break; strcpy(reply, &infile_name1[i+1]); if (temp_c == MAX_OPTION_CLASSIFICATION) { summary = fopen("SUMMARY.bcp", "w"); summary1 = fopen("SUMMARY1.bcp", "w"); } if (num_file == 0) { num_file = 0; while (!feof(infile)) { memset(errfile, 0, MXSTRLEN); fscanf(infile, "%s", errfile); num_file++; ndb_clean_string(errfile); if (strcmp(errfile, "") && strcmp(errfile, "\n") && strcmp(errfile, "\t")) maxit(temp_c, num_file, errfile, support_file, summary, summary1); } } else { maxit(temp_c, num_file, infile_name1, support_file, summary, summary1); } if (summary) fclose (summary); if (summary1) fclose (summary1); fclose(infile); } } temp_c = 0; memset(infile_name1, 0, MXSTRLEN); if (commandLine) break; } ndb_filterlib_close(); ndb_close_log(); return 0; } static void maxit(const int choice, const int num_file, const char *infile_name, const char *support_file, FILE *summary, FILE *summary1) { int fd, i, compressFlag = 0; char tmp_infile[MXSTRLEN], tmpfile[MXSTRLEN], name[100]; char outfile_name[MXSTRLEN], buffer[100], command[800], templateFileName[9] = "./XXXXXX"; CifString message(""); FILE *tlog = NULL; struct stat stat1; struct utsname sname; if (stat(infile_name, &stat1) < 0) { fprintf(stdout, "File %s did not exist.\n", infile_name); ndb_log_message(NDB_MSG_ERR, "File %s did not exist.\n", infile_name); return; } if (strcmp(support_file, "") && stat(support_file, &stat1) < 0) { fprintf(stdout, "File %s did not exist.\n", support_file); ndb_log_message(NDB_MSG_ERR, "File %s did not exist.\n", support_file); return; } strcpy(name, templateFileName); fd = mkstemp(name); close (fd); for (i = strlen(name) - 1; i >= 0; i--) { if (name[i] == '/') break; } strcpy(tmp_infile, &name[i + 1]); strcpy(tmpfile, infile_name); for (i = strlen(tmpfile) - 1; i >= 0; i--) { if (tmpfile[i] == '/') { strcpy(tmpfile, &tmpfile[i + 1]); break; } } compressFlag = 0; if (!strcmp(&tmpfile[strlen(tmpfile)-2], ".Z")) { compressFlag = 1; tmpfile[strlen(tmpfile)-2] = '\0'; strcpy(name, templateFileName); fd = mkstemp(name); close (fd); for (i = strlen(name) - 1; i >= 0; i--) { if (name[i] == '/') { strcpy(name, &name[i + 1]); break; } } sprintf(command, "zcat %s > %s", infile_name, name); system(command); preprocess_file(name, tmp_infile); sprintf(command, "rm %s", name); system(command); } else if (!strcmp(&tmpfile[strlen(tmpfile)-3], ".gz")) { compressFlag = 2; tmpfile[strlen(tmpfile)-3] = '\0'; strcpy(name, templateFileName); fd = mkstemp(name); close (fd); for (i = strlen(name) - 1; i >= 0; i--) { if (name[i] == '/') { strcpy(name, &name[i + 1]); break; } } uname(&sname); if (!strncmp(sname.sysname, "Linux", 5)) sprintf(command, "zcat %s > %s", infile_name, name); else sprintf(command, "gzcat %s > %s", infile_name, name); system(command); preprocess_file(name, tmp_infile); sprintf(command, "rm %s", name); system(command); } else preprocess_file(infile_name, tmp_infile); if (strcmp(support_file, "")) { strcpy(name, templateFileName); fd = mkstemp(name); close (fd); for (i = strlen(name) - 1; i >= 0; i--) { if (name[i] == '/') { strcpy(name, &name[i + 1]); break; } } sprintf(command, "mv %s %s", support_file, name); system(command); preprocess_file(name, support_file); sprintf(command, "rm %s", name); system(command); } maxit_check_files(choice, tmpfile, outfile_name); if (strcmp(object_name, "")) strcpy(outfile_name, object_name); switch (choice) { case MAX_OPTION_PDB_TO_CIF: fprintf(stdout, "Translating a PDB format file [%d] %s to a mmCIF file %s\n", num_file, tmpfile, outfile_name); pdb_to_cif(tmpfile, tmp_infile, outfile_name, is_binary, public_flag, standardized, is_iupac, id_option, exchange_out, together, no_deriv, support_file, keep_contact_author, no_pdbx_strand_id, is_nmr_view); break; case MAX_OPTION_CIF_TO_PDB: fprintf(stdout, "Translating a CIF format file [%d] %s to a PDB file %s\n", num_file, tmpfile, outfile_name); cif_to_pdb(tmpfile, tmp_infile, outfile_name, remark, is_binary, is_special, is_iupac, exchange_in, symmetry_flag, support_file, is_nmr_view); break; case MAX_OPTION_PDB_TO_NDB: fprintf(stdout, "Translating a PDB format file [%d] %s to a NDB file %s\n", num_file, tmpfile, outfile_name); pdb_to_ndb(tmpfile, tmp_infile, outfile_name, output_ndb_format, public_flag, short_version, support_file, is_nmr_view); break; case MAX_OPTION_NDB_TO_PDB: fprintf(stdout, "Translating a NDB format file [%d] %s to a PDB file %s\n", num_file, tmpfile, outfile_name); ndb_to_pdb(tmpfile, tmp_infile, outfile_name, remark, is_iupac); break; case MAX_OPTION_NDB_TO_CIF: fprintf(stdout, "Translating a NDB format file [%d] %s to a mmCIF file %s\n", num_file, tmpfile, outfile_name); ndb_to_cif(tmpfile, tmp_infile, outfile_name, is_binary, standardized, is_iupac, id_option, exchange_out, together, no_deriv, keep_contact_author, no_pdbx_strand_id); break; case MAX_OPTION_CIF_TO_NDB: fprintf(stdout, "Translating a CIF format file [%d] %s to a NDB file %s\n", num_file, tmpfile, outfile_name); cif_to_ndb(tmpfile, tmp_infile, outfile_name, output_ndb_format, is_binary, is_special, exchange_in, short_version, symmetry_flag, support_file, is_nmr_view); break; case MAX_OPTION_PDB_TO_ENCIF: fprintf(stdout, "Translating a PDB format file [%d] %s to a encapsulated CIF file %s\n", num_file, tmpfile, outfile_name); pdb_to_encapsulated_cif(tmpfile, tmp_infile, outfile_name, id_option, exchange_out, is_nmr_view); break; case MAX_OPTION_CIF_TO_CIF: fprintf(stdout, "Translating a CIF format file [%d] %s to a mmCIF file %s\n", num_file, tmpfile, outfile_name); cif_to_cif(tmpfile, tmp_infile, outfile_name, 0, is_binary, standardized, is_special, delete_atom, is_iupac, recover_asym, id_option, exchange_in, exchange_out, together, no_deriv, symmetry_flag, support_file, keep_contact_author, no_pdbx_strand_id, is_nmr_view); break; case MAX_OPTION_VALIDATION_PDB: fprintf(stdout, "Validation of a PDB format file [%d] %s\n", num_file, tmpfile); validation_pdb(tmpfile, tmp_infile, is_separate, is_prev_check, is_short_cut, File_ID, NULL, public_flag, is_nmr_view); memset(File_ID, 0, 100); break; case MAX_OPTION_VALIDATION_NDB: fprintf(stdout, "Validation of a NDB format file [%d] %s\n", num_file, tmpfile); validation_ndb(tmpfile, tmp_infile, is_separate, is_prev_check, is_short_cut, File_ID, public_flag); memset(File_ID, 0, 100); break; case MAX_OPTION_VALIDATION_CIF: fprintf(stdout, "Validation of a CIF format file [%d] %s\n", num_file, tmpfile); validation_cif(tmpfile, tmp_infile, is_separate, is_prev_check, is_short_cut, File_ID, NULL, public_flag, exchange_in, is_nmr_view); memset(File_ID, 0, 100); break; case MAX_OPTION_SYMMETRY_NDB: fprintf(stdout, "Generate symmetry related strands to NDB files(s) "); fprintf(stdout, "for [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); generate_sym_strands_NDB(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_SYMMETRY_CIF: fprintf(stdout, "Generate symmetry related strands to CIF files(s) "); fprintf(stdout, "for [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); generate_sym_strands_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_NCS_NDB: fprintf(stdout, "Generate NCS related strands to NDB files(s) for "); fprintf(stdout, "[%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); generate_ncs_strands_NDB(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_NCS_CIF: fprintf(stdout, "Generate NCS related strands to CIF files(s) for "); fprintf(stdout, "[%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); generate_ncs_strands_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_CHIRALITY_NDB: fprintf(stdout, "Correct Chirality of O1P/O2P and H atoms of NDB file "); fprintf(stdout, "[%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); correction_chirality_NDB(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_CHIRALITY_CIF: fprintf(stdout, "Correct Chirality of O1P/O2P and H atoms of mmCIF file "); fprintf(stdout, "[%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); correction_chirality_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_CORRESPND_NDB: fprintf(stdout, "Create Correspondences between deposited and standard hydrogen atoms"); fprintf(stdout, " of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); restraints_correspondences_NDB(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_CORRESPND_CIF: fprintf(stdout, "Create Correspondences between deposited and standard hydrogen atoms"); fprintf(stdout, " of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); restraints_correspondences_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_HYDROGEN_NDB: fprintf(stdout, "Remove Hydrogen atom(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); remove_hydrogen_NDB(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_HYDROGEN_CIF: fprintf(stdout, "Remove Hydrogen atom(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); remove_hydrogen_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_ORTH_TO_FRAC: fprintf(stdout, "Convert orthogonal coordinates to fractional for NDB file "); fprintf(stdout, "[%d] %s, the output file will be %s\n", num_file, tmpfile, outfile_name); orthogonal_to_fractional(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_FRAC_TO_ORTH: fprintf(stdout, "Convert fractional coordinates to orthogonal for NDB file "); fprintf(stdout, "[%d] %s, the output file will be %s\n", num_file, tmpfile, outfile_name); fractional_to_orthogonal(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_NDB_TO_NDBCIF: fprintf(stdout, "Translating a NDB format file [%d] %s to NDBCIF file %s\n", num_file, tmpfile, outfile_name); ndb_to_ndb(tmpfile, tmp_infile, outfile_name, NDB_FILE_FORMAT_NDBCIF); break; case MAX_OPTION_NDBCIF_TO_NDB: fprintf(stdout, "Translating a NDBCIF format file [%d] %s to NDB file %s\n", num_file, tmpfile, outfile_name); ndb_to_ndb(tmpfile, tmp_infile, outfile_name, NDB_FILE_FORMAT_NDB); break; case MAX_OPTION_DEL_ATOM_NDB: fprintf(stdout, "Delete atom(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); delete_atoms_NDB(tmpfile, tmp_infile, outfile_name, support_file, output_ndb_format); break; case MAX_OPTION_DEL_ATOM_CIF: fprintf(stdout, "Delete atom(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); delete_atoms_CIF(tmpfile, tmp_infile, outfile_name, support_file, is_binary); break; case MAX_OPTION_ADD_ATOM_NDB: fprintf(stdout, "Insert atom(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); insert_atoms_NDB(tmpfile, tmp_infile, outfile_name, support_file, output_ndb_format); break; case MAX_OPTION_ADD_ATOM_CIF: fprintf(stdout, "Insert atom(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); insert_atoms_CIF(tmpfile, tmp_infile, outfile_name, support_file, is_binary); break; case MAX_OPTION_DEL_RESIDUE_NDB: fprintf(stdout, "Delete residue(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); delete_residues_NDB(tmpfile, tmp_infile, outfile_name, support_file, output_ndb_format); break; case MAX_OPTION_DEL_RESIDUE_CIF: fprintf(stdout, "Delete residue(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); delete_residues_CIF(tmpfile, tmp_infile, outfile_name, support_file, is_binary); break; case MAX_OPTION_ADD_RESIDUE_NDB: fprintf(stdout, "Insert residue(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); insert_residues_NDB(tmpfile, tmp_infile, outfile_name, support_file, output_ndb_format); break; case MAX_OPTION_ADD_RESIDUE_CIF: fprintf(stdout, "Insert residue(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); insert_residues_CIF(tmpfile, tmp_infile, outfile_name, support_file, is_binary); break; case MAX_OPTION_MERGE_RMK_NDB: fprintf(stdout, "Merge Remarks of %s into NDB file [%d] %s, output file will be %s\n", support_file, num_file, tmpfile, outfile_name); merge_remarks_NDB(tmpfile, tmp_infile, outfile_name, support_file, output_ndb_format); break; case MAX_OPTION_MERGE_RMK_CIF: fprintf(stdout, "Merge Remarks of %s into mmCIF file [%d] %s, output file will be %s\n", support_file, num_file, tmpfile, outfile_name); merge_remarks_CIF(tmpfile, tmp_infile, outfile_name, support_file, is_binary); break; case MAX_OPTION_MERGE_COR_NDB: fprintf(stdout, "Merge Coordinates of %s into NDB file [%d] %s, output file will be %s\n", support_file, num_file, tmpfile, outfile_name); merge_coordinates_NDB(tmpfile, tmp_infile, outfile_name, support_file, output_ndb_format); break; case MAX_OPTION_MERGE_COR_CIF: fprintf(stdout, "Merge Coordinates of %s into mmCIF file [%d] %s, output file will be %s\n", support_file, num_file, tmpfile, outfile_name); merge_coordinates_CIF(tmpfile, tmp_infile, outfile_name, support_file, is_binary); break; case MAX_OPTION_MOVE_HOH_NDB: fprintf(stdout, "Moving Water(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); moving_waters_NDB(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_MOVE_HOH_CIF: fprintf(stdout, "Moving Water(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); moving_waters_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_RES_NAME_NDB: fprintf(stdout, "Switch Residue Name(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); switch_residue_names_NDB(tmpfile, tmp_infile, outfile_name, output_ndb_format); break; case MAX_OPTION_RES_NAME_CIF: fprintf(stdout, "Switch Residue Name(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); switch_residue_names_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_GET_MATRIX: fprintf(stdout, "Get Virus Matrices of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); get_virus_matrix_from_remark_350(tmpfile, tmp_infile, outfile_name, identical_flag); break; case MAX_OPTION_UPDATE_HYDROGEN: fprintf(stdout, "Update Hydrogen Nomenclature of PDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); update_hydrogen_nomenclature(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_CHECK_FILE: fprintf(stdout, "Checking PDB file [%d] %s\n", num_file, tmpfile); strcpy(buffer, templateFileName); fd = mkstemp(buffer); close (fd); tlog = fopen(buffer, "w"); check_file(tmpfile, tmp_infile, tlog, public_flag); fclose (tlog); tlog = fopen(buffer, "r"); while (!feof(tlog)) { fgets(command, 199, tlog); if (feof(tlog)) break; message += command; } fclose (tlog); sprintf(command, "rm -f %s", buffer); system(command); if (message != "") ndb_log_message(NDB_MSG_WARN, "%s\n", message.Text()); break; case MAX_OPTION_CLASSIFICATION: fprintf(stdout, "Get Classification of PDB file [%d] %s\n", num_file, tmpfile); classification(tmpfile, tmp_infile, summary, summary1); break; case MAX_OPTION_LAYER1_TO_2: fprintf(stdout, "Update REVDAT of Layer1 CIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); cif_layer1_to_layer2(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_CHANGE_SYMMETRY: fprintf(stdout, "Changing coordinates of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); change_coordinates_symm_CIF(tmpfile, tmp_infile, outfile_name, support_file); break; case MAX_OPTION_CHANGE_NON_SYMM: fprintf(stdout, "Changing coordinates of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); change_coordinates_non_symm_CIF(tmpfile, tmp_infile, outfile_name, support_file); break; case MAX_OPTION_COMPLEXITY: fprintf(stdout, "Search Complexity of mmCIF file [%d] %s\n", num_file, tmpfile); search_complexity(tmpfile, tmp_infile); break; case MAX_OPTION_FRAC_TO_ORTH_CIF: fprintf(stdout, "Changing coordinates from Fractional to Orthogonal\n"); fractional_to_orthogonal(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_Q_ATOM_CIF: fprintf(stdout, "Remove Q atom(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); remove_Q_atoms_CIF(tmpfile, tmp_infile, outfile_name, is_binary); break; case MAX_OPTION_MERGE_WATER: fprintf(stdout, "Reorder Het Group(s) and Waters of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); merge_waters_CIF(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_REP_RESIDUE_NDB: fprintf(stdout, "Replace residue(s) of NDB file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); replace_residues_NDB(tmpfile, tmp_infile, outfile_name, support_file, output_ndb_format); break; case MAX_OPTION_REP_RESIDUE_CIF: fprintf(stdout, "Replace residue(s) of mmCIF file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); replace_residues_CIF(tmpfile, tmp_infile, outfile_name, support_file); break; case MAX_OPTION_UPDATE_NA_FEATURE: fprintf(stdout, "Update NA features of mmCIF format file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); cif_to_cif(tmpfile, tmp_infile, outfile_name, 1, is_binary, standardized, is_special, 0, 0, 0, id_option, 0, 0, 0, 0, 0, "", keep_contact_author, 0, 0); break; case MAX_OPTION_RENUMBER_PDB: fprintf(stdout, "Re-number PDB numbers of mmCIF format file [%d] %s, output file will be %s\n", num_file, tmpfile, outfile_name); renumber_pdb_number_CIF(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_BIOL_UNIT: fprintf(stdout, "Creat biological unit PDB file(s) %s from CIF format file [%d] %s\n", outfile_name, num_file, tmpfile); cif_to_biol_unit_pdb(tmpfile, tmp_infile, outfile_name, exchange_in, id_option & 1); break; case MAX_OPTION_ONE_LETTER_CODE: fprintf(stdout, "Get one letter sequence from coordinates for file [%d] %s\n", num_file, tmpfile); get_one_letter_code_from_coordinates(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_HPUB_LETTER: fprintf(stdout, "Get letter for 'HOLD FOR PUBLICATION' file [%d] %s\n", num_file, tmpfile); get_hpub_letter(tmp_infile); break; case MAX_OPTION_EXCHANGE: fprintf(stdout, "Convert exchange format mmCIF %s into internal format mmCIF [%d] %s\n", outfile_name, num_file, tmpfile); exchange_cif_to_internal_cif(tmpfile, tmp_infile, outfile_name); break; case MAX_OPTION_PACKING: fprintf(stdout, "Creat packing unit PDB file(s) %s from CIF format file [%d] %s\n", outfile_name, num_file, tmpfile); cif_to_packing_pdb(tmpfile, tmp_infile, outfile_name, exchange_in); break; } sprintf(command, "rm -rf %s", tmp_infile); system(command); if (compressFlag == 1) { sprintf(command, "compress -f %s", outfile_name); system(command); } else if (compressFlag == 2) { sprintf(command, "gzip -f %s", outfile_name); system(command); } } static void maxit_check_files(const int choice, const char *infile_name, char *outfile_name) { memset(outfile_name, 0, MXSTRLEN); switch(choice){ case MAX_OPTION_PDB_TO_CIF: case MAX_OPTION_NDB_TO_CIF: case MAX_OPTION_PDB_TO_ENCIF: case MAX_OPTION_CIF_TO_CIF: case MAX_OPTION_SYMMETRY_CIF: case MAX_OPTION_NCS_CIF: case MAX_OPTION_CHIRALITY_CIF: case MAX_OPTION_HYDROGEN_CIF: case MAX_OPTION_DEL_ATOM_CIF: case MAX_OPTION_ADD_ATOM_CIF: case MAX_OPTION_DEL_RESIDUE_CIF: case MAX_OPTION_ADD_RESIDUE_CIF: case MAX_OPTION_MERGE_RMK_CIF: case MAX_OPTION_MERGE_COR_CIF: case MAX_OPTION_MOVE_HOH_CIF: case MAX_OPTION_RES_NAME_CIF: case MAX_OPTION_GET_MATRIX: case MAX_OPTION_LAYER1_TO_2: case MAX_OPTION_CHANGE_SYMMETRY: case MAX_OPTION_CHANGE_NON_SYMM: case MAX_OPTION_FRAC_TO_ORTH_CIF: case MAX_OPTION_Q_ATOM_CIF: case MAX_OPTION_MERGE_WATER: case MAX_OPTION_REP_RESIDUE_CIF: case MAX_OPTION_UPDATE_NA_FEATURE: case MAX_OPTION_RENUMBER_PDB: case MAX_OPTION_EXCHANGE: sprintf(outfile_name, "%s.cif", infile_name); break; case MAX_OPTION_CIF_TO_PDB: case MAX_OPTION_NDB_TO_PDB: case MAX_OPTION_UPDATE_HYDROGEN: case MAX_OPTION_BIOL_UNIT: case MAX_OPTION_PACKING: sprintf(outfile_name, "%s.pdb", infile_name); break; case MAX_OPTION_PDB_TO_NDB: case MAX_OPTION_CIF_TO_NDB: case MAX_OPTION_SYMMETRY_NDB: case MAX_OPTION_NCS_NDB: case MAX_OPTION_CHIRALITY_NDB: case MAX_OPTION_HYDROGEN_NDB: case MAX_OPTION_ORTH_TO_FRAC: case MAX_OPTION_FRAC_TO_ORTH: case MAX_OPTION_NDBCIF_TO_NDB: case MAX_OPTION_DEL_ATOM_NDB: case MAX_OPTION_ADD_ATOM_NDB: case MAX_OPTION_DEL_RESIDUE_NDB: case MAX_OPTION_ADD_RESIDUE_NDB: case MAX_OPTION_MERGE_RMK_NDB: case MAX_OPTION_MERGE_COR_NDB: case MAX_OPTION_MOVE_HOH_NDB: case MAX_OPTION_RES_NAME_NDB: case MAX_OPTION_REP_RESIDUE_NDB: sprintf(outfile_name, "%s.ndb", infile_name); break; case MAX_OPTION_CORRESPND_NDB: case MAX_OPTION_CORRESPND_CIF: sprintf(outfile_name, "%s.cor", infile_name); break; case MAX_OPTION_NDB_TO_NDBCIF: sprintf(outfile_name, "%s.ndbcif", infile_name); break; case MAX_OPTION_ONE_LETTER_CODE: sprintf(outfile_name, "%s.seq", infile_name); break; } } static void maxit_usage(const char *prog_name) { fprintf(stdout, "Usage: %s [-f file -i file -M merge_file -o num -replace ", prog_name); fprintf(stdout, "-path -filename -p -adit -s -standard -exchange_in -exchange_out -pdbids -ndbids -public -together -short -no_deriv -get_biol_unit]\n"); fprintf(stdout," [-f batch_file_name ]\n"); fprintf(stdout," [-i single_file_name]\n"); fprintf(stdout," [-o 1: Translate PDB format file(s) to CIF format file(s)]\n"); fprintf(stdout," [-o 2: Translate CIF format file(s) to PDB format file(s)]\n"); fprintf(stdout," [-o 3: Translate PDB format file(s) to NDB format file(s)]\n"); fprintf(stdout," [-o 4: Translate NDB format file(s) to PDB format file(s)]\n"); fprintf(stdout," [-o 5: Translate NDB format file(s) to mmCIF format file(s)]\n"); fprintf(stdout," [-o 6: Translate CIF format file(s) to NDB format file(s)]\n"); fprintf(stdout," [-o 7: Translate PDB format file(s) to encapsulated CIF file(s)\n"); fprintf(stdout," [-o 8: Translate CIF format file(s) to mmCIF format file(s)\n"); fprintf(stdout," [-o 9: Validation: PDB format file(s)]\n"); fprintf(stdout," [-o 10: Validation: NDB format file(s)]\n"); fprintf(stdout," [-o 11: Validation: CIF format file(s)]\n"); fprintf(stdout," [-o 12: Generate symmetry related strands to NDB files(s)]\n"); fprintf(stdout," [-o 13: Generate symmetry related strands to mmCIF files(s)]\n"); fprintf(stdout," [-o 14: Generate NCS related strands to NDB file(s)]\n"); fprintf(stdout," [-o 15: Generate NCS related strands to mmCIF file(s)]\n"); fprintf(stdout," [-o 16: Correct Chirality of O1P/O2P and H atoms to NDB file(s)]\n"); fprintf(stdout," [-o 17: Correct Chirality of O1P/O2P and H atoms to mmCIF file(s)]\n"); fprintf(stdout," [-o 18: Create Correspondences between deposited and standard hydrogen atoms to NDB file(s)]\n"); fprintf(stdout," [-o 19: Create Correspondences between deposited and standard hydrogen atoms to mmCIF file(s)]\n"); fprintf(stdout," [-o 20: Remove Hydrogen atom(s) to NDB file(s)]\n"); fprintf(stdout," [-o 21: Remove Hydrogen atom(s) to mmCIF file(s)]\n"); fprintf(stdout," [-o 22: Delete Atom(s) to NDB file(s)]\n"); fprintf(stdout," [-o 23: Delete Atom(s) to mmCIF file(s)]\n"); fprintf(stdout," [-o 24: Insert Atom(s) to NDB file(s)]\n"); fprintf(stdout," [-o 25: Insert Atom(s) to mmCIF file(s)]\n"); fprintf(stdout," [-o 26: Delete Residue(s) to NDB file(s)]\n"); fprintf(stdout," [-o 27: Delete Residue(s) to mmCIF file(s)]\n"); fprintf(stdout," [-o 28: Insert Residue(s) to NDB file(s)]\n"); fprintf(stdout," [-o 29: Insert Residue(s) to mmCIF file(s)]\n"); fprintf(stdout," [-o 30: Merge Remarks to NDB file]\n"); fprintf(stdout," [-o 31: Merge Remarks to mmCIF file]\n"); fprintf(stdout," [-o 32: Merge Coordinates to NDB file]\n"); fprintf(stdout," [-o 33: Merge Coordinates to mmCIF file]\n"); fprintf(stdout," [-o 34: Moving Water(s) to NDB file(s)]\n"); fprintf(stdout," [-o 35: Moving Water(s) to CIF file(s)]\n"); fprintf(stdout," [-o 36: Switch Residue Name(s) to NDB file(s)]\n"); fprintf(stdout," [-o 37: Switch Residue Name(s) to CIF file(s)]\n"); fprintf(stdout," [-o 38: Replace Residue(s) to NDB file(s)]\n"); fprintf(stdout," [-o 39: Replace Residue(s) to mmCIF file(s)]\n"); fprintf(stdout," [-o 40: Moving coordinates using symmetry operation to mmCIF file(s)]\n"); fprintf(stdout," [-o 41: Moving coordinates using non-symmetry operation to mmCIF file(s)]\n"); fprintf(stdout," [-o 42: Update NA features to mmCIF file(s)]\n"); fprintf(stdout," [-o 43: Convert orthogonal coordinates to fractional using NDB files(s)]\n"); fprintf(stdout," [-o 44: Convert fractional coordinates to orthogonal using NDB files(s)]\n"); fprintf(stdout," [-o 45: Convert fractional coordinates to orthogonal using mmCIF file(s)]\n"); fprintf(stdout," [-o 46: Translating NDB format file(s) to NDBCIF format file(s)]\n"); fprintf(stdout," [-o 47: Translating NDBCIF format file(s) to NDB format file(s)]\n"); fprintf(stdout," [-o 48: Adding REVDAT for Layer1 to Layer2 using CIF file(s)]\n"); fprintf(stdout," [-o 49: Remove Q atom(s) to mmCIF file(s)]\n"); fprintf(stdout," [-o 50: Reorder Het group(s) and Waters to mmCIF file(s)]\n"); fprintf(stdout," [-o 51: Get Virus Matrices to mmCIF file(s)]\n"); fprintf(stdout," [-o 52: Update Hydrogen Nomenclature to PDB file(s)]\n"); fprintf(stdout," [-o 53: Check PDB file(s)]\n"); fprintf(stdout," [-o 54: Get Classification of PDB file(s)]\n"); fprintf(stdout," [-o 55: Get Biological Unit PDB file(s)]\n"); fprintf(stdout," [-o 56: Convert mmCIF from exchange to internal dictionary]\n"); fprintf(stdout," [-o 57: Get one letter sequence from coordinates]\n"); fprintf(stdout," [-o 58: Get letter for 'HOLD FOR PUBLICATION' structures]\n"); }