/* FILE: ndb_cifparse_main.C */ /* VERSION: 3.101 */ /* DATE: 8/27/2004 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2004 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. 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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. */ /* PURPOSE: DDL 2.1 compliant CIF data file access library test program... */ #include #include #include #include #include "ndb_cifparse.h" #include "ndb_misclib.h" #define MAX_ID2_LEN 10 #define MAX_ID1_LEN 10 void ndb_usage(const char *prog_name); void build_new_datablocks(CifHandle *cif); void test_write_file(CifHandle *cif,const char *fname); int test_read_file(CifHandle *cif,const char *fname); void test_build_block_write_block(CifHandle *cif,const char *fname); void test_remove_block(CifHandle *cif,int iblock); void test_print_all_datablocks(CifHandle *cif); void build_new_datablock_from_pdb_file(CifHandle *cif); int get_category_index(CifHandle *cif,int blockIndex, const char *categoryName); int get_column_index(CifHandle *cif,int blockIndex, int categoryIndex, const char *columnName); void pr_coords_for_component_from_cif(CifHandle *cif,const char *cifName, const char *blockId, const char *compId); void test_write_file_pretty(CifHandle *cif,const char *fname); CifHandle NdbCif; int main(int argc, char *argv[]) { int level=10, i, itest,ret; char *prog_name, *fname=NULL,*fname2=NULL, *oname=NULL, *dbname=NULL, *compid=NULL; char *fname_default = "test.cif"; char *oname_default = "test.ocif"; prog_name = argv[0]; ndb_open_log(prog_name,"cifparse.log"); /* * Process command line arguments ... */ for (i=1; i < argc; i++) { if ( argv[i][0] == '-' ) { if (strcmp(argv[i],"-f") == 0 ) { /*input file */ i++; fname= argv[i]; } else if (strcmp(argv[i],"-f2") == 0 ) { /*input file2 */ i++; fname2= argv[i]; } else if (strcmp(argv[i],"-o") == 0 ) { /*output file */ i++; oname= argv[i]; } else if (strcmp(argv[i],"-v") == 0 ) { /* debug level */ i++; level = atoi(argv[i]); } else if (strcmp(argv[i],"-t") == 0 ) { /* test # */ i++; itest = atoi(argv[i]); } else if (strcmp(argv[i],"-db") == 0 ) { /* dblock name */ i++; dbname= argv[i]; } else if (strcmp(argv[i],"-compid") == 0 ) { /* component id */ i++; compid= argv[i]; } else { ndb_usage(prog_name); exit(1); } } else { ndb_usage(prog_name); exit(1); } } if (fname == NULL) fname = fname_default; if (oname == NULL) oname = oname_default; ndb_set_debug_level(level); ndb_log_message(NDB_MSG_DEBUG4,"Starting CIFparse test program"); ndb_log_message(NDB_MSG_DEBUG4,"Current number of data blocks is %d", ndb_cif_count_datablock(&NdbCif)); ndb_log_message(NDB_MSG_DEBUG4,"Current data block is %d", ndb_cif_current_datablock(&NdbCif)); switch (itest) { case 1: ndb_cif_init(&NdbCif); test_read_file(&NdbCif,fname); test_write_file(&NdbCif,oname); ndb_cif_close(&NdbCif); break; case 2: ndb_cif_init(&NdbCif); test_build_block_write_block(&NdbCif,oname); ndb_cif_close(&NdbCif); break; case 3: ndb_cif_init(&NdbCif); build_new_datablocks(&NdbCif); ndb_cif_print_datablocks(&NdbCif,stdout); ndb_cif_rewind_datablock(&NdbCif); ndb_cif_print_datablocks(&NdbCif,stdout); ndb_cif_close(&NdbCif); break; case 4: ndb_cif_init(&NdbCif); build_new_datablocks(&NdbCif); ndb_cif_move_datablock_by_id(&NdbCif,1); test_write_file(&NdbCif,oname); ndb_cif_close(&NdbCif); break; case 5: ndb_cif_init(&NdbCif); test_read_file(&NdbCif,fname); test_print_all_datablocks(&NdbCif); ndb_cif_close(&NdbCif); break; case 6: for (i=0; i < 10; i++) { fprintf(stderr,"Beginning read/write %d cycle on file %s\n",i+1,fname); ndb_cif_init(&NdbCif); test_read_file(&NdbCif,fname); test_write_file(&NdbCif,oname); ndb_cif_close(&NdbCif); } break; case 7: pr_coords_for_component_from_cif(&NdbCif,fname,dbname, compid); break; case 8: ndb_cif_init(&NdbCif); test_read_file(&NdbCif,fname); test_write_file_pretty(&NdbCif,oname); ndb_cif_close(&NdbCif); break; case 9: ndb_cif_init(&NdbCif); ret=test_read_file(&NdbCif,fname); ndb_cif_close(&NdbCif); if (ret==0) fprintf(stderr,"Parser error in file %s\n",fname); else fprintf(stderr,"%d Datablock(s) in file%s\n",ret,fname); ndb_cif_init(&NdbCif); ret=test_read_file(&NdbCif,fname2); ndb_cif_close(&NdbCif); if (ret==0) fprintf(stderr,"Parser error in file %s\n",fname2); else fprintf(stderr,"%d Datablock(s) in file %s\n",ret,fname2); break; } ndb_log_message(NDB_MSG_DEBUG4,"All done ... "); ndb_close_log(); } void build_new_datablocks(CifHandle *cif) { int nblocks=10, ncats=10, nrows=100, ncols=8; int iblock, icat, irow, icol; char block[20], category[20],keyword[20],value[20]; for (iblock=1; iblock<=nblocks; iblock++) { sprintf(block,"block_%d",iblock); ndb_cif_new_datablock(cif,block); ndb_log_message(NDB_MSG_DEBUG4,"Building block %d of %d", ndb_cif_current_datablock(cif), ndb_cif_count_datablock(cif)); for (icat=1; icat <= ncats; icat++) { sprintf(category,"category_%d",icat); ndb_cif_new_category(cif,category); for (icol=1; icol <= ncols; icol++) { sprintf(keyword,"keyword_%d",icol); ndb_cif_put_item_keyword(cif,keyword); } for (irow=1; irow <= nrows; irow++) { ndb_cif_new_row(cif); for (icol=1; icol <= ncols; icol++) { sprintf(value,"Value[%3d,%3d]",irow,icol); ndb_cif_put_item_value(cif,icol,value); } } } } } void ndb_usage(const char *prog_name) { fprintf(stdout,"Usage: %s\n",prog_name); fprintf(stdout," [-f input CIF1 ]\n"); fprintf(stdout," [-f2 input CIF2 ]\n"); fprintf(stdout," [-o output CIF ]\n"); fprintf(stdout," [-t test number (1-6)]\n"); fprintf(stdout," [-v debug level (1-10)]\n"); fprintf(stdout," [-db data block name\n"); fprintf(stdout," [-compid component id\n"); } int test_read_file(CifHandle *cif,const char *fname) { FILE *fp; int iret; /* * Read file ... */ if ((fp = fopen(fname,"r")) == NULL ) { ndb_log_message(NDB_MSG_DEBUG4,"Unable to open file %s",fname); exit(1); } iret = ndb_cif_read_file(cif,fp); ndb_log_message(NDB_MSG_DEBUG4,"Read CIF file %s and returned %d datablock(s)", fname,iret); ndb_log_message(NDB_MSG_DEBUG4,"Current number of data blocks is %d", ndb_cif_count_datablock(cif)); ndb_log_message(NDB_MSG_DEBUG4,"Current data block is %d", ndb_cif_current_datablock(cif)); fclose(fp); return iret; } void test_write_file(CifHandle *cif,const char *fname) { FILE *fp; /* * Write file */ ndb_cif_rewind_file(cif); if ((fp = fopen(fname,"w")) == NULL ) { ndb_log_message(NDB_MSG_DEBUG4,"Unable to open %s",fname); exit(1); } ndb_cif_write_file(cif,fp); ndb_log_message(NDB_MSG_DEBUG4,"Wrote CIF file %s",fname); fclose(fp); ndb_log_message(NDB_MSG_DEBUG4,"Current number of data blocks is %d", ndb_cif_count_datablock(cif)); ndb_log_message(NDB_MSG_DEBUG4,"Current data block is %d", ndb_cif_current_datablock(cif)); } void test_write_file_pretty(CifHandle *cif,const char *fname) { FILE *fp; /* * Write file */ ndb_cif_rewind_file(cif); if ((fp = fopen(fname,"w")) == NULL ) { ndb_log_message(NDB_MSG_DEBUG4,"Unable to open %s",fname); exit(1); } ndb_cif_write_file_pr(cif,fp); ndb_log_message(NDB_MSG_DEBUG4,"Wrote CIF file %s",fname); fclose(fp); ndb_log_message(NDB_MSG_DEBUG4,"Current number of data blocks is %d", ndb_cif_count_datablock(cif)); ndb_log_message(NDB_MSG_DEBUG4,"Current data block is %d", ndb_cif_current_datablock(cif)); } void test_build_block_write_block(CifHandle *cif,const char *fname) { FILE *fp; ndb_log_message(NDB_MSG_DEBUG4,"Building data blocks"); build_new_datablocks(cif); ndb_cif_rewind_datablock(cif); ndb_log_message(NDB_MSG_DEBUG4,"Current number of data blocks is %d", ndb_cif_count_datablock(cif)); ndb_log_message(NDB_MSG_DEBUG4,"Current data block is %d", ndb_cif_current_datablock(cif)); ndb_log_message(NDB_MSG_DEBUG4,"Writing new data blocks"); if ((fp = fopen(fname,"w")) == NULL ) { ndb_log_message(NDB_MSG_DEBUG4,"Unable to open file %s",fname); exit(1); } ndb_cif_write_file(cif,fp); ndb_log_message(NDB_MSG_DEBUG4,"Wrote CIF file %s",fname); fclose(fp); } void test_remove_block(CifHandle *cif,int iblock) { int nblocks; ndb_log_message(NDB_MSG_DEBUG4,"Current number of data blocks is %d", ndb_cif_count_datablock(cif)); ndb_log_message(NDB_MSG_DEBUG4,"Current data block is %d", ndb_cif_current_datablock(cif)); nblocks = ndb_cif_count_datablock(cif); if (iblock < nblocks ) { ndb_log_message(NDB_MSG_DEBUG4,"Removing data block %d ",iblock); ndb_cif_remove_datablock_by_id(cif,iblock); ndb_log_message(NDB_MSG_DEBUG4,"Current number of data blocks is %d", ndb_cif_count_datablock(cif)); ndb_log_message(NDB_MSG_DEBUG4,"Current data block is %d", ndb_cif_current_datablock(cif)); } } void test_print_all_datablocks(CifHandle *cif) { int datablockId; ndb_cif_rewind_datablock(cif); datablockId = ndb_cif_rewind_datablock(cif); do { ndb_cif_pretty_print_datablock(cif,stdout); datablockId = ndb_cif_next_datablock(cif); } while (datablockId); } void pr_coords_for_component_from_cif(CifHandle *cif,const char *cifName, const char *blockId, const char *compId) /* * Example: function which reads coordinates for component 'compid' from the * atom_site category of data block 'blockId. * */ { int i, stat, iblock; FILE *fp=NULL; int iCat, irow, nRow; int col1,col2,col3,col4,col5,col6,col7,col8,col9,col10,col11,col12; int col2a,col4a,col5a,col6a; char atom_id[MAX_ID2_LEN+1]; char name[MAX_ID2_LEN+1]; char nameAuth[MAX_ID2_LEN+1]; char type[MAX_ID2_LEN+1]; char compid[MAX_ID2_LEN+1]; char compidAuth[MAX_ID2_LEN+1]; char asymid[MAX_ID1_LEN+1]; char asymidAuth[MAX_ID1_LEN+1]; char seqid[MAX_ID1_LEN+1]; char seqidAuth[MAX_ID1_LEN+1]; char altid[MAX_ID1_LEN+1]; double x,y,z,occ,biso; ndb_cif_init(cif); ndb_log_message(NDB_MSG_INFO,"Reading CIF file %s",cifName); if ((fp = fopen(cifName, "r")) == NULL) { ndb_log_message(NDB_MSG_INFO,"Unable to open %s",cifName); return; } stat = ndb_cif_read_file(cif,fp); fclose(fp); ndb_log_message(NDB_MSG_INFO,"Read %d datablocks from %s [status = %d]", ndb_cif_count_datablock(cif),cifName,stat); /* * Check for target data block. */ iblock = -1; for (i=0; i< (*cif).numDatablock; i++) { if (!strcmp(blockId,(*cif).datablocks[i].datablockName)) { iblock = i; break; } } if (iblock == -1 ) { ndb_log_message(NDB_MSG_ERR,"Target data block %s is not in file %s", blockId,cifName); return; } /******************************************************************************************* * Load atom information and coordinates... * Get category id for category "atom_site" in this datablock.. */ iCat = get_category_index(cif,iblock,"atom_site"); if (iCat == -1) { ndb_log_message(NDB_MSG_ERR,"Target category %s is not in data block %d", "atom_site",iblock); return; } else { ndb_log_message(NDB_MSG_INFO,"Read %d rows in category %d", (*cif).datablocks[iblock].categories[iCat].numRow, iCat); col1 = get_column_index(cif,iblock,iCat,"id"); col2 = get_column_index(cif,iblock,iCat,"label_atom_id"); col3 = get_column_index(cif,iblock,iCat,"type_symbol"); col4 = get_column_index(cif,iblock,iCat,"label_comp_id"); col5 = get_column_index(cif,iblock,iCat,"label_asym_id"); col6 = get_column_index(cif,iblock,iCat,"label_seq_id"); col7 = get_column_index(cif,iblock,iCat,"label_alt_id"); col8 = get_column_index(cif,iblock,iCat,"cartn_x"); col9 = get_column_index(cif,iblock,iCat,"cartn_y"); col10 = get_column_index(cif,iblock,iCat,"cartn_z"); col11 = get_column_index(cif,iblock,iCat,"occupancy"); col12 = get_column_index(cif,iblock,iCat,"B_iso_or_equiv"); col2a = get_column_index(cif,iblock,iCat,"auth_atom_id"); col4a = get_column_index(cif,iblock,iCat,"auth_comp_id"); col5a = get_column_index(cif,iblock,iCat,"auth_asym_id"); col6a = get_column_index(cif,iblock,iCat,"auth_seq_id"); nRow=0; for (i=0; i < (*cif).datablocks[iblock].categories[iCat].numRow; i++) { if (!strcmp((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4],compId)) { nRow++; } } if (nRow > 0 ) { for (i=0; i < (*cif).datablocks[iblock].categories[iCat].numRow; i++) { if (!strcmp((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4],compId)) { if ((col1 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col1] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col1]) > 0)) { strncpy(atom_id, (*cif).datablocks[iblock].categories[iCat].rows[i].columns[col1],MAX_ID2_LEN); } if ((col2 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col2] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col2]) > 0)) { strncpy(name,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col2],MAX_ID2_LEN); } if ((col2a != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col2a] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col2a]) > 0)) { strncpy(nameAuth,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col2a],MAX_ID2_LEN); } if ((col3 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col3] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col3]) > 0)) { strncpy(type,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col3],2); } if ((col4 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4]) > 0)) { strncpy(compid,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4],MAX_ID2_LEN); } if ((col4a != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4a] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4a]) > 0)) { strncpy(compidAuth,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col4a],MAX_ID2_LEN); } if ((col5 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col5] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col5]) > 0)) { strncpy(asymid,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col5],MAX_ID1_LEN); } if ((col5a != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col5a] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col5a]) > 0)) { strncpy(asymidAuth,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col5a],MAX_ID1_LEN); } if ((col6 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col6] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col6]) > 0)) { strncpy(seqid,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col6],MAX_ID1_LEN); } if ((col6a != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col6a] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col6a]) > 0)) { strncpy(seqidAuth,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col6a],MAX_ID1_LEN); } if ((col7 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col7] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col7]) > 0)) { strncpy(altid,(*cif).datablocks[iblock].categories[iCat].rows[i].columns[col7],MAX_ID1_LEN); } if ((col8 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col8] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col8]) > 0)) { x = atof((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col8]); } if ((col9 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col9] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col9]) > 0)) { y = atof((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col9]); } if ((col10 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col10] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col10]) > 0)) { z = atof((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col10]); } if ((col11 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col11] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col11]) > 0)) { occ = atof((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col11]); } if ((col12 != -1) && ((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col12] != NULL) && (strlen((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col12]) > 0)) { biso = atof((*cif).datablocks[iblock].categories[iCat].rows[i].columns[col12]); } irow++; printf("%-5s %-5s %-5s %-5s %-5s %8.3f %8.3f %8.3f %8.3f %8.3f\n", atom_id,name,type,compid,seqid,x,y,z,occ,biso); } } } } ndb_cif_close(cif); } int get_column_index(CifHandle *cif,int blockIndex, int categoryIndex, const char *columnName) /* * Return the index of for 'columnName' in the data block and category * specified by 'blockIndex' and 'categoryIndex'. */ { int icol, k; icol = -1; for (k=0; k < (*cif).datablocks[blockIndex].categories[categoryIndex].numCol; k++) { if (!strcmp(columnName,(*cif).datablocks[blockIndex].categories[categoryIndex].colNames[k])) { icol = k; break; } } return icol; } int get_category_index(CifHandle *cif,int blockIndex, const char *categoryName) /* * Return the index of for 'categoryName' in the data block * specified by 'blockIndex'. */ { int icat, i; icat = -1; for (i=0; i< (*cif).datablocks[blockIndex].numCategory; i++) { if (!strcmp(categoryName,(*cif).datablocks[blockIndex].categories[i].categoryName)) { icat = i; break; } } return(icat); }