/* FILE: cif_to_ndb.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. 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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 "ndb_misclib.h" #include "util.h" #include "_maxit.h" #include "erf_category.h" #include "erf_util.h" #define N_SWITCH_CATEGORY 3 #define N_R_MERGE 4 #define N_ENTITY 46 typedef struct { const char *category; const char *high_item; const char *low_item; } _Switch_Category; typedef struct { const char *catetory; const char *item; } _R_Merge; static _Switch_Category _switch_category[N_SWITCH_CATEGORY] = { { "refine", "ls_d_res_high", "ls_d_res_low" }, { "reflns", "d_resolution_high", "d_resolution_low" }, { "reflns_shell", "d_res_high", "d_res_low" } }; static _R_Merge _r_merge[N_R_MERGE] = { { "reflns", "ndb_Rmerge_I_obs" }, { "reflns", "ndb_Rsym_value" }, { "reflns_shell", "Rmerge_I_obs" }, { "reflns_shell", "ndb_Rsym_value" } }; static const char entity_token[N_ENTITY][7] = { "ENTAIL", "ENTKEY", "ENTMUT", "FRAGMT", "ISOTYP", "ECNUM", "BINEMD", "BIOUNI", "ENTNAM", "ENTSYS", "PROTEI", "SRCNNM", "SRCNSP", "SRCNTS", "SRCNSE", "SRCNDS", "SRCNFR", "SRCNSC", "SRCNCC", "SRCNOR", "SRCNPL", "SRCGFR", "SRCGNM", "SRCNN1", "SRCGST", "SRCGSP", "SRCGCC", "SRCGTS", "SRCGTI", "SRCGDS", "SRCSYN", "SRCGE1", "SRCGE2", "SRCGE3", "SRCGE4", "SRCGE5", "SRCGHN", "SRCGHS", "SRCGH1", "SRCGHT", "SRCGHV", "SRCGHC", "SRCGVE", "SRCGHD", "SRCGPL", "TARGET" }; #define NUM_CENTER 20 static const int is_psi_center[NUM_CENTER] = { 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1 }; static const char *_full_name_of_center[NUM_CENTER] = { "Bacterial targets at IGS-CNRS, France", "Berkeley Structural Genomics Center", "Center for Eukaryotic Structural Genomics", "Israel Structural Proteomics Center", "Joint Center for Structural Genomics", "Marseilles Structural Genomics Program @ AFMB", "Midwest Center for Structural Genomics", "Montreal-Kingston Bacterial Structural Genomics Initiative", "Mycobacterium Tuberculosis Structural Proteomics Project", "New York Structural Genomics Research Consortium", "Northeast Structural Genomics Consortium", "Oxford Protein Production Facility", "Paris-Sud Yeast Structural Genomics", "Protein Structure Factory", "RIKEN Structural Genomics/Proteomics Initiative", "Southeast Collaboratory for Structural Genomics", "Structural Genomics of Pathogenic Protozoa Consortium", "Structural Proteomics in Europe", "Structure 2 Function Project", "TB Structural Genomics Consortium" }; static const char *_initials_of_center[NUM_CENTER] = { "BIGS", "BSGC", "CESG", "ISPC", "JCSG", "MSGP", "MCSG", "BSGI", "XMTB", "NYSGRC", "NESG", "OPPF", "YSG", "PSF", "RSGI", "SECSG", "SGPP", "SPINE", "S2F", "TBSGC" }; static int get_number_strands(ISTable *Table, const char *sheet_id); static int get_sense(ISTable *Table, const char *sheet_id, const char *id_1, const char *id_2); static void get_hbond(_MOLECULE *mol, ISTable *Table, const int chain_index, const char *sheet_id, const char *range_id, CifString &curAtom, int &curIndex, int &curRes, CifString &prevAtom, int &prevIndex, int &prevRes); static void cif_to_ndb_find_serial_no(ISTable *Table, const int id, const int irow, const int tokenid, int *idfield, char idvalue[10][82], char SerialNo[10][82]); void _MAXIT::cif_to_ndb_general(const int transfer, const int flag, const int special, const int recover_asym, const int exchange, const int together, const int short_version, const int symmetry_flag, const int is_nmr_view) { int fd, i, k, is_same, card_id, rowNo, entity_id, full_index, initial_index; int is_PSI_entry = 0, is_SG_entry = 0, name_index, db_name_index, db_id_index; int project_index, rowNo1, target_index, len; char buffer[5000], buffer1[100], *p = NULL; CifString cifstring, cifstring1, target, project, full_name, initials; ISTable *Struct_Ref = NULL, *Table = NULL; One_Card_Info_Format *pCard = NULL; ReVarCifArray colData; int input_format = NDB_FILE_FORMAT_PDB; read_mmcif_file(input_format, special, exchange, short_version, symmetry_flag, 0, is_nmr_view); ndb_processing_requests(); ndb_processing_em_software(); ndb_processing_struct_category(); ndb_processing_struct_sheet_hbond(); ndb_processing_ndb_database_PDB_obs_spr_category(); ndb_processing_struct_ref_seq_and_diff(); if (transfer != 2) seq_alignment(1); if (_file_status == FILE_STATUS_MMCIF_PLUS_MOL) { char filename[100], line[200]; char templateFileName[9] = "./XXXXXX"; strcpy(filename, templateFileName); fd = mkstemp(filename); close (fd); FILE *tlog = fopen(filename, "w"); ndb_check_file(tlog, NUM_TOKEN, Check_Format, NUM_CHECK_CATEGORY, check_category, 1, 0); input_structural_features(NDB_FILE_FORMAT_PDB); fclose (tlog); tlog = fopen(filename, "r"); CifString message(""); while (!feof(tlog)) { fgets(line, 199, tlog); if (feof(tlog)) break; message += line; } fclose (tlog); sprintf(line, "rm -f %s", filename); system(line); if (message != "") ndb_log_message(NDB_MSG_WARN, "%s\n", message.Text()); } if (flag) processing_r_factor(100.0); Table = _CifObj->GetTablePtr(_StructureId, "pdbx_SG_project"); if (!is_empty_table(Table)) { project_index = Table->GetColumnIndex("project_name"); full_index = Table->GetColumnIndex("full_name_of_center"); initial_index = Table->GetColumnIndex("initial_of_center"); rowNo1 = Table->GetNumRows(); for (k = 0; k < rowNo1; k++) { cifstring.Clear(); Table->GetCell(cifstring, full_index, k); for (i = 0; i < NUM_CENTER; i++) { if (!strcasecmp(cifstring.Text(), _full_name_of_center[i])) { cifstring.Copy(_full_name_of_center[i]); Table->UpdateCell(cifstring, full_index, k); cifstring.Copy(_initials_of_center[i]); Table->UpdateCell(cifstring, initial_index, k); _CifObj->WriteTable(Table, _StructureId, "pdbx_SG_project"); is_SG_entry = 1; if (is_psi_center[i]) is_PSI_entry = 1; break; } } } if (is_SG_entry) { Struct_Ref = _CifObj->GetTablePtr(_StructureId, "ndb_database_status"); if (!is_empty_table(Struct_Ref)) { cifstring.Copy("Y"); name_index = Struct_Ref->GetColumnIndex("SG_entry"); if (name_index < 0) { Struct_Ref->AddColumn("SG_entry"); name_index = Struct_Ref->GetColumnIndex("SG_entry"); colData.Clear(); colData.Add(cifstring); Struct_Ref->FillColumn(colData, name_index); } Struct_Ref->UpdateCell(cifstring, name_index, 0); _CifObj->WriteTable(Struct_Ref, _StructureId, "ndb_database_status"); } for (k = 0; k < rowNo1; k++) { Table->GetCell(project, project_index, k); if (project == "?" || project == ".") project.Copy(""); Table->GetCell(full_name, full_index, k); if (full_name == "?" || full_name == ".") full_name.Copy(""); Table->GetCell(initials, initial_index, k); if (initials == "?" || initials == ".") initials.Copy(""); if (full_name != "") { Struct_Ref = _CifObj->GetTablePtr(_StructureId, "audit_author"); if (is_empty_table(Struct_Ref)) { _CifObj->DeleteTable(_StructureId, "audit_author"); Struct_Ref = new ISTable("audit_author"); Struct_Ref->AddColumn("name"); _CifObj->WriteTable(Struct_Ref, _StructureId, "audit_author"); } name_index = Struct_Ref->GetColumnIndex("name"); rowNo = Struct_Ref->GetNumRows(); for (i = 0; i < rowNo; i++) { Struct_Ref->GetCell(cifstring, name_index, i); if (strstr(cifstring.Text(), full_name.Text()) && strstr(cifstring.Text(), initials.Text())) break; } if (i == rowNo) { Struct_Ref->AddRow(); cifstring.Copy(full_name.Text()); if (initials != "") { cifstring += " ("; cifstring += initials.Text(); cifstring += ")"; } Struct_Ref->UpdateCell(cifstring, name_index, rowNo); _CifObj->WriteTable(Struct_Ref, _StructureId, "audit_author"); } } Struct_Ref = _CifObj->GetTablePtr(_StructureId, "struct_keywords"); if (is_empty_table(Struct_Ref)) { _CifObj->DeleteTable(_StructureId, "struct_keywords"); Struct_Ref = new ISTable("struct_keywords"); Struct_Ref->AddColumn("entry_id"); Struct_Ref->AddColumn("ndb_keywords"); Struct_Ref->AddColumn("text"); Struct_Ref->AddRow(); cifstring.Copy(_StructureId); Struct_Ref->UpdateCell(cifstring, 0, 0); _CifObj->WriteTable(Struct_Ref, _StructureId, "struct_keywords"); } name_index = Struct_Ref->GetColumnIndex("text"); cifstring.Clear(); Struct_Ref->GetCell(cifstring, name_index, 0); if (cifstring == "?" || cifstring == ".") cifstring.Clear(); strcpy(buffer, cifstring.Text()); ndb_set_string_to_upper(buffer); if (!strstr(buffer, "STRUCTURAL GENOMICS")) { if (cifstring != "") cifstring += ", "; cifstring += "Structural Genomics"; } if (is_PSI_entry) { if (!strstr(buffer, "PSI")) { if (cifstring != "") cifstring += ", "; cifstring += "PSI"; } if (!strstr(buffer, "PROTEIN STRUCTURE INITIATIVE")) { if (cifstring != "") cifstring += ", "; cifstring += "Protein Structure Initiative"; } } else { strcpy(buffer1, project.Text()); ndb_set_string_to_upper(buffer1); if (strcmp(buffer1, "") && !strstr(buffer, buffer1)) { if (cifstring != "") cifstring += ", "; cifstring += project.Text(); } } strcpy(buffer1, full_name.Text()); ndb_set_string_to_upper(buffer1); if (strcmp(buffer1, "") && !strstr(buffer, buffer1)) { if (cifstring != "") cifstring += ", "; cifstring += full_name.Text(); } strcpy(buffer1, initials.Text()); ndb_set_string_to_upper(buffer1); if (strcmp(buffer1, "") && !strstr(buffer, buffer1)) { if (cifstring != "") cifstring += ", "; cifstring += initials.Text(); } Struct_Ref->UpdateCell(cifstring, name_index, 0); _CifObj->WriteTable(Struct_Ref, _StructureId, "struct_keywords"); } Table = _CifObj->GetTablePtr(_StructureId, "entity_poly"); if (!is_empty_table(Table)) { target_index = Table->GetColumnIndex("pdbx_target_identifier"); rowNo1 = Table->GetNumRows(); for (i = 0; i < rowNo1; i++) { cifstring.Clear(); Table->GetCell(cifstring, target_index, i); if (cifstring == "." || cifstring == "?") cifstring.Clear(); if (cifstring != "") break; } if (i < rowNo1) { Struct_Ref = _CifObj->GetTablePtr(_StructureId, "rcsb_database_related"); if (is_empty_table(Struct_Ref)) { _CifObj->DeleteTable(_StructureId, "rcsb_database_related"); Struct_Ref = new ISTable("rcsb_database_related"); Struct_Ref->AddColumn("db_name"); Struct_Ref->AddColumn("db_id"); _CifObj->WriteTable(Struct_Ref, _StructureId, "rcsb_database_related"); } db_name_index = Struct_Ref->GetColumnIndex("db_name"); db_id_index = Struct_Ref->GetColumnIndex("db_id"); rowNo = Struct_Ref->GetNumRows(); for (k = 0; k < rowNo1; k++) { target.Clear(); Table->GetCell(target, target_index, k); if (target == "." || target == "?" || target == "") continue; strcpy(buffer, target.Text()); len = strlen(buffer); for (i = 0; i < len; i++) { if (buffer[i] == ',' || buffer[i] == ';') buffer[i] = ' '; } ndb_clean_string(buffer); p = buffer; while (p) { p = get_word(p, buffer1); if (!strcmp(buffer1, "")) continue; for (i = 0; i < rowNo; i++) { Struct_Ref->GetCell(cifstring, db_name_index, i); Struct_Ref->GetCell(cifstring1, db_id_index, i); if (!strcasecmp(cifstring.Text(), "TargetDB") && !strcasecmp(cifstring1.Text(), buffer1)) break; } if (i == rowNo) { Struct_Ref->AddRow(); cifstring.Copy("TargetDB"); Struct_Ref->UpdateCell(cifstring, db_name_index, rowNo); cifstring.Copy(buffer1); Struct_Ref->UpdateCell(cifstring, db_id_index, rowNo); _CifObj->WriteTable(Struct_Ref, _StructureId, "rcsb_database_related"); rowNo++; } } } } } } } ndb_processing_categories_mapping(transfer); if (transfer != 2) { find_missing_residues(); // update_pdb_and_pub_numbers(); // Input_Stbiol(); if (!recover_asym) Get_Stbiol(exchange); Reorder_Stbiol(); Input_Entity(); get_seqifo(0, together); match_entity_with_molecules(); match_stbiol_with_molecules(); if (_file_status == FILE_STATUS_MMCIF_PLUS_MOL) { is_same = 1; for (i = 0; i < _n_entity; i++) { if (_entity[i].Entity_ID != _entity[i].Old_Entity_ID) { is_same = 0; break; } } if (!is_same) { for (i = 0; i < N_ENTITY; i++) { card_id = find_card_id(entity_token[i]); if (card_id == -1) continue; pCard = _CardInfo[card_id].Head(); while (pCard) { for (k = 0; k < _n_entity; k++) { if (!strcmp(entity_token[i], "BINEMD")) { if (atoi(pCard->Field(3)) == _entity[k].Old_Entity_ID) { pCard->AddElementToField(_entity[k].Entity_ID, 3); break; } } else { if (atoi(pCard->Field(1)) == _entity[k].Old_Entity_ID) { pCard->AddElementToField(_entity[k].Entity_ID, 1); break; } } } pCard = pCard->Next(); } _CardInfo[card_id].reorder_cards(1, INTEGER_COMPARE, ASCENT); } Table = _CifObj->GetTablePtr(_StructureId, "rcsb_entity_name"); if (!is_empty_table(Table)) { rowNo = Table->GetNumRows(); entity_id = Table->GetColumnIndex("entity_id"); if (entity_id >= 0) { for (i = 0; i < rowNo; i++) { get_value(cifstring, Table, entity_id, i); if (cifstring != "") { for (k = 0; _n_entity; k++) { if (atoi(cifstring.Text()) == _entity[k].Old_Entity_ID) { sprintf(buffer, "%d", _entity[k].Entity_ID); cifstring.Copy(buffer); Table->UpdateCell(cifstring, entity_id, i); break; } } } } } _CifObj->WriteTable(Table, _StructureId, "rcsb_entity_name"); } Struct_Ref = _CifObj->GetTablePtr(_StructureId, "struct_ref"); if (!is_empty_table(Struct_Ref)) { rowNo = Struct_Ref->GetNumRows(); entity_id = Struct_Ref->GetColumnIndex("entity_id"); if (entity_id >= 0) { for (i = 0; i < rowNo; i++) { get_value(cifstring, Struct_Ref, entity_id, i); if (cifstring != "") { for (k = 0; _n_entity; k++) { if (atoi(cifstring.Text()) == _entity[k].Old_Entity_ID) { sprintf(buffer, "%d", _entity[k].Entity_ID); cifstring.Copy(buffer); Struct_Ref->UpdateCell(cifstring, entity_id, i); break; } } } } } _CifObj->WriteTable(Struct_Ref, _StructureId, "struct_ref"); } } } Table = _CifObj->GetTablePtr(_StructureId, "rcsb_struct_link"); if (!is_empty_table(Table)) cifndb_process_rcsb_link(Table); get_entity_card(); get_compnd_card(); } check_terminal_atoms(cifstring); if (strcmp(cifstring.Text(), "")) ndb_log_message(NDB_MSG_WARN, "%s\n", cifstring.Text()); post_processing_from_cif_to_ndb(); } void _MAXIT::cif_to_ndb_exchange(const int exchange, const int is_nmr_view) { int input_format = NDB_FILE_FORMAT_PDB; read_mmcif_file(input_format, 0, exchange, 0, 0, 0, is_nmr_view); seq_alignment(0); ndb_processing_em_software(); ndb_processing_struct_category(); ndb_processing_struct_sheet_hbond(); ndb_processing_ndb_database_PDB_obs_spr_category(); ndb_processing_struct_ref_seq_and_diff(); processing_r_factor(100.0); ndb_processing_categories_mapping(0); Get_Stbiol(exchange); } void _MAXIT::ndb_processing_categories_mapping(const int transfer) { int i, card_id, struct_ref_id = -1; ISTable *Struct_Ref = NULL, *Table = NULL; for (i = 0; i < MxCategory; i++) { if (transfer && !(transfer & CifCategory[i].transfer)) continue; if (!strcmp(CifCategory[i].category, "struct_conf_type") || !strcmp(CifCategory[i].category, "struct_conn_type") || !strcmp(CifCategory[i].category, "struct_sheet_order") || !strcmp(CifCategory[i].category, "struct_sheet_range") || !strcmp(CifCategory[i].category, "struct_sheet_hbond") || !strcmp(CifCategory[i].category, "rcsb_struct_sheet_hbond") || !strcmp(CifCategory[i].category, "atom_site") || !strcmp(CifCategory[i].category, "atom_site_anisotrop") || !strcmp(CifCategory[i].category, "struct_asym") || !strcmp(CifCategory[i].category, "entity_poly_seq") || !strcmp(CifCategory[i].category, "ndb_nonstandard_list") || !strcmp(CifCategory[i].category, "ndb_poly_seq_scheme") || !strcmp(CifCategory[i].category, "database_PDB_rev_record")) continue; Table = _CifObj->GetTablePtr(_StructureId, CifCategory[i].category); if (is_empty_table(Table)) continue; if (!strcmp(CifCategory[i].category, "struct_ref")) { Struct_Ref = Table; struct_ref_id = i; continue; } if (!strcmp(CifCategory[i].category, "struct_conf")) cifndb_process_struct_conf(Table); else if (!strcmp(CifCategory[i].category, "struct_sheet")) cifndb_process_sheet(); else if (!strcmp(CifCategory[i].category, "struct_conn")) cifndb_process_struct_conn(Table); else if (!strcmp(CifCategory[i].category, "refine_ls_restr")) cifndb_process_refine_ls_restr(Table); else if (!strcmp(CifCategory[i].category, "struct_site_gen")) cifndb_process_struct_site_gen(Table); else if (!strcmp(CifCategory[i].category, "rcsb_struct_link")) cifndb_process_rcsb_link(Table); else if (!strcmp(CifCategory[i].category, "database_PDB_rev")) cifndb_process_database_pdb_rev(Table); else if (!strcmp(CifCategory[i].category, "database_PDB_remark") || !strcmp(CifCategory[i].category, "rcsb_database_PDB_remark")) { if (!strcmp(CifCategory[i].category, "database_PDB_remark")) cifndb_process_remark(Table, PREMRK_TOKEN-1, 2); else { card_id = find_card_id("PDBRMK"); cifndb_process_remark(Table, card_id, 3); } } else if (!strcmp(CifCategory[i].category, "ndb_database_remark") || !strcmp(CifCategory[i].category, "ndb_pdb_compnd") || !strcmp(CifCategory[i].category, "ndb_pdb_source")) { cifndb_process_general_category(Table, i, 1); } else if (CifCategory[i].general) cifndb_process_general_category(Table, i, 0); else if (CifCategory[i].xray_or_nmr & 4) cifndb_process_matrix(Table, i); else cifndb_process_category(Table, i, 0); } if (Struct_Ref) cifndb_process_category(Struct_Ref, struct_ref_id, 1); } void _MAXIT::cifndb_process_category(ISTable *Table, const int id, const int is_special) { int i, j, k, irow, icol, tokenid, jrnlid, fieldno; int idfield[10], SerialNoField[10], cols[200]; char SerialNo[10][82], idValue[10][82]; CifString string; int colNo = Table->GetNumColumns(); int rowNo = Table->GetNumRows(); ReVarCifArray *ColumnNames = Table->GetColumnNames(); for (i = 0; i < 10; i++) idfield[i] = -1; for (i = 0; i < colNo; i++) { for (j = 0; j < CifCategory[id].nkeywords; j++) { if (!strcasecmp((*ColumnNames)[i].Text(), CifCategory[id].keywords[j].name)) break; } if (j == CifCategory[id].nkeywords) cols[i] = -1; else cols[i] = j; for (k = 0; k < CifCategory[id].nCifKeyField; k++) { if (j == CifCategory[id].CifKeyField[k]) idfield[k] = i; } } if (ColumnNames) delete ColumnNames; for (irow = 0; irow < rowNo; irow++) { for (icol = 0; icol < colNo; icol++) { j = cols[icol]; if (j < 0 || j > CifCategory[id].nkeywords) continue; Table->GetCell(string, icol, irow); if (string == "" || string == "." || string == "?") continue; for (i = 0; i < CifCategory[id].keywords[j].numNdbInfo; i++) { tokenid = CifCategory[id].keywords[j].NdbInfo[i].NdbTokenId-1; jrnlid = CifCategory[id].keywords[j].NdbInfo[i].JrnlTokenId-1; fieldno = CifCategory[id].keywords[j].NdbInfo[i].NdbFieldNo-1; for (k = 0; k < CifCategory[id].nCifKeyField; k++) SerialNoField[k] = CifCategory[id].keywords[j]. NdbInfo[i].NdbTokenKeyFieldNo[k]; if (tokenid < 0 || tokenid >= MxTokens || fieldno <= 0) continue; cif_to_ndb_find_serial_no(Table, id, irow, tokenid, idfield, idValue, SerialNo); if (CifCategory[id].nCifKeyField) { for (k = 0; k < CifCategory[id].nCifKeyField; k++) { if (strcmp(idValue[k], "") && strcasecmp(idValue[k], CifCategory[id].keywords[j].NdbInfo[i]. JrnlTokenName_Type)) break; } if (k < CifCategory[id].nCifKeyField) continue; } if (tokenid == JRNL_TOKEN - 1) { if (!strcasecmp(JrnlToken[jrnlid].TokenName, "AUTH") && !strcasecmp(CifCategory[id].category, "citation")) continue; cifndb_process_general(jrnlid, fieldno, CifCategory[id].nCifKeyField, SerialNoField, SerialNo, string.Text(), TRUE); } else if (is_special) cifndb_process_special(tokenid, fieldno, CifCategory[id].nCifKeyField, SerialNoField, SerialNo, string.Text()); else cifndb_process_general(tokenid, fieldno, CifCategory[id].nCifKeyField, SerialNoField, SerialNo, string.Text(), FALSE); } } } } void _MAXIT::cifndb_process_general(const int tokenid, const int fieldno, const int NumKey, int *SerialNoField, char SerialNo[10][82], char *value, const int IsJrnl) { One_Card_Info_Format *pCard = NULL; int i, vField = 5, logical = FALSE, jrnl_id; char buffer[1000]; if (tokenid == NDBFIL_TOKEN - 1 && !strcasecmp(value, "DEPOSIT-0")) { pCard = _CardInfo[tokenid].Head(); if (pCard && strcmp(pCard->Field(fieldno), "")) return; } if (IsJrnl) { pCard = _JrnlCardInfo[tokenid].Head(); while (pCard) { if (NumKey) { for (i = 0; i < NumKey; i++) { if (SerialNoField[i] > 0 && strcasecmp(SerialNo[i], pCard->Field(SerialNoField[i]))) break; } if (i == NumKey) break; } else if (JrnlToken[tokenid].SeqField != 0 && !strcasecmp(SerialNo[0], pCard->Field(JrnlToken[tokenid].SeqField-1))) break; else if (!strcmp(pCard->Field(fieldno), "")) break; pCard = pCard->Next(); } } else if (tokenid == AUTHOR_TOKEN-1) pCard = _CardInfo[tokenid].Tail(); else { pCard = _CardInfo[tokenid].Head(); while (pCard) { if (NumKey) { for (i = 0; i < NumKey; i++) { if (SerialNoField[i] > 0 && strcasecmp(SerialNo[i], pCard->Field(SerialNoField[i]))) break; } if (i == NumKey) break; } else if (NdbToken[tokenid].SeqField != 0 && !strcasecmp(SerialNo[0], pCard->Field(NdbToken[tokenid].SeqField-1))) break; else if ((tokenid == HEADER_TOKEN - 1 || tokenid == PDBFIL_TOKEN - 1 || tokenid == NDBFIL_TOKEN - 1) && !strcasecmp(value, pCard->Field(fieldno))) break; else if (!strcmp(pCard->Field(fieldno), "")) break; pCard = pCard->Next(); } } if (IsJrnl && pCard == NULL) { pCard = _JrnlCardInfo[tokenid].add_a_new_card(JrnlToken[tokenid], 1); if (NumKey) { for (i = 0; i < NumKey; i++) { if (SerialNoField[i] > 0) pCard->AddElementToField(SerialNo[i], SerialNoField[i]); } } else if (atoi(SerialNo[0]) != 0 && JrnlToken[tokenid].SeqField != 0) pCard->AddElementToField(SerialNo[0], JrnlToken[tokenid].SeqField-1); } else if (!IsJrnl && pCard == NULL) { pCard = _CardInfo[tokenid].add_a_new_card(NdbToken[tokenid], 0); if (NumKey) { for (i = 0; i < NumKey; i++) { if (SerialNoField[i] > 0) pCard->AddElementToField(SerialNo[i], SerialNoField[i]); } } else if (strcmp(SerialNo[0], "") && NdbToken[tokenid].SeqField != 0) pCard->AddElementToField(SerialNo[0], NdbToken[tokenid].SeqField-1); } for (i = 0; i < NumKey; i++) { if (fieldno == SerialNoField[i]) logical = TRUE; } if (!IsJrnl && (logical || fieldno == NdbToken[tokenid].SeqField - 1) || IsJrnl && fieldno == JrnlToken[tokenid].SeqField -1) {} else if (!IsJrnl && !strcmp(NdbToken[tokenid].TokenName, "AUTHOR")) { ndb_name_conversion_first_last(value); if (!strcmp(pCard->Field(fieldno), "")) strcpy(buffer, value); else sprintf(buffer, "%s, %s", pCard->Field(fieldno), value); pCard->AddElementToField(buffer, fieldno); } else if (!IsJrnl || IsJrnl && (!strcmp(pCard->Field(fieldno), "") || strcmp(JrnlToken[tokenid].TokenName, "AUTH") && strcmp(JrnlToken[tokenid].TokenName, "EDIT"))) { if (IsJrnl) { jrnl_id = find_jrnl_id("REF"); if (jrnl_id == tokenid && fieldno == vField + 1) pCard->AddElementToField("V.", vField); if (!strcmp(JrnlToken[tokenid].TokenName, "AUTH") || !strcmp(JrnlToken[tokenid].TokenName, "EDIT")) ndb_name_conversion_first_last(value); } pCard->AddElementToField(value, fieldno); } else if (atoi(SerialNo[0]) == atoi(pCard->Field(JrnlToken[tokenid].SeqField-1))) { ndb_name_conversion_first_last(value); sprintf(buffer, "%s, %s", pCard->Field(fieldno), value); pCard->AddElementToField(buffer, fieldno); } } void _MAXIT::cifndb_process_special(const int tokenid, const int fieldno, const int NumKey, int *SerialNoField, char SerialNo[10][82], const char *value) { int i; One_Card_Info_Format *pCard = _CardInfo[tokenid].Head(); while (pCard) { for (i = 0; i < NumKey; i++) { if (SerialNoField[i] > 0 && strcmp(SerialNo[i], pCard->Field(SerialNoField[i]))) break; } if (i == NumKey) pCard->AddElementToField(value, fieldno); pCard = pCard->Next(); } } void _MAXIT::cifndb_process_general_category(ISTable *Table, const int id, const int is_remark) { int ndb_tokenid = -1, ndb_fieldno, i, j, tmp_id, row, col; char value[10000], buffer[62], *p; CifString string; One_Card_Info_Format *pCard = NULL, *qCard = NULL; int colNo = Table->GetNumColumns(); int rowNo = Table->GetNumRows(); ReVarCifArray *ColumnNames = Table->GetColumnNames(); int *cols = new int[colNo]; for (i = 0; i < colNo; i++) { for (j = 0; j < CifCategory[id].nkeywords; j++) { if (!strcasecmp((*ColumnNames)[i].Text(), CifCategory[id].keywords[j].name)) { tmp_id = CifCategory[id].keywords[j].NdbInfo[0].NdbTokenId-1; if (tmp_id != HEADER_TOKEN-1 && tmp_id >= 0) ndb_tokenid = tmp_id; break; } } if (j == CifCategory[id].nkeywords) cols[i] = -1; else cols[i] = j; } if (ColumnNames) delete ColumnNames; if (ndb_tokenid == -1) { delete cols; return; } for (row = 0; row < rowNo; row++) { pCard = _CardInfo[ndb_tokenid].add_a_new_card(NdbToken[ndb_tokenid], 0); for (col = 0; col < colNo; col++) { j = cols[col]; if (j < 0 || j > CifCategory[id].nkeywords) continue; string.Clear(); Table->GetCell(string, col, row); if (string == "?" || string == "." || string == "" || string == "@") continue; ndb_fieldno = CifCategory[id].keywords[j]. NdbInfo[0].NdbFieldNo - 1; if (ndb_fieldno < 0) continue; strcpy(value, string.Text()); if (is_remark) { if (strstr(value, "'") && value[0] == '\n') strcpy(value, &value[1]); } else ndb_clean_string(value); if (is_remark && ndb_tokenid == PREMRK_TOKEN-1 && strlen(value) > 60) { ndb_clean_string(value); p = get_max_length_word(value, buffer, 60); pCard->AddElementToField(buffer, ndb_fieldno); while (p) { p = get_max_length_word(p, buffer, 60); ndb_clean_string(buffer); if (!strcmp(buffer, "")) break; qCard = _CardInfo[ndb_tokenid]. add_a_new_card(NdbToken[ndb_tokenid], 0); qCard->AddElementToField(pCard->Field(1), 1); qCard->AddElementToField(buffer, ndb_fieldno); } } else pCard->AddElementToField(value, ndb_fieldno); } } delete [] cols; if (ndb_tokenid == REMARK_TOKEN-1 || ndb_tokenid == PCOMPN_TOKEN-1 || ndb_tokenid == PSOURC_TOKEN-1) { pCard = _CardInfo[ndb_tokenid].Head(); while (pCard) { if (!strcmp(pCard->Field(2), "") || !strcmp(pCard->Field(2), "@") || !strcmp(pCard->Field(2), "?")) pCard = _CardInfo[ndb_tokenid].delete_a_card(pCard); else pCard = pCard->Next(); } } } void _MAXIT::cifndb_process_remark(ISTable *Table, const int card_id, const int field_no) { CifString id, text, old_id; char buffer[62], *value, *p; int irow, count, length, i, first = 1; One_Card_Info_Format *pCard = NULL; int rowNo = Table->GetNumRows(); int id_idx = Table->GetColumnIndex("id"); int txt_idx = Table->GetColumnIndex("text"); if (id_idx < 0 || txt_idx < 0) return; old_id.Copy("-1"); for (irow = 0; irow < rowNo; irow++) { Table->GetCell(id, id_idx, irow); Table->GetCell(text, txt_idx, irow); if (id != old_id) { old_id.Copy(id); first = 1; } else first = 0; count = 0; length = strlen(text.Text()); for (i = 0; i < length; i++) { if (text.Text()[i] != '\n') count++; else { if (count > 60) break; count = 0; } } if (count > 60) { value = new char[length + 1]; strcpy(value, text.Text()); ndb_clean_string(value); p = value; while (p) { p = get_max_length_word(p, buffer, 60); ndb_clean_string(buffer); if (!strcmp(buffer, "")) break; pCard = _CardInfo[card_id]. add_a_new_card(NdbToken[card_id], 0); pCard->AddElementToField(id.Text(), 1); pCard->AddElementToField(buffer, field_no); } delete [] value; } else { count = 0; for (i = 0; i < length; i++) { if (text.Text()[i] != '\n') { buffer[count++] = text.Text()[i]; } else { buffer[count] = '\0'; if (!strcmp(buffer, "?")) strcpy(buffer, ""); if (strcmp(buffer, "") || !strcmp(buffer, "") && !first) { pCard = _CardInfo[card_id]. add_a_new_card(NdbToken[card_id], 0); pCard->AddElementToField(id.Text(), 1); pCard->AddElementToField(buffer, field_no); first = 0; } count = 0; } } if (count) { buffer[count] = '\0'; if (!strcmp(buffer, "?")) strcpy(buffer, ""); if (strcmp(buffer, "") || !strcmp(buffer, "") && !first) { pCard = _CardInfo[card_id]. add_a_new_card(NdbToken[card_id], 0); pCard->AddElementToField(id.Text(), 1); pCard->AddElementToField(buffer, field_no); } } } } } void _MAXIT::cifndb_process_refine_ls_restr(ISTable *Table) { int rowNo = Table->GetNumRows(); int type_index = Table->GetColumnIndex("type"); if (type_index < 0) return; int ave_index = Table->GetColumnIndex("dev_ideal"); int std_index = Table->GetColumnIndex("dev_ideal_target"); int weight_index = Table->GetColumnIndex("weight"); int number_index = Table->GetColumnIndex("number"); int ndb_tokenid, ndb_fieldno, irow, i; CifString value; for (irow = 0; irow < rowNo; irow++) { get_value(value, Table, type_index, irow); for (i = 0; i < mxRmsRecords; i++) { if (!strcasecmp(value.Text(), rmsRecords[i].type)) break; } if (i == mxRmsRecords) continue; if (ave_index >= 0 && get_value(value, Table, ave_index, irow)) { ndb_tokenid = rmsRecords[i].tokens[0]; ndb_fieldno = rmsRecords[i].fields[0]; put_into_card(value.Text(), ndb_tokenid, ndb_fieldno); } if (std_index >= 0 && get_value(value, Table, std_index, irow)) { ndb_tokenid = rmsRecords[i].tokens[1]; ndb_fieldno = rmsRecords[i].fields[1]; put_into_card(value.Text(), ndb_tokenid, ndb_fieldno); } if (weight_index >= 0 && get_value(value, Table, weight_index, irow)) { ndb_tokenid = rmsRecords[i].tokens[2]; ndb_fieldno = rmsRecords[i].fields[2]; put_into_card(value.Text(), ndb_tokenid, ndb_fieldno); } if (number_index >= 0 && get_value(value, Table, number_index, irow)) { ndb_tokenid = rmsRecords[i].tokens[3]; ndb_fieldno = rmsRecords[i].fields[3]; put_into_card(value.Text(), ndb_tokenid, ndb_fieldno); } } } void _MAXIT::cifndb_process_matrix(ISTable *Table, const int id) { int colNo = Table->GetNumColumns(); int rowNo = Table->GetNumRows(); ReVarCifArray *ColumnNames = Table->GetColumnNames(); int *cols = new int[colNo]; int ndb_tokenid = -1, i, j, tokenid, fieldno, tmp_id, row; CifString value; One_Card_Info_Format *pCard1 = NULL, *pCard2 = NULL, *pCard3 = NULL; for (i = 0; i < colNo; i++) { for (j = 0; j < CifCategory[id].nkeywords; j++) { if (!strcasecmp((*ColumnNames)[i].Text(), CifCategory[id].keywords[j].name)) { tmp_id = CifCategory[id].keywords[j]. NdbInfo[0].NdbTokenId - 1; if (tmp_id != HEADER_TOKEN-1 && tmp_id >= 0) ndb_tokenid = tmp_id; break; } } if (j == CifCategory[id].nkeywords) cols[i] = -1; else cols[i] = j; } if (ndb_tokenid == -1) { if (ColumnNames) delete ColumnNames; delete cols; return; } for (row = 0; row < rowNo; row++) { pCard1 = _CardInfo[ndb_tokenid].add_a_new_card(NdbToken[ndb_tokenid], 0); pCard2 = _CardInfo[ndb_tokenid].add_a_new_card(NdbToken[ndb_tokenid], 0); pCard3 = _CardInfo[ndb_tokenid].add_a_new_card(NdbToken[ndb_tokenid], 0); for (i = 0; i < colNo; i++) { j = cols[i]; if (j < 0 || j > CifCategory[id].nkeywords) continue; if (!get_value(value, Table, i, row)) continue; tokenid = CifCategory[id].keywords[j].NdbInfo[0].NdbTokenId-1; fieldno = CifCategory[id].keywords[j].NdbInfo[0].NdbFieldNo-1; if (fieldno < 0 || tokenid != ndb_tokenid) continue; if (strstr((*ColumnNames)[i].Text(), "x[1]") || strstr((*ColumnNames)[i].Text(), "vector[1]")) { pCard1->AddElementToField(value.Text(), fieldno); } else if (strstr((*ColumnNames)[i].Text(), "x[2]") || strstr((*ColumnNames)[i].Text(), "vector[2]")) { pCard2->AddElementToField(value.Text(), fieldno); } else if (strstr((*ColumnNames)[i].Text(), "x[3]") || strstr((*ColumnNames)[i].Text(), "vector[3]")) { pCard3->AddElementToField(value.Text(), fieldno); } else { if (value == "given") value.Copy("1"); else if (value == "generate") value.Copy(""); pCard1->AddElementToField(value.Text(), fieldno); pCard2->AddElementToField(value.Text(), fieldno); pCard3->AddElementToField(value.Text(), fieldno); } } } if (ColumnNames) delete ColumnNames; delete [] cols; } void _MAXIT::cifndb_process_struct_site_gen(ISTable *Table) { if (_num_mol == 0 || _molecules == NULL) return; int rowNo = Table->GetNumRows(); int site_id_index = Table->GetColumnIndex("site_id"); int label_comp_id = Table->GetColumnIndex("label_comp_id"); int label_asym_id = Table->GetColumnIndex("label_asym_id"); int label_seq_id = Table->GetColumnIndex("label_seq_id"); int auth_comp_id = Table->GetColumnIndex("auth_comp_id"); int auth_asym_id = Table->GetColumnIndex("auth_asym_id"); int auth_seq_id = Table->GetColumnIndex("auth_seq_id"); int ndb_ins_code = Table->GetColumnIndex("ndb_label_ins_code"); CifString site_id; int irow, FstIndex, FstRes; for (irow = 0; irow < rowNo; irow++) { get_value(site_id, Table, site_id_index, irow); if (get_residue_index(_molecules[0], Table, irow, label_comp_id, label_asym_id, label_seq_id, auth_comp_id, auth_asym_id, auth_seq_id, ndb_ins_code, FstIndex, FstRes)) { Insert_a_Site(site_id.Text(), FstIndex, FstRes); } } } void _MAXIT::cifndb_process_rcsb_link(ISTable *Table) { int rowNo, irow, BegIndex, BegRes, EndIndex, EndRes, beg, end; int ptnr1_label_alt_id, ptnr1_label_asym_id, ptnr1_label_atom_id; int ptnr1_label_comp_id, ptnr1_label_seq_id, ptnr1_label_ins_code; int ptnr1_symmetry, ptnr2_label_alt_id, ptnr2_label_asym_id; int ptnr2_label_atom_id, ptnr2_label_comp_id, ptnr2_label_seq_id; int ptnr2_label_ins_code, ptnr2_symmetry, details; CifString comment, atom1, loc1, atom2, loc2, symm1, symm2; if (_num_mol == 0 || _molecules == NULL) return; rowNo = Table->GetNumRows(); ptnr1_label_alt_id = Table->GetColumnIndex("ptnr1_label_alt_id"); ptnr1_label_asym_id = Table->GetColumnIndex("ptnr1_label_asym_id"); ptnr1_label_atom_id = Table->GetColumnIndex("ptnr1_label_atom_id"); ptnr1_label_comp_id = Table->GetColumnIndex("ptnr1_label_comp_id"); ptnr1_label_seq_id = Table->GetColumnIndex("ptnr1_label_seq_id"); ptnr1_label_ins_code = Table->GetColumnIndex("ptnr1_label_ins_code"); ptnr1_symmetry = Table->GetColumnIndex("ptnr1_symmetry"); ptnr2_label_alt_id = Table->GetColumnIndex("ptnr2_label_alt_id"); ptnr2_label_asym_id = Table->GetColumnIndex("ptnr2_label_asym_id"); ptnr2_label_atom_id = Table->GetColumnIndex("ptnr2_label_atom_id"); ptnr2_label_comp_id = Table->GetColumnIndex("ptnr2_label_comp_id"); ptnr2_label_seq_id = Table->GetColumnIndex("ptnr2_label_seq_id"); ptnr2_label_ins_code = Table->GetColumnIndex("ptnr2_label_ins_code"); ptnr2_symmetry = Table->GetColumnIndex("ptnr2_symmetry"); details = Table->GetColumnIndex("details"); for (irow = 0; irow < rowNo; irow++) { get_value(comment, Table, details, irow); get_value(loc1, Table, ptnr1_label_alt_id, irow); get_value(atom1, Table, ptnr1_label_atom_id, irow); get_value(symm1, Table, ptnr1_symmetry, irow); get_value(loc2, Table, ptnr2_label_alt_id, irow); get_value(atom2, Table, ptnr2_label_atom_id, irow); get_value(symm2, Table, ptnr2_symmetry, irow); beg = get_residue_index(_molecules[0], Table, irow, -1, -1, -1, ptnr1_label_comp_id, ptnr1_label_asym_id, ptnr1_label_seq_id, ptnr1_label_ins_code, BegIndex, BegRes); end = get_residue_index(_molecules[0], Table, irow, -1, -1, -1, ptnr2_label_comp_id, ptnr2_label_asym_id, ptnr2_label_seq_id, ptnr2_label_ins_code, EndIndex, EndRes); if (!beg || !end) continue; if (symm1 == "1_555") symm1.Clear(); if (symm2 == "1_555") symm2.Clear(); Insert_a_Link(atom1.Text(), loc1.Text(), BegIndex, BegRes, atom2.Text(), loc2.Text(), EndIndex, EndRes, symm1.Text(), symm2.Text(), comment.Text()); } } void _MAXIT::cifndb_process_struct_conf(ISTable *Table) { int BegIndex = -1, BegRes = -1, EndIndex = -1, EndRes = -1, beg = -1, end = -1; int irow, rowNo, id_index, pdb_index, beg_label_comp_id, beg_label_asym_id; int beg_label_seq_id, beg_label_ins_code, beg_auth_comp_id, beg_auth_asym_id; int beg_auth_seq_id, end_label_comp_id, end_label_asym_id, end_label_seq_id; int end_label_ins_code, end_auth_comp_id, end_auth_asym_id, end_auth_seq_id; int class_index, details_index; CifString pdb_id, type, comment, class_type; _CHAIN *chain = NULL; if (_num_mol == 0 || _molecules == NULL) return; rowNo = Table->GetNumRows(); id_index = Table->GetColumnIndex("conf_type_id"); pdb_index = Table->GetColumnIndex("pdb_id"); beg_label_comp_id = Table->GetColumnIndex("beg_label_comp_id"); beg_label_asym_id = Table->GetColumnIndex("beg_label_asym_id"); beg_label_seq_id = Table->GetColumnIndex("beg_label_seq_id"); beg_label_ins_code = Table->GetColumnIndex("ndb_beg_label_ins_code_pdb"); beg_auth_comp_id = Table->GetColumnIndex("beg_auth_comp_id"); beg_auth_asym_id = Table->GetColumnIndex("beg_auth_asym_id"); beg_auth_seq_id = Table->GetColumnIndex("beg_auth_seq_id"); end_label_comp_id = Table->GetColumnIndex("end_label_comp_id"); end_label_asym_id = Table->GetColumnIndex("end_label_asym_id"); end_label_seq_id = Table->GetColumnIndex("end_label_seq_id"); end_label_ins_code = Table->GetColumnIndex("ndb_end_label_ins_code_pdb"); end_auth_comp_id = Table->GetColumnIndex("end_auth_comp_id"); end_auth_asym_id = Table->GetColumnIndex("end_auth_asym_id"); end_auth_seq_id = Table->GetColumnIndex("end_auth_seq_id"); class_index = Table->GetColumnIndex("ndb_helix_class_pdb"); details_index = Table->GetColumnIndex("details"); for (irow = 0; irow < rowNo; irow++) { beg = get_residue_index(_molecules[0], Table, irow, beg_label_comp_id, beg_label_asym_id, beg_label_seq_id, beg_auth_comp_id, beg_auth_asym_id, beg_auth_seq_id, beg_label_ins_code, BegIndex, BegRes); end = get_residue_index(_molecules[0], Table, irow, end_label_comp_id, end_label_asym_id, end_label_seq_id, end_auth_comp_id, end_auth_asym_id, end_auth_seq_id, end_label_ins_code, EndIndex, EndRes); if (beg && end && BegIndex == EndIndex) { chain = _molecules[0]->GetIndexChain(BegIndex); if (chain) { get_value(type, Table, id_index, irow); get_value(pdb_id, Table, pdb_index, irow); get_value(comment, Table, details_index, irow); if (!strcasecmp(type.Text(), "HELX_P")) { get_value(class_type, Table, class_index, irow); chain->Insert_a_Helix(pdb_id.Text(), BegRes, EndRes, atoi(class_type.Text()), comment.Text()); _exist_helix = 1; } else if (!strcasecmp(type.Text(), "TURN_P")) { chain->Insert_a_Turn(pdb_id.Text(), BegRes, EndRes, comment.Text()); } } } } } void _MAXIT::cifndb_process_sheet() { if (_num_mol == 0 || _molecules == NULL) return; ISTable *Table = _CifObj->GetTablePtr(_StructureId, "struct_sheet_range"); if (is_empty_table(Table)) return; ISTable *Table1 = _CifObj->GetTablePtr(_StructureId, "rcsb_struct_sheet_hbond"); ISTable *Table2 = _CifObj->GetTablePtr(_StructureId, "struct_sheet_order"); ISTable *Table3 = _CifObj->GetTablePtr(_StructureId, "struct_sheet"); int rowNo = Table->GetNumRows(); int sheet_id_index = Table->GetColumnIndex("sheet_id"); int id_index = Table->GetColumnIndex("id"); int beg_label_comp_id = Table->GetColumnIndex("beg_label_comp_id"); int beg_label_asym_id = Table->GetColumnIndex("beg_label_asym_id"); int beg_label_seq_id = Table->GetColumnIndex("beg_label_seq_id"); int ndb_beg_label_ins_code_pdb = Table->GetColumnIndex("ndb_beg_label_ins_code_pdb"); int end_label_comp_id = Table->GetColumnIndex("end_label_comp_id"); int end_label_asym_id = Table->GetColumnIndex("end_label_asym_id"); int end_label_seq_id = Table->GetColumnIndex("end_label_seq_id"); int ndb_end_label_ins_code_pdb = Table->GetColumnIndex("ndb_end_label_ins_code_pdb"); int beg_auth_comp_id = Table->GetColumnIndex("beg_auth_comp_id"); int beg_auth_asym_id = Table->GetColumnIndex("beg_auth_asym_id"); int beg_auth_seq_id = Table->GetColumnIndex("beg_auth_seq_id"); int end_auth_comp_id = Table->GetColumnIndex("end_auth_comp_id"); int end_auth_asym_id = Table->GetColumnIndex("end_auth_asym_id"); int end_auth_seq_id = Table->GetColumnIndex("end_auth_seq_id"); int row, BegIndex, BegRes, EndIndex, EndRes, beg, end, number_strands; int sense = 0, curIndex = -1, curRes = -1, prevIndex = -1, prevRes = -1; CifString sheet_id, id, prev_id, curAtom, prevAtom; prev_id[0] = '\0'; prev_id.Clear(); id.Clear(); for (row = 0; row < rowNo; row++) { prev_id.Copy(id); sheet_id.Clear(); id.Clear(); get_value(sheet_id, Table, sheet_id_index, row); get_value(id, Table, id_index, row); beg = get_residue_index(_molecules[0], Table, row, beg_label_comp_id, beg_label_asym_id, beg_label_seq_id, beg_auth_comp_id, beg_auth_asym_id, beg_auth_seq_id, ndb_beg_label_ins_code_pdb, BegIndex, BegRes); end = get_residue_index(_molecules[0], Table, row, end_label_comp_id, end_label_asym_id, end_label_seq_id, end_auth_comp_id, end_auth_asym_id, end_auth_seq_id, ndb_end_label_ins_code_pdb, EndIndex, EndRes); if (beg && end && BegIndex == EndIndex) { sense = 0; curIndex = -1; curRes = -1; prevIndex = -1; prevRes = -1; curAtom.Clear(); prevAtom.Clear(); number_strands = get_number_strands(Table3, sheet_id.Text()); if (row) { get_hbond(_molecules[0], Table1, BegIndex, sheet_id.Text(), id.Text(), curAtom, curIndex, curRes, prevAtom, prevIndex, prevRes); sense = get_sense(Table2, sheet_id.Text(), prev_id.Text(), id.Text()); } Insert_a_Sheet(sheet_id.Text(), number_strands, BegIndex, BegRes, EndIndex, EndRes, sense, curAtom.Text(), curIndex, curRes, prevAtom.Text(), prevIndex, prevRes); _exist_sheet = 1; } } } #ifdef SUN_OS #ifdef __cplusplus extern "C" { #endif #endif static int pdb_rev_compare(const void *a, const void *b) { return (((PDB_REV *) b)->num - ((PDB_REV *) a)->num); } #ifdef SUN_OS #ifdef __cplusplus } #endif #endif void _MAXIT::cifndb_process_database_pdb_rev(ISTable *Table) { int rowNo = Table->GetNumRows(); PDB_REV *pdb_rev = (PDB_REV *) calloc(rowNo, sizeof(PDB_REV)); int n_rev = rowNo; int num_index = Table->GetColumnIndex("num"); int date_index = Table->GetColumnIndex("date"); int original_index = Table->GetColumnIndex("date_original"); int replaces_index = Table->GetColumnIndex("replaces"); int type_index = Table->GetColumnIndex("mod_type"); int revised_index[4]; revised_index[0] = Table->GetColumnIndex("rcsb_record_revised_1"); revised_index[1] = Table->GetColumnIndex("rcsb_record_revised_2"); revised_index[2] = Table->GetColumnIndex("rcsb_record_revised_3"); revised_index[3] = Table->GetColumnIndex("rcsb_record_revised_4"); int irow, i, len, serial_no, pos; CifString cifstring, value; char buffer[20], *p; One_Card_Info_Format *pCard = NULL; for (irow = 0; irow < rowNo; irow++) { pdb_rev[irow].num = 0; pdb_rev[irow].date[0] = '\0'; pdb_rev[irow].replaces[0] = '\0'; pdb_rev[irow].mod_type = 0; pdb_rev[irow].record = NULL; if (num_index >= 0) { get_value(cifstring, Table, num_index, irow); pdb_rev[irow].num = atoi(cifstring.Text()); } if (date_index >= 0) { get_value(cifstring, Table, date_index, irow); strcpy(pdb_rev[irow].date, cifstring.Text()); } if (replaces_index >= 0) { get_value(cifstring, Table, replaces_index, irow); strcpy(pdb_rev[irow].replaces, cifstring.Text()); } if (type_index >= 0) { get_value(cifstring, Table, type_index, irow); pdb_rev[irow].mod_type = atoi(cifstring.Text()); } if (original_index >= 0 && !pdb_rev[irow].mod_type) { get_value(cifstring, Table, original_index, irow); if (cifstring != "") { pCard = _CardInfo[HEADER_TOKEN-1].Head(); if (!pCard) pCard = _CardInfo[HEADER_TOKEN-1]. add_a_new_card(NdbToken[HEADER_TOKEN-1], 0); pCard->AddElementToField(cifstring.Text(), 2); } } for (i = 0; i < 4; i++) { if (revised_index[i] < 0) continue; get_value(cifstring, Table, revised_index[i], irow); if (cifstring == "") continue; if (pdb_rev[irow].record == NULL) { len = strlen(cifstring.Text())+1; pdb_rev[irow].record = (char *) calloc(len, sizeof(char)); strcpy(pdb_rev[irow].record, cifstring.Text()); } else if (!strstr(pdb_rev[irow].record, cifstring.Text())) { len = strlen(cifstring.Text()) + 2 + strlen(pdb_rev[irow].record); pdb_rev[irow].record = (char *) realloc(pdb_rev[irow].record, len * sizeof(char)); strcat(pdb_rev[irow].record, " "); strcat(pdb_rev[irow].record, cifstring.Text()); } } } Table = _CifObj->GetTablePtr(_StructureId, "database_PDB_rev_record"); if (!is_empty_table(Table)) { rowNo = Table->GetNumRows(); num_index = Table->GetColumnIndex("rev_num"); type_index = Table->GetColumnIndex("type"); for (irow = 0; irow < rowNo; irow++) { get_value(cifstring, Table, num_index, irow); get_value(value, Table, type_index, irow); if (cifstring == "" || value == "") continue; for (i = 0; i < n_rev; i++) if (pdb_rev[i].num == atoi(cifstring.Text())) break; if (i < n_rev) { if (pdb_rev[i].record == NULL) { len = strlen(value.Text())+1; pdb_rev[i].record = (char *) calloc(len, sizeof(char)); strcpy(pdb_rev[i].record, value.Text()); } else if (!strstr(pdb_rev[i].record, value.Text())) { len = strlen(value.Text()) + 2 + strlen(pdb_rev[i].record); pdb_rev[i].record = (char *) realloc(pdb_rev[i].record, len * sizeof(char)); strcat(pdb_rev[i].record, " "); strcat(pdb_rev[i].record, value.Text()); } } } } if (n_rev > 1) qsort((void *) pdb_rev, n_rev, sizeof(PDB_REV), pdb_rev_compare); for (i = 0; i < n_rev; i++) { if (!pdb_rev[i].num) continue; pCard = _CardInfo[REVDAT_TOKEN-1]. add_a_new_card(NdbToken[REVDAT_TOKEN-1], 0); pCard->AddElementToField(pdb_rev[i].num, 1); pCard->AddElementToField(pdb_rev[i].date, 3); pCard->AddElementToField(pdb_rev[i].replaces, 4); pCard->AddElementToField(pdb_rev[i].mod_type, 5); p = pdb_rev[i].record; serial_no = 2; pos = 6; while (p) { if (pos > 9) { pCard = _CardInfo[REVDAT_TOKEN-1]. add_a_new_card(NdbToken[REVDAT_TOKEN-1], 0); pCard->AddElementToField(pdb_rev[i].num, 1); pCard->AddElementToField(serial_no, 2); pCard->AddElementToField(pdb_rev[i].mod_type, 5); serial_no++; pos = 6; } p = get_word(p, buffer); pCard->AddElementToField(buffer, pos); pos++; } } for (i = 0; i < n_rev; i++) { if (pdb_rev[i].record) free ((void *) pdb_rev[i].record); } free ((void *) pdb_rev); } void _MAXIT::cifndb_process_struct_conn(ISTable *Table) { if (_num_mol == 0 || _molecules == NULL) return; int rowNo = Table->GetNumRows(); int id_index = Table->GetColumnIndex("conn_type_id"); int pdb_index = Table->GetColumnIndex("ndb_PDB_id"); int name_index = Table->GetColumnIndex("ndb_ptnr1_mod_name"); int sugar_index = Table->GetColumnIndex("ndb_ptnr1_sugar_name"); int replaced_index = Table->GetColumnIndex("ndb_ptnr1_replaced_atom"); int standard_index = Table->GetColumnIndex("ndb_ptnr1_standard_comp_id"); int ptnr1_label_comp_id = Table->GetColumnIndex("ptnr1_label_comp_id"); int ptnr1_label_asym_id = Table->GetColumnIndex("ptnr1_label_asym_id"); int ptnr1_label_seq_id = Table->GetColumnIndex("ptnr1_label_seq_id"); int ptnr1_label_atom_id = Table->GetColumnIndex("ptnr1_label_atom_id"); int ndb_ptnr1_label_alt_loc = Table->GetColumnIndex("ndb_ptnr1_label_alt_loc"); int ptnr1_label_ins_code = Table->GetColumnIndex("ndb_ptnr1_label_ins_code"); int ptnr1_symmetry = Table->GetColumnIndex("ptnr1_symmetry"); int ptnr2_label_comp_id = Table->GetColumnIndex("ptnr2_label_comp_id"); int ptnr2_label_asym_id = Table->GetColumnIndex("ptnr2_label_asym_id"); int ptnr2_label_seq_id = Table->GetColumnIndex("ptnr2_label_seq_id"); int ptnr2_label_atom_id = Table->GetColumnIndex("ptnr2_label_atom_id"); int ndb_ptnr2_label_alt_loc = Table->GetColumnIndex("ndb_ptnr2_label_alt_loc"); int ptnr2_label_ins_code = Table->GetColumnIndex("ndb_ptnr2_label_ins_code"); int ptnr2_symmetry = Table->GetColumnIndex("ptnr2_symmetry"); int ptnr1_auth_comp_id = Table->GetColumnIndex("ptnr1_auth_comp_id"); int ptnr1_auth_asym_id = Table->GetColumnIndex("ptnr1_auth_asym_id"); int ptnr1_auth_seq_id = Table->GetColumnIndex("ptnr1_auth_seq_id"); int ptnr2_auth_comp_id = Table->GetColumnIndex("ptnr2_auth_comp_id"); int ptnr2_auth_asym_id = Table->GetColumnIndex("ptnr2_auth_asym_id"); int ptnr2_auth_seq_id = Table->GetColumnIndex("ptnr2_auth_seq_id"); int ndb_ptnr3_label_atom_id = Table->GetColumnIndex("ndb_ptnr3_label_atom_id"); int ndb_ptnr3_label_seq_id = Table->GetColumnIndex("ndb_ptnr3_label_seq_id"); int ndb_ptnr3_label_asym_id = Table->GetColumnIndex("ndb_ptnr3_label_asym_id"); int ndb_ptnr3_label_alt_loc = Table->GetColumnIndex("ndb_ptnr3_label_alt_loc"); int details_index = Table->GetColumnIndex("details"); int irow, BegIndex, BegRes, EndIndex, EndRes, beg, end, H_Index, H_Res; CifString type, atom1, loc1, atom2, loc2, symm1, symm2, comment, name; CifString Replaced_Atom, atom3, loc3, standard, pdb_id, sugar; CifString seq_id1, seq_id2, seq_id3, chain_id1, chain_id2, chain_id3; for (irow = 0; irow < rowNo; irow++) { get_value(type, Table, id_index, irow); if (type == "") continue; get_value(atom1, Table, ptnr1_label_atom_id, irow); get_value(loc1, Table, ndb_ptnr1_label_alt_loc, irow); get_value(symm1, Table, ptnr1_symmetry, irow); get_value(atom2, Table, ptnr2_label_atom_id, irow); get_value(loc2, Table, ndb_ptnr2_label_alt_loc, irow); get_value(symm2, Table, ptnr2_symmetry, irow); get_value(comment, Table, details_index, irow); get_value(name, Table, name_index, irow); get_value(Replaced_Atom, Table, replaced_index, irow); if (symm1 == "1_555") symm1.Clear(); if (symm2 == "1_555") symm2.Clear(); beg = get_residue_index(_molecules[0], Table, irow, ptnr1_label_comp_id, ptnr1_label_asym_id, ptnr1_label_seq_id, ptnr1_auth_comp_id, ptnr1_auth_asym_id, ptnr1_auth_seq_id, ptnr1_label_ins_code, BegIndex, BegRes); end = get_residue_index(_molecules[0], Table, irow, ptnr2_label_comp_id, ptnr2_label_asym_id, ptnr2_label_seq_id, ptnr2_auth_comp_id, ptnr2_auth_asym_id, ptnr2_auth_seq_id, ptnr2_label_ins_code, EndIndex, EndRes); if (!beg) continue; if (!strcasecmp(type.Text(), "hydrog")) { if (end) { if (!strcasecmp(comment.Text(), "WATSON-CRICK") || !strcasecmp(comment.Text(), "REVERSED WATSON-CRICK") || !strcasecmp(comment.Text(), "HOOGSTEEN") || !strcasecmp(comment.Text(), "REVERSED HOOGSTEEN") || strstr(comment.Text(), "PAIR") || strstr(comment.Text(), "pair")) Insert_a_Bspair(atom1.Text(), BegIndex, BegRes, atom2.Text(), EndIndex, EndRes, symm2.Text(), comment.Text()); else { seq_id3.Copy("ZZZ"); chain_id3.Copy("ZZZ"); get_value(atom3, Table, ndb_ptnr3_label_atom_id, irow); get_value(loc3, Table, ndb_ptnr3_label_alt_loc, irow); get_value(seq_id1, Table, ptnr1_label_seq_id, irow); get_value(chain_id1, Table, ptnr1_label_asym_id, irow); get_value(seq_id2, Table, ptnr2_label_seq_id, irow); get_value(chain_id2, Table, ptnr2_label_asym_id, irow); if (ndb_ptnr3_label_seq_id >= 0) get_value(seq_id3, Table, ndb_ptnr3_label_seq_id, irow); if (ndb_ptnr3_label_asym_id >= 0) get_value(chain_id3, Table, ndb_ptnr3_label_asym_id, irow); H_Index = -1; H_Res = -1; if (seq_id1 == seq_id3 && chain_id1 == chain_id3) { H_Index = BegIndex; H_Res = BegRes; } else if (seq_id2 == seq_id3 && chain_id2 == chain_id3) { H_Index = EndIndex; H_Res = EndRes; } Insert_a_Hydbnd(atom1.Text(), loc1.Text(), BegIndex, BegRes, atom3.Text(), loc3.Text(), H_Index, H_Res, atom2.Text(), loc2.Text(), EndIndex, EndRes, symm1.Text(), symm2.Text()); } } } else if (!strcasecmp(type.Text(), "hydbnd")) { if (end) { seq_id3.Copy("ZZZ"); chain_id3.Copy("ZZZ"); get_value(atom3, Table, ndb_ptnr3_label_atom_id, irow); get_value(loc3, Table, ndb_ptnr3_label_alt_loc, irow); get_value(seq_id1, Table, ptnr1_label_seq_id, irow); get_value(chain_id1, Table, ptnr1_label_asym_id, irow); get_value(seq_id2, Table, ptnr2_label_seq_id, irow); get_value(chain_id2, Table, ptnr2_label_asym_id, irow); if (ndb_ptnr3_label_seq_id >= 0) get_value(seq_id3, Table, ndb_ptnr3_label_seq_id, irow); if (ndb_ptnr3_label_asym_id >= 0) get_value(chain_id3, Table, ndb_ptnr3_label_asym_id, irow); H_Index = -1; H_Res = -1; if (seq_id1 == seq_id3 && chain_id1 == chain_id3) { H_Index = BegIndex; H_Res = BegRes; } else if (seq_id2 == seq_id3 && chain_id2 == chain_id3) { H_Index = EndIndex; H_Res = EndRes; } Insert_a_Hydbnd(atom1.Text(), loc1.Text(), BegIndex, BegRes, atom3.Text(), loc3.Text(), H_Index, H_Res, atom2.Text(), loc2.Text(), EndIndex, EndRes, symm1.Text(), symm2.Text()); } } else if (!strcasecmp(type.Text(), "link") || !strcasecmp(type.Text(), "covale")) { if (end) Insert_a_Link(atom1.Text(), loc1.Text(), BegIndex, BegRes, atom2.Text(), loc2.Text(), EndIndex, EndRes, symm1.Text(), symm2.Text(), comment.Text()); } else if (!strcasecmp(type.Text(), "modres")) { get_value(pdb_id, Table, pdb_index, irow); get_value(standard, Table, standard_index, irow); Insert_a_Modres(pdb_id.Text(), BegIndex, BegRes, standard.Text(), comment.Text()); } else if (!strcasecmp(type.Text(), "sltbrg") || !strcasecmp(type.Text(), "saltbr")) { if (end) Insert_a_Sltbrg(atom1.Text(), loc1.Text(), BegIndex, BegRes, atom2.Text(), loc2.Text(), EndIndex, EndRes, symm1.Text(), symm2.Text()); } else if (!strcasecmp(type.Text(), "disulf")) { if (end) { Insert_a_SSbond(BegIndex, BegRes, EndIndex, EndRes, symm1.Text(), symm2.Text()); _exist_ssbond = 1; } } else if (!strcasecmp(type.Text(), "mismat")) { if (end) Insert_a_Mismat(BegIndex, BegRes, EndIndex, EndRes); } else if (!strcasecmp(type.Text(), "covale_base")) { if (end) Insert_a_Modifb(name.Text(), atom1.Text(), BegIndex, BegRes, atom2.Text(), EndIndex, EndRes, Replaced_Atom.Text()); } else if (!strcasecmp(type.Text(), "covale_sugar")) { if (end) { get_value(sugar, Table, sugar_index, irow); Insert_a_Modifs(name.Text(), atom1.Text(), BegIndex, BegRes, atom2.Text(), EndIndex, EndRes, Replaced_Atom.Text(), sugar.Text()); } } else if (!strcasecmp(type.Text(), "covale_phosphate")) { if (end) Insert_a_Modifp(name.Text(), atom1.Text(), BegIndex, BegRes, atom2.Text(), EndIndex, EndRes, Replaced_Atom.Text()); } } } void _MAXIT::put_into_card(const char *value, const int tokenid, const int fieldno) { if (tokenid < 0 || tokenid >= MxTokens || fieldno < 0 || fieldno >= NdbToken[tokenid].NumField) return; One_Card_Info_Format *pCard = _CardInfo[tokenid].Tail(); if (pCard == NULL || strcmp(pCard->Field(fieldno), "")) pCard = _CardInfo[tokenid].add_a_new_card(NdbToken[tokenid], 0); pCard->AddElementToField(value, fieldno); } void _MAXIT::ndb_processing_em_software() { int idx; CifString string, string1; ISTable *Table = NULL; Table = _CifObj->GetTablePtr(_StructureId, "em_3d_fitting"); if (is_empty_table(Table)) return; idx = Table->GetColumnIndex("software_name"); if (idx < 0) return; Table->GetCell(string, idx, 0); if (string == "" || string == "." || string == "?") return; Table = _CifObj->GetTablePtr(_StructureId, "em_2d_projection_selection"); if (!Table) { Table = new ISTable("em_2d_projection_selection"); Table->AddColumn("entry_id"); Table->AddColumn("software_name"); Table->AddColumn("num_particles"); Table->AddRow(); _CifObj->WriteTable(Table, _StructureId, "em_2d_projection_selection"); } idx = Table->GetColumnIndex("software_name"); Table->GetCell(string1, idx, 0); if (string1 == "" || string1 == "." || string1 == "?") Table->UpdateCell(string, idx, 0); } void _MAXIT::ndb_processing_struct_category() { ISTable *Table = _CifObj->GetTablePtr(_StructureId, "struct"); if (is_empty_table(Table)) return; int ndb_descriptor = Table->GetColumnIndex("ndb_descriptor"); int ndb_title_text = Table->GetColumnIndex("ndb_title_text"); int title_index = Table->GetColumnIndex("title"); if (ndb_title_text >= 0 && title_index >= 0 && ndb_descriptor < 0) { ISTable *Table1 = new ISTable("struct"); Table1->AddColumn("entry_id"); Table1->AddColumn("title"); Table1->AddColumn("ndb_descriptor"); Table1->AddColumn("rcsb_model_details"); Table1->AddColumn("ndb_details"); Table1->AddRow(); CifString string(_StructureId); Table1->UpdateCell(string, 0, 0); Table->GetCell(string, ndb_title_text, 0); Table1->UpdateCell(string, 1, 0); Table->GetCell(string, title_index, 0); Table1->UpdateCell(string, 2, 0); int detail_index = Table->GetColumnIndex("rcsb_model_details"); if (detail_index >= 0) { Table->GetCell(string, detail_index, 0); Table1->UpdateCell(string, 3, 0); } detail_index = Table->GetColumnIndex("ndb_details"); if (detail_index >= 0) { Table->GetCell(string, detail_index, 0); Table1->UpdateCell(string, 4, 0); } _CifObj->DeleteTable(_StructureId, "struct"); _CifObj->WriteTable(Table1, _StructureId, "struct"); } } void _MAXIT::ndb_processing_struct_sheet_hbond() { ISTable *Table = _CifObj->GetTablePtr(_StructureId, "struct_sheet_hbond"); if (is_empty_table(Table)) return; ISTable *Table1 = new ISTable("rcsb_struct_sheet_hbond"); Table1->AddColumn("sheet_id"); Table1->AddColumn("range_id_2"); Table1->AddColumn("range_1_label_atom_id"); Table1->AddColumn("range_1_label_comp_id"); Table1->AddColumn("range_1_label_asym_id"); Table1->AddColumn("range_1_label_seq_id"); Table1->AddColumn("range_1_PDB_ins_code"); Table1->AddColumn("range_1_auth_comp_id"); Table1->AddColumn("range_1_auth_asym_id"); Table1->AddColumn("range_1_auth_seq_id"); Table1->AddColumn("range_2_label_atom_id"); Table1->AddColumn("range_2_label_comp_id"); Table1->AddColumn("range_2_label_asym_id"); Table1->AddColumn("range_2_label_seq_id"); Table1->AddColumn("range_2_PDB_ins_code"); Table1->AddColumn("range_2_auth_comp_id"); Table1->AddColumn("range_2_auth_asym_id"); Table1->AddColumn("range_2_auth_seq_id"); int rowNo = Table->GetNumRows(); int sheet_id = Table->GetColumnIndex("sheet_id"); int range_id_1 = Table->GetColumnIndex("range_id_1"); int beg_label_atom_id = Table->GetColumnIndex("range_1_beg_label_atom_id"); int beg_label_comp_id = Table->GetColumnIndex("ndb_range_1_beg_label_comp_id"); int beg_label_asym_id = Table->GetColumnIndex("ndb_range_1_beg_label_asym_id"); int beg_label_seq_id = Table->GetColumnIndex("range_1_beg_label_seq_id"); int beg_label_ins_code = Table->GetColumnIndex("ndb_range_1_beg_label_ins_code"); int beg_auth_comp_id = Table->GetColumnIndex("ndb_range_1_beg_auth_comp_id"); int beg_auth_asym_id = Table->GetColumnIndex("ndb_range_1_beg_auth_asym_id"); int beg_auth_seq_id = Table->GetColumnIndex("range_1_beg_auth_seq_id"); int end_label_atom_id = Table->GetColumnIndex("range_1_end_label_atom_id"); int end_label_comp_id = Table->GetColumnIndex("ndb_range_1_end_label_comp_id"); int end_label_asym_id = Table->GetColumnIndex("ndb_range_1_end_label_asym_id"); int end_label_seq_id = Table->GetColumnIndex("range_1_end_label_seq_id"); int end_label_ins_code = Table->GetColumnIndex("ndb_range_1_end_label_ins_code"); int end_auth_comp_id = Table->GetColumnIndex("ndb_range_1_end_auth_comp_id"); int end_auth_asym_id = Table->GetColumnIndex("ndb_range_1_end_auth_asym_id"); int end_auth_seq_id = Table->GetColumnIndex("range_1_end_auth_seq_id"); CifString string; for (int i = 0; i < rowNo; i++) { Table1->AddRow(); if (sheet_id >= 0) { Table->GetCell(string, sheet_id, i); Table1->UpdateCell(string, 0, i); } if (range_id_1 >= 0) { Table->GetCell(string, range_id_1, i); Table1->UpdateCell(string, 1, i); } if (end_label_atom_id >= 0) { Table->GetCell(string, end_label_atom_id, i); Table1->UpdateCell(string, 2, i); } if (end_label_comp_id >= 0) { Table->GetCell(string, end_label_comp_id, i); Table1->UpdateCell(string, 3, i); } if (end_label_asym_id >= 0) { Table->GetCell(string, end_label_asym_id, i); Table1->UpdateCell(string, 4, i); } if (end_label_seq_id >= 0) { Table->GetCell(string, end_label_seq_id, i); Table1->UpdateCell(string, 5, i); } if (end_label_ins_code >= 0) { Table->GetCell(string, end_label_ins_code, i); Table1->UpdateCell(string, 6, i); } if (end_auth_comp_id >= 0) { Table->GetCell(string, end_auth_comp_id, i); Table1->UpdateCell(string, 7, i); } if (end_auth_asym_id >= 0) { Table->GetCell(string, end_auth_asym_id, i); Table1->UpdateCell(string, 8, i); } if (end_auth_seq_id >= 0) { Table->GetCell(string, end_auth_seq_id, i); Table1->UpdateCell(string, 9, i); } if (beg_label_atom_id >= 0) { Table->GetCell(string, beg_label_atom_id, i); Table1->UpdateCell(string, 10, i); } if (beg_label_comp_id >= 0) { Table->GetCell(string, beg_label_comp_id, i); Table1->UpdateCell(string, 11, i); } if (beg_label_asym_id >= 0) { Table->GetCell(string, beg_label_asym_id, i); Table1->UpdateCell(string, 12, i); } if (beg_label_seq_id >= 0) { Table->GetCell(string, beg_label_seq_id, i); Table1->UpdateCell(string, 13, i); } if (beg_label_ins_code >= 0) { Table->GetCell(string, beg_label_ins_code, i); Table1->UpdateCell(string, 14, i); } if (beg_auth_comp_id >= 0) { Table->GetCell(string, beg_auth_comp_id, i); Table1->UpdateCell(string, 15, i); } if (beg_auth_asym_id >= 0) { Table->GetCell(string, beg_auth_asym_id, i); Table1->UpdateCell(string, 16, i); } if (beg_auth_seq_id >= 0) { Table->GetCell(string, beg_auth_seq_id, i); Table1->UpdateCell(string, 17, i); } } _CifObj->DeleteTable(_StructureId, "struct_sheet_hbond"); _CifObj->WriteTable(Table1, _StructureId, "rcsb_struct_sheet_hbond"); } void _MAXIT::ndb_processing_ndb_database_PDB_obs_spr_category() { ISTable *Table = _CifObj->GetTablePtr(_StructureId, "ndb_database_PDB_obs_spr"); if (is_empty_table(Table)) return; int id, nrow, i; CifString value; id = Table->GetColumnIndex("id"); if (id >= 0) { nrow = Table->GetNumRows(); for (i = 0; i < nrow; i++) { value.Clear(); Table->GetCell(value, id, i); if (strcmp(value.Text(), "SPRSDE") && strcmp(value.Text(), "OBSLTE")) { value.Copy("SPRSDE"); Table->UpdateCell(value, id, i); } } } _CifObj->WriteTable(Table, _StructureId, "ndb_database_PDB_obs_spr"); } void _MAXIT::ndb_processing_struct_ref_seq_and_diff() { int i, rowNo, auth_beg_idx, auth_end_idx, beg_idx, end_idx; CifString string; ISTable *Table = NULL; Table = _CifObj->GetTablePtr(_StructureId, "struct_ref_seq"); if (!is_empty_table(Table)) { rowNo = Table->GetNumRows(); auth_beg_idx = Table->GetColumnIndex("ndb_auth_seq_align_beg"); auth_end_idx = Table->GetColumnIndex("ndb_auth_seq_align_end"); beg_idx = Table->GetColumnIndex("seq_align_beg"); end_idx = Table->GetColumnIndex("seq_align_end"); if (auth_beg_idx >= 0 && auth_end_idx >= 0 && beg_idx >= 0 && end_idx >= 0) { for (i = 0; i < rowNo; i++) { Table->GetCell(string, auth_beg_idx, i); if (string != "?" && string != "" && string != ".") Table->UpdateCell(string, beg_idx, i); Table->GetCell(string, auth_end_idx, i); if (string != "?" && string != "" && string != ".") Table->UpdateCell(string, end_idx, i); } } } Table = _CifObj->GetTablePtr(_StructureId, "struct_ref_seq_dif"); if (!is_empty_table(Table)) { rowNo = Table->GetNumRows(); auth_beg_idx = Table->GetColumnIndex("ndb_auth_seq_num"); beg_idx = Table->GetColumnIndex("seq_num"); if (auth_beg_idx >= 0 && beg_idx >= 0) { for (i = 0; i < rowNo; i++) { Table->GetCell(string, auth_beg_idx, i); if (string != "?" && string != "" && string != ".") Table->UpdateCell(string, beg_idx, i); } } } } void _MAXIT::post_processing_from_cif_to_ndb() { int Auth_Token; One_Card_Info_Format *pCard = NULL; Auth_Token = find_jrnl_id("AUTH"); if (_JrnlCardInfo[Auth_Token].Head() && _CardInfo[AUTHOR_TOKEN-1].Head() == NULL && strcmp(_JrnlCardInfo[Auth_Token].Head()->Field(4), "")) { pCard = _CardInfo[AUTHOR_TOKEN-1].add_a_new_card(NdbToken[AUTHOR_TOKEN-1], 0); pCard->AddElementToField(_JrnlCardInfo[Auth_Token].Head()->Field(4), 2); } get_refn_card(); _JrnlCardInfo[Auth_Token].reorder_cards(1, INTEGER_COMPARE, ASCENT); Auth_Token = find_jrnl_id("TITL"); _JrnlCardInfo[Auth_Token].reorder_cards(1, INTEGER_COMPARE, ASCENT); Auth_Token = find_jrnl_id("EDIT"); _JrnlCardInfo[Auth_Token].reorder_cards(1, INTEGER_COMPARE, ASCENT); Auth_Token = find_jrnl_id("REF"); _JrnlCardInfo[Auth_Token].reorder_cards(1, INTEGER_COMPARE, ASCENT); Auth_Token = find_jrnl_id("PUBL"); _JrnlCardInfo[Auth_Token].reorder_cards(1, INTEGER_COMPARE, ASCENT); Auth_Token = find_jrnl_id("REFN"); _JrnlCardInfo[Auth_Token].reorder_cards(1, INTEGER_COMPARE, ASCENT); Auth_Token = find_card_id("TITLE"); pCard = _CardInfo[Auth_Token].Head(); while (pCard) { pCard->CleanStringDash(2); pCard = pCard->Next(); } if ((_CardInfo[STATUS_TOKEN-1].Head() == NULL || !strcmp(_CardInfo[STATUS_TOKEN-1].Head()->Field(6), "")) && _CardInfo[HEADER_TOKEN-1].Head() && strcmp(_CardInfo[HEADER_TOKEN-1].Head()->Field(2), "")) { pCard = _CardInfo[STATUS_TOKEN-1].Head(); if (pCard == NULL) pCard = _CardInfo[STATUS_TOKEN-1]. add_a_new_card(NdbToken[STATUS_TOKEN-1], 0); pCard->AddElementToField(_CardInfo[HEADER_TOKEN-1].Head()->Field(2), 6); } pCard = _CardInfo[PROCES_TOKEN-1].Head(); if (pCard == NULL) pCard = _CardInfo[PROCES_TOKEN-1]. add_a_new_card(NdbToken[PROCES_TOKEN-1], 0); if (!strcmp(pCard->Field(5), "")) pCard->AddElementToField("RCSB", 5); _CardInfo[RADIAT_TOKEN-1].reorder_cards(1, INTEGER_COMPARE, ASCENT); pCard = _CardInfo[REFMET_TOKEN-1].Head(); if (pCard && (!strncasecmp(pCard->Field(3), "CNS", 3) || !strncasecmp(pCard->Field(3), "X-PLOR", 6))) { pCard = _CardInfo[RFACTR_TOKEN-1].Head(); if (pCard) { if (!strcmp(pCard->Field(10), "") && strcmp(pCard->Field(7), "")) pCard->AddElementToField(pCard->Field(7), 10); else if (strcmp(pCard->Field(10), "") && !strcmp(pCard->Field(7), "")) pCard->AddElementToField(pCard->Field(10), 7); } } delete_null_cards(); } void _MAXIT::update_encapsulated_cif() { int count = 0; One_Card_Info_Format *pCard = NULL; if (_file_status == FILE_STATUS_MMCIF_PLUS_MOL) { pCard = _CardInfo[COMPND_TOKEN-1].Head(); while (pCard) { count++; pCard = pCard->Next(); } pCard = _CardInfo[SOURCE_TOKEN-1].Head(); if (pCard && count > 2) pdb_to_ndb_proc_compnd_and_source(0); } } static int get_number_strands(ISTable *Table, const char *sheet_id) { int id_index, num_index, rowNo, irow; CifString id, number; if (is_empty_table(Table)) return 1; id_index = Table->GetColumnIndex("id"); num_index = Table->GetColumnIndex("number_strands"); if (id_index < 0 || num_index < 0) return 1; rowNo = Table->GetNumRows(); for (irow = 0; irow < rowNo; irow++) { get_value(id, Table, id_index, irow); get_value(number, Table, num_index, irow); if (!strcasecmp(sheet_id, id.Text())) { return (atoi(number.Text())); } } return 1; } static int get_sense(ISTable *Table, const char *sheet_id, const char *id_1, const char *id_2) { int id_index, range_id_1, range_id_2, sense_index, rowNo, irow; char sense[50]; CifString id, range_1, range_2, cifstring; if (is_empty_table(Table)) return 0; id_index = Table->GetColumnIndex("sheet_id"); range_id_1 = Table->GetColumnIndex("range_id_1"); range_id_2 = Table->GetColumnIndex("range_id_2"); sense_index = Table->GetColumnIndex("sense"); if (id_index < 0 || range_id_1 < 0 || range_id_2 < 0 || sense_index < 0) return 0; rowNo = Table->GetNumRows(); for (irow = 0; irow < rowNo; irow++) { get_value(id, Table, id_index, irow); get_value(range_1, Table, range_id_1, irow); get_value(range_2, Table, range_id_2, irow); get_value(cifstring, Table, sense_index, irow); if (!strcasecmp(sheet_id, id.Text()) && !strcasecmp(id_1, range_1.Text()) && !strcasecmp(id_2, range_2.Text())) { strcpy(sense, cifstring.Text()); ndb_clean_string(sense); if (sense[0] == '-' || isdigit(sense[0])) return (atoi(sense)); else if (!strcasecmp(sense, "anti-parallel")) return (-1); else if (!strcasecmp(sense, "parallel")) return (1); } } return 0; } static void get_hbond(_MOLECULE *mol, ISTable *Table, const int chain_index, const char *sheet_id, const char *range_id, CifString &curAtom, int &curIndex, int &curRes, CifString &prevAtom, int &prevIndex, int &prevRes) { if (is_empty_table(Table)) return; int id_index = Table->GetColumnIndex("sheet_id"); int range_id_2 = Table->GetColumnIndex("range_id_2"); int beg_label_atom_id = Table->GetColumnIndex("range_2_label_atom_id"); int beg_label_comp_id = Table->GetColumnIndex("range_2_label_comp_id"); int beg_label_asym_id = Table->GetColumnIndex("range_2_label_asym_id"); int beg_label_seq_id = Table->GetColumnIndex("range_2_label_seq_id"); int beg_label_ins_code = Table->GetColumnIndex("range_2_PDB_ins_code"); int beg_auth_comp_id = Table->GetColumnIndex("range_2_auth_comp_id"); int beg_auth_asym_id = Table->GetColumnIndex("range_2_auth_asym_id"); int beg_auth_seq_id = Table->GetColumnIndex("range_2_auth_seq_id"); int end_label_atom_id = Table->GetColumnIndex("range_1_label_atom_id"); int end_label_comp_id = Table->GetColumnIndex("range_1_label_comp_id"); int end_label_asym_id = Table->GetColumnIndex("range_1_label_asym_id"); int end_label_seq_id = Table->GetColumnIndex("range_1_label_seq_id"); int end_label_ins_code = Table->GetColumnIndex("range_1_PDB_ins_code"); int end_auth_comp_id = Table->GetColumnIndex("range_1_auth_comp_id"); int end_auth_asym_id = Table->GetColumnIndex("range_1_auth_asym_id"); int end_auth_seq_id = Table->GetColumnIndex("range_1_auth_seq_id"); int rowNo = Table->GetNumRows(); int irow, BegIndex, BegRes, EndIndex, EndRes, beg, end; CifString id, range_2; for (irow = 0; irow < rowNo; irow++) { get_value(id, Table, id_index, irow); get_value(range_2, Table, range_id_2, irow); if (!strcasecmp(sheet_id, id.Text()) && !strcasecmp(range_id, range_2.Text())) { beg = get_residue_index(mol, Table, irow, beg_label_comp_id, beg_label_asym_id, beg_label_seq_id, beg_auth_comp_id, beg_auth_asym_id, beg_auth_seq_id, beg_label_ins_code, BegIndex, BegRes); end = get_residue_index(mol, Table, irow, end_label_comp_id, end_label_asym_id, end_label_seq_id, end_auth_comp_id, end_auth_asym_id, end_auth_seq_id, end_label_ins_code, EndIndex, EndRes); if (beg && end && (BegIndex == chain_index || EndIndex == chain_index)) { curIndex = BegIndex; curRes = BegRes; prevIndex = EndIndex; prevRes = EndRes; get_value(curAtom, Table, beg_label_atom_id, irow); get_value(prevAtom, Table, end_label_atom_id, irow); } return; } } } static void cif_to_ndb_find_serial_no(ISTable *Table, const int id, const int irow, const int tokenid, int *idfield, char idvalue[10][82], char SerialNo[10][82]) { int i, j, k; unsigned int str_len; CifString value; for (j = 0; j < 10; j++) { SerialNo[j][0] = '\0'; idvalue[j][0] = '\0'; } if (CifCategory[id].nCifKeyField) { for (i = 0; i < CifCategory[id].nCifKeyField; i++) { j = CifCategory[id].CifKeyField[i]; get_value(value, Table, idfield[i], irow); if (tokenid == JRNL_TOKEN-1) { if (value == "primary") strcpy(SerialNo[i], "0"); else if (value != "") strcpy(SerialNo[i], value.Text()); else sprintf(SerialNo[i], "%d", irow); } else if (value != "") { strcpy(SerialNo[i], value.Text()); for (k = 0; k < CifCategory[id].keywords[j].numNdbInfo; k++) { str_len = strlen(CifCategory[id].keywords[j].NdbInfo[k]. JrnlTokenName_Type); if (str_len != 0 && strlen(value.Text()) >= str_len && !strncmp(value.Text(), CifCategory[id].keywords[j].NdbInfo[k]. JrnlTokenName_Type, str_len)) { strcpy(SerialNo[i], &value.Text()[str_len]); strcpy(idvalue[i], CifCategory[id].keywords[j]. NdbInfo[k].JrnlTokenName_Type); break; } } } else sprintf(SerialNo[i], "%d", irow + 1); } } else sprintf(SerialNo[0], "%d", irow + 1); } void _MAXIT::ndb_processing_requests() { int i, j, k, ph_idx, mtd_idx, tmp_idx, det_idx, rowNo; char buffer[1000]; ISTable *Table = NULL, *Table1 = NULL; CifString pH, method, temp, rcsb_details; if (_experiment_type == EXPERIMENT_TYPE_NMR) { Table = _CifObj->GetTablePtr(_StructureId, "exptl"); if (!is_empty_table(Table)) { mtd_idx = Table->GetColumnIndex("method"); method.Clear(); Table->GetCell(method, mtd_idx, 0); // if (strcasecmp(method.Text(), "NMR, RESTRAINED REGULARIZED MEAN STRUCTURE")) { if (!strstr(method.Text(), "REGULARIZED MEAN STRUCTURE")) { if (_num_mol > 1) sprintf(buffer, "NMR, %d STRUCTURES", _num_mol); else if (_num_mol == 1) { strcpy(buffer, "NMR"); Table1 = _CifObj->GetTablePtr(_StructureId, "rcsb_nmr_representative"); if (!is_empty_table(Table1)) { tmp_idx = Table1->GetColumnIndex("selection_criteria"); temp.Clear(); Table1->GetCell(temp, tmp_idx, 0); if (!strcasecmp(temp.Text(), "minimized average structure")) { strcpy(buffer, "NMR, minimized average structure"); } } } else strcpy(buffer, "NMR"); method.Copy(buffer); Table->UpdateCell(method, mtd_idx, 0); _CifObj->WriteTable(Table, _StructureId, "exptl"); } } Table = _CifObj->GetTablePtr(_StructureId, "rcsb_nmr_software"); if (!is_empty_table(Table)) { mtd_idx = Table->GetColumnIndex("classification"); rowNo = Table->GetNumRows(); tmp_idx = -1; det_idx = -1; for (i = 0; i < rowNo; i++) { Table->GetCell(method, mtd_idx, i); if (!strcasecmp(method.Text(), "structure solution")) tmp_idx = i; if (!strcasecmp(method.Text(), "refinement")) det_idx = i; } if (tmp_idx >= 0 && det_idx < 0) { ph_idx = Table->GetNumColumns(); Table->AddRow(); for (i = 0; i < ph_idx; i++) { if (i == mtd_idx) method.Copy("refinement"); else Table->GetCell(method, i, tmp_idx); Table->UpdateCell(method, i, rowNo); } _CifObj->WriteTable(Table, _StructureId, "rcsb_nmr_software"); } } } for (i = 0; i < N_R_MERGE; i++) { Table = _CifObj->GetTablePtr(_StructureId, _r_merge[i].catetory); if (is_empty_table(Table)) continue; mtd_idx = Table->GetColumnIndex(_r_merge[i].item); if (mtd_idx < 0) continue; rowNo = Table->GetNumRows(); for (j = 0; j < rowNo; j++) { Table->GetCell(method, mtd_idx, j); if (method == "" || method == "?" || method == ".") continue; if (atof(method.Text()) > 0.99) { sprintf(buffer, "%.7f", atof(method.Text()) / 100.0); for (k = strlen(buffer) - 1; k >= 0; k--) { if (buffer[k] == '0') buffer[k] = '\0'; else break; } method.Copy(buffer); Table->UpdateCell(method, mtd_idx, j); } } _CifObj->WriteTable(Table, _StructureId, _r_merge[i].catetory); } for (i = 0; i < N_SWITCH_CATEGORY; i++) { Table = _CifObj->GetTablePtr(_StructureId, _switch_category[i].category); if (is_empty_table(Table)) continue; mtd_idx = Table->GetColumnIndex(_switch_category[i].high_item); tmp_idx = Table->GetColumnIndex(_switch_category[i].low_item); if (mtd_idx < 0 || tmp_idx < 0) continue; Table->GetCell(method, mtd_idx, 0); Table->GetCell(temp, tmp_idx, 0); if (method == "" || method == "?" || method == "." || temp == "" || temp == "?" || temp == ".") continue; if (atof(method.Text()) > atof(temp.Text())) { Table->UpdateCell(temp, mtd_idx, 0); Table->UpdateCell(method, tmp_idx, 0); _CifObj->WriteTable(Table, _StructureId, _switch_category[i].category); } } Table = _CifObj->GetTablePtr(_StructureId, "struct_keywords"); if (!is_empty_table(Table)) { ph_idx = Table->GetColumnIndex("ndb_keywords"); mtd_idx = Table->GetColumnIndex("text"); pH.Clear(); Table->GetCell(pH, ph_idx, 0); if (pH == "" || pH == "?" || pH == ".") pH.Clear(); method.Clear(); Table->GetCell(method, mtd_idx, 0); if (method == "" || method == "?" || method == ".") method.Clear(); if (pH != "" && method == "") { Table->UpdateCell(pH, mtd_idx, 0); _CifObj->WriteTable(Table, _StructureId, "struct_keywords"); } } Table = _CifObj->GetTablePtr(_StructureId, "exptl_crystal_grow"); if (!is_empty_table(Table)) { rowNo = Table->GetNumRows(); ph_idx = Table->GetColumnIndex("pH"); mtd_idx = Table->GetColumnIndex("method"); tmp_idx = Table->GetColumnIndex("temp"); det_idx = Table->GetColumnIndex("rcsb_details"); for (i = 0; i < rowNo; i++) { rcsb_details.Clear(); Table->GetCell(rcsb_details, det_idx, i); if (rcsb_details == "" || rcsb_details == "?" || rcsb_details == ".") rcsb_details.Clear(); pH.Clear(); Table->GetCell(pH, ph_idx, i); if (pH == "" || pH == "?" || pH == ".") pH.Clear(); if (pH != "" && !strstr(rcsb_details.Text(), pH.Text())) { if (rcsb_details != "") rcsb_details += ", "; rcsb_details += "pH "; rcsb_details += pH; } method.Clear(); Table->GetCell(method, mtd_idx, i); if (method == "" || method == "?" || method == ".") method.Clear(); if (method != "" && !strstr(rcsb_details.Text(), method.Text())) { if (rcsb_details != "") rcsb_details += ", "; rcsb_details += method; } temp.Clear(); Table->GetCell(temp, tmp_idx, i); if (temp == "" || temp == "?" || temp == ".") temp.Clear(); if (temp != "" && !strstr(rcsb_details.Text(), temp.Text())) { if (rcsb_details != "") rcsb_details += ", temperature "; rcsb_details += temp; rcsb_details += "K"; } Table->UpdateCell(rcsb_details, det_idx, i); } _CifObj->WriteTable(Table, _StructureId, "exptl_crystal_grow"); } Table = _CifObj->GetTablePtr(_StructureId, "ndb_xplor_file"); if (!is_empty_table(Table)) { rowNo = Table->GetNumRows(); mtd_idx = Table->GetColumnIndex("param_file"); tmp_idx = Table->GetColumnIndex("topol_file"); for (i = 0; i < rowNo; i++) { Table->GetCell(method, mtd_idx, i); if (method != "" && method != "?" && method != ".") { strcpy(buffer, method.Text()); for (j = strlen(buffer) - 1; j >= 0; j--) { if (buffer[j] == '/') break; } method.Copy(&buffer[j + 1]); Table->UpdateCell(method, mtd_idx, i); } Table->GetCell(method, tmp_idx, i); if (method != "" && method != "?" && method != ".") { strcpy(buffer, method.Text()); for (j = strlen(buffer) - 1; j >= 0; j--) { if (buffer[j] == '/') break; } method.Copy(&buffer[j + 1]); Table->UpdateCell(method, tmp_idx, i); } } _CifObj->WriteTable(Table, _StructureId, "ndb_xplor_file"); } Table = _CifObj->GetTablePtr(_StructureId, "database_PDB_remark"); if (!is_empty_table(Table)) { rowNo = Table->GetNumRows(); mtd_idx = Table->GetColumnIndex("id"); if (mtd_idx >= 0) { for (i = 0; i < rowNo; i++) { Table->GetCell(method, mtd_idx, i); if (method != "" && method != "?" && method != ".") { strcpy(buffer, method.Text()); k = strlen(buffer); for (j = 0; j < k; j++) { if (!isdigit(buffer[j])) break; } if (j < k) { Table->DeleteRow(i); /* Table->RemoveRow(i); i--; rowNo--; */ } } } Table->CompressTable(); _CifObj->WriteTable(Table, _StructureId, "database_PDB_remark"); } } }