/* FILE: ndb_to_cif.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. 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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 "dict_exchange.h" #include "_maxit.h" #include "erf_category.h" #include "erf_util.h" #include "util.h" #define N_R_FACTOR 16 #define NKEYWORDS 10 #define MAXIMUM_DB 200 static const char *pdbx_nonpoly_scheme[NKEYWORDS] = { "asym_id", "entity_id", "mon_id", "ndb_num", "pdb_num", "auth_num", "pdb_mon_id", "auth_mon_id", "pdb_id", "pdb_ins_code" }; typedef struct { const char *catetory; const char *item; } R_FACTOR; static R_FACTOR r_factor[N_R_FACTOR] = { { "ndb_refine", "R_factor_all_4sig_cutoff" }, { "ndb_refine", "R_factor_all_no_cutoff" }, { "ndb_refine", "R_factor_obs_4sig_cutoff" }, { "ndb_refine", "R_factor_obs_no_cutoff" }, { "ndb_refine", "free_R_factor_4sig_cutoff" }, { "ndb_refine", "free_R_factor_no_cutoff" }, { "refine", "ls_R_factor_R_free" }, { "refine", "ls_R_factor_R_work" }, { "refine", "ls_R_factor_all" }, { "refine", "ls_R_factor_obs" }, { "refine_ls_shell", "R_factor_R_free" }, { "refine_ls_shell", "R_factor_R_work" }, { "reflns", "ndb_Rmerge_I_obs" }, { "reflns", "ndb_Rsym_value" }, { "reflns_shell", "Rmerge_I_obs" }, { "reflns_shell", "ndb_Rsym_value" } }; #define NUM_TML 6 static R_FACTOR tml_token[NUM_TML] = { { "RFTPOS", "tight positional" }, { "RFMPOS", "medium positional" }, { "RFLPOS", "loose positional" }, { "RFTTHR", "tight thermal" }, { "RFMTHR", "medium thermal" }, { "RFLTHR", "loose thermal" } }; static ISTable *create_new_table(CIF_CATEGORY *cifcategory); static ISTable *create_atom_table(CIF_CATEGORY *cifcategory, const int standardized); static void put_atom_to_atom_site(ISTable *Table, CIF_CATEGORY *cifcategory, const int model, const int entity_id, const int card_id, const int format, _ATOM *atom, const int standardized); static void put_atom_to_atom_site_anisotrop(ISTable *Table, CIF_CATEGORY *cifcategory, _ATOM *atom, int &row, const int card_id); static int Insert_Struct_Conf(ISTable *Table, int &nrow, _CHAIN *chain, const char *type, const char *ID, const int fst, const int snd, const char *clas, const char *comment, const int category_id, const int serial_no); static void Insert_Sheet_Range(ISTable *Table, int &nrow, _CHAIN *chain, const char *sheetID, const int initRes, const int endRes, const int id, CIF_CATEGORY *category); static void Insert_Sheet_Hbond(ISTable *Table, int &nrow, _CHAIN *curchain, _CHAIN *prevchain, const char *sheetID, const char *curAtom, const int curRes, const char *prevAtom, const int prevRes, const int id, CIF_CATEGORY *ctg); static int Insert_Struct_Conn(ISTable *Table, int &nrow, const char *type, const char *PDB_id, const char *mod_name, const char *sugar_name, const char *atom_id, const char *standard_id, _CHAIN *fst_chain, const char *fst_atom, const char *fst_loc, const int fst, const char *sym_op1, _CHAIN *snd_chain, const char *snd_atom, const char *snd_loc, const int snd, const char *sym_op2, _CHAIN *trd_chain, const char *trd_atom, const char *trd_loc, const int trd, const char *comment, const int id, const int serial_no); #ifdef SUN_OS #ifdef __cplusplus extern "C" { #endif #endif static int pdb_rev_compare(const void *a, const void *b); #ifdef SUN_OS #ifdef __cplusplus } #endif #endif void _MAXIT::ndb_to_cif_general(const int cif_type, const int transfer, const int standardized, const int keep_contact_author, const int no_pdbx_strand_id) { int i, j, card_id, id, xray_or_nmr, category_id, ndb_tokenid, ndb_jrnlid; int tokenid, rowNo, row, is_ids; char buffer[82], WEIGHT[20], *p, *q, db_name[MAXIMUM_DB][20], db_code[MAXIMUM_DB][20]; double weight; _CHAIN *chain = NULL; CifString string; ISTable *Table = NULL, *Table1 = NULL; One_Card_Info_Format *pCard = NULL, *qCard = NULL; _RESIDUE *residue = NULL; pCard = _CardInfo[FORMUL_TOKEN-1].Head(); while (pCard) { WEIGHT[0] = '\0'; weight = get_molecule_weight(pCard->Field(2)); if (weight >= 0.0) sprintf(WEIGHT, "%11.3f", weight); if (strcmp(WEIGHT, "")) { ndb_clean_string(WEIGHT); pCard->AddElementToField(WEIGHT, 4); } strcpy(buffer, pCard->Field(5)); p = strstr(buffer, "("); q = strstr(buffer, ")"); if (p && q) { *q = '\0'; strcpy(buffer, p + 1); pCard->AddElementToField(buffer, 5); } if (!strcmp(pCard->Field(2), "HOH")) { qCard = _CardInfo[HETNAM_TOKEN-1]. add_a_new_card(NdbToken[HETNAM_TOKEN-1], 0); qCard->AddElementToField(pCard->Field(2), 2); qCard->AddElementToField("WATER", 3); } pCard = pCard->Next(); } 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); } } card_id = find_card_id("RCSBID"); if (card_id != -1) { pCard = _CardInfo[card_id].Head(); qCard = _CardInfo[NDBFIL_TOKEN-1].Head(); if (qCard && strcmp(qCard->Field(1), "")) { if (!pCard) pCard = _CardInfo[card_id].add_a_new_card(NdbToken[card_id], 0); if (!strcmp(pCard->Field(1), "")) pCard->AddElementToField(qCard->Field(1), 1); } } for (i = 0; i < MAXIMUM_DB; i++) { db_name[i][0] = '\0'; db_code[i][0] = '\0'; } id = 0; pCard = _CardInfo[DBREF_TOKEN-1].Head(); while (pCard) { for (i = 0; i < id; i++) { if (!strcmp(db_name[i], pCard->Field(7)) && !strcmp(db_code[i], pCard->Field(9))) break; } if (i == id) { id++; strcpy(db_name[i], pCard->Field(7)); strcpy(db_code[i], pCard->Field(9)); } pCard->AddElementToField(i+1, 15); pCard = pCard->Next(); } card_id = find_card_id("SEQADV"); qCard = _CardInfo[card_id].Head(); while (qCard) { pCard = _CardInfo[DBREF_TOKEN-1].Head(); while (pCard) { if (!strcmp(pCard->Field(2), qCard->Field(3))) { qCard->AddElementToField(pCard->Field(14), 11); break; } pCard = pCard->Next(); } qCard = qCard->Next(); } card_id = find_card_id("TMLPTL"); if (card_id >= 0) { pCard = _CardInfo[card_id].Head(); if (!pCard) { for (i = 0; i < NUM_TML; i++) { tokenid = find_card_id(tml_token[i].catetory); if (tokenid < 0) continue; qCard = _CardInfo[tokenid].Head(); while (qCard) { pCard = _CardInfo[card_id]. add_a_new_card(NdbToken[card_id], 0); for (j = 1; j < qCard->NumField(); j++) pCard->AddElementToField(qCard->Field(j), j); pCard->AddElementToField(tml_token[i].item, j); qCard = qCard->Next(); } } } } xray_or_nmr = 1; if (_experiment_type == EXPERIMENT_TYPE_NMR) xray_or_nmr = 2; for (category_id = 0; category_id < MxCategory; category_id++) { if (transfer && !(transfer & CifCategory[category_id].transfer)) continue; if (!(CifCategory[category_id].xray_or_nmr & xray_or_nmr)) continue; if (CifCategory[category_id].nkeywords == 0) continue; if (cif_type == CIF_NDB_TYPE && !CifCategory[category_id].xyz) continue; if (cif_type == CIF_SF_TYPE && !CifCategory[category_id].sf) continue; if (cif_type == CIF_COORDENCE_TYPE && !CifCategory[category_id].coordence) continue; if (cif_type == CIF_DEPOSITION_TYPE && !CifCategory[category_id].deposition) continue; ndb_tokenid = -1; ndb_jrnlid = -1; if (CifCategory[category_id].nkeywords > 1) { for (i = 1; i < CifCategory[category_id].nkeywords; i++) { if (CifCategory[category_id].keywords[i].NdbInfo[0].NdbTokenId > 0) { ndb_tokenid = CifCategory[category_id].keywords[i]. NdbInfo[0].NdbTokenId - 1; if (ndb_tokenid == JRNL_TOKEN-1) { ndb_jrnlid = CifCategory[category_id].keywords[i]. NdbInfo[0].JrnlTokenId -1; if (ndb_jrnlid != -1) break; } else if (ndb_tokenid != -1) break; } } } else if (CifCategory[category_id].nkeywords > 0) ndb_tokenid = CifCategory[category_id].keywords[0].NdbInfo[0].NdbTokenId - 1; if (!strcmp(CifCategory[category_id].category, "atom_site") || !strcmp(CifCategory[category_id].category, "atom_site_anisotrop")) continue; else if (!strcmp(CifCategory[category_id].category, "entity_poly")) continue; else if (!strcmp(CifCategory[category_id].category, "struct_mon_prot_cis")) continue; else if (!strcmp(CifCategory[category_id].category, "struct_asym")) ndbcif_process_stasym(category_id); else if (!strcmp(CifCategory[category_id].category, "entity_poly_seq")) ndbcif_process_entity_poly_seq(category_id, no_pdbx_strand_id); else if (!strcmp(CifCategory[category_id].category, "ndb_poly_seq_scheme")) ndbcif_process_asym_poly_seq_ndb(category_id); else if (!strcmp(CifCategory[category_id].category, "refine_ls_restr")) ndbcif_process_refine_ls_restr(category_id); else if (!strcmp(CifCategory[category_id].category, "struct_site_gen")) ndbcif_process_site_gen(category_id); else if (!strcmp(CifCategory[category_id].category, "rcsb_struct_link")) ndbcif_process_rcsb_link(category_id); else if (!strcmp(CifCategory[category_id].category, "struct_sheet")) ndbcif_process_struct_sheet(category_id); else if (!strcmp(CifCategory[category_id].category, "struct_sheet_order") || !strcmp(CifCategory[category_id].category, "struct_sheet_range") || !strcmp(CifCategory[category_id].category, "struct_sheet_hbond") || !strcmp(CifCategory[category_id].category, "rcsb_struct_sheet_hbond")) continue; else if (!strcmp(CifCategory[category_id].category, "struct_conn")) ndbcif_process_struct_conn(category_id); else if (!strcmp(CifCategory[category_id].category, "struct_conn_type")) continue; else if (!strcmp(CifCategory[category_id].category, "ndb_nonstandard_list")) ndbcif_process_nonstandard_list(category_id); else if (!strcmp(CifCategory[category_id].category, "struct_conf")) ndbcif_process_struct_conf(category_id); else if (!strcmp(CifCategory[category_id].category, "struct_conf_type")) continue; else if (!strcmp(CifCategory[category_id].category, "database_PDB_rev")) ndbcif_process_database_pdb_rev(category_id); else if (!strcmp(CifCategory[category_id].category, "database_PDB_rev_record")) continue; else if (ndb_tokenid != -1 && NdbToken[ndb_tokenid].MatrixType != 0) ndbcif_process_matrix(category_id); else if (ndb_tokenid == JRNL_TOKEN - 1 && (!strcmp(JrnlToken[ndb_jrnlid].TokenName, "AUTH") && strcmp(CifCategory[category_id].category, "citation") || !strcmp(JrnlToken[ndb_jrnlid].TokenName, "EDIT"))) ndbcif_process_name(category_id); else if (!strcmp(CifCategory[category_id].category, "audit_author")) ndbcif_process_name(category_id); else if (ndb_tokenid == PREMRK_TOKEN - 1) ndbcif_process_remark(category_id, ndb_tokenid); else if (CifCategory[category_id].general) ndbcif_process_general_category(category_id, ndb_tokenid); else ndbcif_process_general(category_id); if (!strncmp(CifCategory[category_id].category, "em_", 3)) { Table = _CifObj->GetTablePtr(_StructureId, CifCategory[category_id].category); if (is_empty_table(Table)) continue; rowNo = Table->GetNumRows(); for (i = 0; i < CifCategory[category_id].nkeywords; i++) { tokenid = CifCategory[category_id].keywords[i].NdbInfo[0].NdbTokenId-1; if (tokenid >= 0) continue; is_ids = 0; if (strstr(CifCategory[category_id].keywords[i].name, "id")) is_ids = 1; for (j = 0; j < rowNo; j++) { if (is_ids) { sprintf(buffer, "%d", j + 1); string.Copy(buffer); } else string.Copy("."); Table->UpdateCell(string, i, j); } } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } } ndbcif_postprocessing_molecule_weight(); ndbcif_postprocessing_exptl_crystal(); ndbcif_postprocessing_wavelength_id(); ndbcif_postprocessing_ncs_oper(); processing_r_factor(0.01); ndbcif_postprocessing_cif_standard(standardized, keep_contact_author); calculate_all_contact(5.0, 1); get_molecule_topology(); get_ebi_validate_contact(); get_ebi_validate_bond(); get_ebi_validate_angle(); get_ebi_validate_torsion(); get_ebi_validate_peptide_omega(); if (!_num_mol) return; Table = _CifObj->GetTablePtr(_StructureId, "entity"); if (is_empty_table(Table)) return; rowNo = Table->GetNumRows(); id = Table->GetColumnIndex("id"); card_id = Table->GetColumnIndex("type"); tokenid = Table->GetColumnIndex("ndb_description"); if (_CifObj->IsTablePresent(_StructureId, "rcsb_entity_nonpoly")) _CifObj->DeleteTable(_StructureId, "rcsb_entity_nonpoly"); Table1 = new ISTable("rcsb_entity_nonpoly"); Table1->AddColumn("entity_id"); Table1->AddColumn("name"); Table1->AddColumn("comp_id"); row = 0; for (i = 0; i < rowNo; i++) { Table->GetCell(string, card_id, i); if (string == "polymer") continue; Table->GetCell(string, id, i); chain = _molecules[0]->GetFirstChain(); while (chain) { if (atoi(string.Text()) == chain->entity_id()) break; chain = _molecules[0]->GetNextChain(); } if (!chain) continue; Table1->AddRow(); Table1->UpdateCell(string, 0, row); Table->GetCell(string, tokenid, i); Table1->UpdateCell(string, 1, row); residue = chain->GetFirstResidue(); string.Copy(residue->ResName()); Table1->UpdateCell(string, 2, row); row++; } if (!row) delete Table1; else _CifObj->WriteTable(Table1, _StructureId, "rcsb_entity_nonpoly"); } void _MAXIT::ndbcif_process_general(const int category_id) { int i, j, k, tokenid, fieldno, IsJrnl, nrow, NoKey, SerialNo, logical; int comp_id, crystal_id, keyField, found, serialNo1; char keyValue[10][82], Value[10][82], value[82]; CifString string, string1; ISTable *Table = NULL; One_Card_Info_Format *pCard = NULL, *qCard = NULL; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); nrow = 0; Table = create_new_table(&CifCategory[category_id]); for (i = 0; i < CifCategory[category_id].nkeywords; i++) { NoKey = CifCategory[category_id].nCifKeyField; for (j = 0; j < CifCategory[category_id].keywords[i].numNdbInfo; j++) { tokenid = CifCategory[category_id].keywords[i].NdbInfo[j].NdbTokenId-1; fieldno = CifCategory[category_id].keywords[i].NdbInfo[j].NdbFieldNo-1; IsJrnl = FALSE; if (tokenid == JRNL_TOKEN-1) { tokenid = CifCategory[category_id].keywords[i].NdbInfo[j].JrnlTokenId-1; IsJrnl = TRUE; } if (tokenid < 0 || fieldno < 0) continue; pCard = NULL; if (!IsJrnl) pCard = _CardInfo[tokenid].Head(); else pCard = _JrnlCardInfo[tokenid].Head(); SerialNo = 0; while (pCard) { if (!strcmp(CifCategory[category_id].category, "struct_ncs_ens_gen") && !strcmp(pCard->Field(9), "")) { pCard = pCard->Next(); continue; } if (pCard == NULL) break; value[0] = '\0'; string.Copy(value); logical = FALSE; for (k = 0; k < NoKey; k++) { if (fieldno == CifCategory[category_id].keywords[i]. NdbInfo[j].NdbTokenKeyFieldNo[k]) logical = TRUE; } if (IsJrnl) { if (fieldno == 1 && (!strcmp(pCard->Field(fieldno), "") || !strcmp(pCard->Field(fieldno), "0"))) string.Copy("primary"); else string.Copy(pCard->Field(fieldno)); } else if (fieldno == 0) { if (strcmp(CifCategory[category_id].keywords[i].NdbInfo[j]. JrnlTokenName_Type, "")) string.Copy(CifCategory[category_id].keywords[i].NdbInfo[j]. JrnlTokenName_Type); else string.Copy(NdbToken[tokenid].TokenName); } else if (logical) { if (strcmp(CifCategory[category_id].keywords[i].NdbInfo[j]. JrnlTokenName_Type, "")) { if (strcmp(pCard->Field(fieldno), "")) sprintf(value, "%s%s", CifCategory[category_id]. keywords[i].NdbInfo[j].JrnlTokenName_Type, pCard->Field(fieldno)); else sprintf(value, "%s1", CifCategory[category_id]. keywords[i].NdbInfo[j].JrnlTokenName_Type); } else { if (strcmp(pCard->Field(fieldno), "")) sprintf(value, "%s", pCard->Field(fieldno)); else strcpy(value, "1"); } string.Copy(value); } else { if (tokenid == CRSOLU_TOKEN-1 && fieldno == 1) { comp_id = 0; crystal_id = atoi(pCard->Field(2)); qCard = _CardInfo[tokenid].Head(); while (qCard) { if (atoi(qCard->Field(2)) == crystal_id) comp_id++; if (!strcmp(pCard->Field(1), qCard->Field(1))) break; qCard = qCard->Next(); } sprintf(value, "%d", comp_id); string.Copy(value); } else string.Copy(pCard->Field(fieldno)); } if (NoKey) { for (k = 0; k < 10; k++) { keyValue[k][0] = '\0'; Value[k][0] = '\0'; } for (k = 0; k < NoKey; k++) { keyField = CifCategory[category_id].keywords[i]. NdbInfo[j].NdbTokenKeyFieldNo[k]; if (keyField > 0) { if (IsJrnl) { if (strcmp(pCard->Field(keyField), "") && strcmp(pCard->Field(keyField), "0")) sprintf(Value[k],"%s", pCard->Field(keyField)); else strcpy(Value[k], "primary"); } else if (strcmp(CifCategory[category_id].keywords[i]. NdbInfo[j].JrnlTokenName_Type, "")) { if (strcmp(pCard->Field(keyField), "")) sprintf(Value[k], "%s%s", CifCategory[category_id].keywords[i]. NdbInfo[j].JrnlTokenName_Type, pCard->Field(keyField)); else sprintf(Value[k], "%s1", CifCategory[category_id].keywords[i]. NdbInfo[j].JrnlTokenName_Type); } else { if (strcmp(pCard->Field(keyField), "")) sprintf(Value[k],"%s", pCard->Field(keyField)); else strcpy(Value[k], "1"); } } else if (keyField == 0) strcpy(Value[k], CifCategory[category_id].keywords[i]. NdbInfo[j].JrnlTokenName_Type); } found = 0; for (serialNo1 = 0; serialNo1 < nrow; serialNo1++) { for (k = 0; k < NoKey; k++) { keyField = CifCategory[category_id].CifKeyField[k]; Table->GetCell(string1, keyField, serialNo1); strcpy(keyValue[k], string1.Text()); ndb_clean_string(keyValue[k]); if (strcmp(keyValue[k], Value[k]) && strcmp(Value[k], "")) break; } if (k == NoKey) { found = 1; Table->UpdateCell(string, i, serialNo1); } } if (!found) { nrow++; Table->AddRow(); Table->UpdateCell(string, i, serialNo1); for (k = 0; k < NoKey; k++) { keyField = CifCategory[category_id].CifKeyField[k]; string1.Copy(Value[k]); Table->UpdateCell(string1, keyField, serialNo1); } } } else { if (IsJrnl) SerialNo = atoi(pCard->Field(JrnlToken[tokenid].SeqField-1)); else if (!strcmp(CifCategory[category_id].category, "audit_contact_author")) SerialNo = atoi(pCard->Field(NdbToken[tokenid].SeqField-1)) - 1; if (SerialNo >= nrow) { nrow++; Table->AddRow(); } Table->UpdateCell(string, i, SerialNo); } pCard = pCard->Next(); SerialNo++; } } } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndbcif_process_site_gen(const int category_id) { if (_num_mol == 0 || _molecules == NULL) return; if (_n_site == 0 || _site == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); ISTable *Table = create_new_table(&CifCategory[category_id]); int nrow = 0, i = 0, j = 0, l = 0; CifString string; char value[10]; _CHAIN *chain = NULL; _FIELD *Init = NULL; for (i = 0; i < _n_site; i++) { for (j = 0; j < _site[i]->numRes; j++) { chain = _molecules[0]->GetIndexChain(_site[i]->initIndex[j]); if (!chain) continue; Init = chain->SeqResIndex(_site[i]->initRes[j]); if (!Init) continue; Table->AddRow(); for (l = 0; l < CifCategory[category_id].nkeywords; l++) { string.Copy(""); if (!strcasecmp(CifCategory[category_id].keywords[l].name, "id")) { sprintf(value, "%d", nrow+1); string.Copy(value); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "site_id")) { string.Copy(_site[i]->SiteID); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ndb_num_res")) { sprintf(value, "%d", _site[i]->numRes); string.Copy(value); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "label_comp_id")) { string.Copy(Init->Field[0]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "label_asym_id")) { string.Copy(chain->ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "label_seq_id")) { if (chain->chain_type() == ATOMP_TOKEN || chain->chain_type() == ATOMN_TOKEN) string.Copy(Init->Field[2]); else string.Copy("."); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ndb_label_ins_code")) { string.Copy(Init->InsCode); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "auth_comp_id")) { string.Copy(Init->Field[3]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "auth_asym_id")) { string.Copy(chain->PDB_ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "auth_seq_id")) { string.Copy(Init->Field[4]); } Table->UpdateCell(string, l, nrow); } nrow++; } } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndbcif_process_rcsb_link(const int category_id) { if (_num_mol == 0 || _molecules == NULL) return; if (_n_link == 0 || _link == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); int nrow = 0, i = 0, l = 0; CifString string; char value[10]; _CHAIN *fst = NULL, *snd = NULL; _FIELD *Fst = NULL, *Snd = NULL; _RESIDUE *fstRes = NULL, *sndRes = NULL; ISTable *Table = create_new_table(&CifCategory[category_id]); for (i = 0; i < _n_link; i++) { fst = _molecules[0]->GetIndexChain(_link[i]->FstIndex); snd = _molecules[0]->GetIndexChain(_link[i]->SndIndex); if (!fst || !snd) continue; Fst = fst->SeqResIndex(_link[i]->FstRes); Snd = snd->SeqResIndex(_link[i]->SndRes); if (!Fst || !Snd) continue; fstRes = Fst->Residue; sndRes = Snd->Residue; if (!fstRes || !sndRes) continue; if (!fstRes->find_atom(_link[i]->FstAtom) || !sndRes->find_atom(_link[i]->SndAtom)) continue; Table->AddRow(); for (l = 0; l < CifCategory[category_id].nkeywords; l++) { string.Copy(""); if (!strcasecmp(CifCategory[category_id].keywords[l].name, "id")) { sprintf(value, "%d", nrow+1); string.Copy(value); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr1_label_alt_id")) { string.Copy(_link[i]->altLoc1); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr1_label_asym_id")) { string.Copy(fst->PDB_ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr1_label_atom_id")) { string.Copy(_link[i]->FstAtom); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr1_label_comp_id")) { string.Copy(Fst->Field[3]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr1_label_seq_id")) { string.Copy(Fst->Field[4]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr1_label_ins_code")) { string.Copy(Fst->InsCode); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr1_symmetry")) { if (strcmp(_link[i]->SymOP_1, "")) string.Copy(_link[i]->SymOP_1); else string.Copy("1_555"); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr2_label_alt_id")) { string.Copy(_link[i]->altLoc2); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr2_label_asym_id")) { string.Copy(snd->PDB_ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr2_label_atom_id")) { string.Copy(_link[i]->SndAtom); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr2_label_comp_id")) { string.Copy(Snd->Field[3]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr2_label_seq_id")) { string.Copy(Snd->Field[4]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr2_label_ins_code")) { string.Copy(Snd->InsCode); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ptnr2_symmetry")) { if (strcmp(_link[i]->SymOP_2, "")) string.Copy(_link[i]->SymOP_2); else string.Copy("1_555"); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "details")) { string.Copy(_link[i]->details); } Table->UpdateCell(string, l, nrow); } nrow++; } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndbcif_process_struct_sheet(const int category_id) { int i, nrow1 = 0, nrow2 = 0, nrow3 = 0, nrow4 = 0; char sheetID[5], value[10]; CifString string; int serial_sheet = 1; _CHAIN *ch1 = NULL, *ch2 = NULL; CIF_CATEGORY *cifcategory = NULL, *cifcategory1 = NULL; ISTable *Table1 = NULL, *Table2 = NULL, *Table3 = NULL, *Table4 = NULL; if (_num_mol == 0 || _molecules == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); Table1 = create_new_table(&CifCategory[category_id]); if (_CifObj->IsTablePresent(_StructureId, "struct_sheet_order")) _CifObj->DeleteTable(_StructureId, "struct_sheet_order"); cifcategory = find_category("struct_sheet_order"); Table2 = create_new_table(cifcategory); if (_CifObj->IsTablePresent(_StructureId, "struct_sheet_range")) _CifObj->DeleteTable(_StructureId, "struct_sheet_range"); cifcategory = find_category("struct_sheet_range"); Table3 = create_new_table(cifcategory); if (_CifObj->IsTablePresent(_StructureId, "rcsb_struct_sheet_hbond")) _CifObj->DeleteTable(_StructureId, "rcsb_struct_sheet_hbond"); cifcategory1 = find_category("rcsb_struct_sheet_hbond"); Table4 = create_new_table(cifcategory1); strcpy(sheetID, "xxx"); for (i = 0; i < _n_sheet; i++) { if (strcmp(sheetID, _sheet[i]->sheetID)) { strcpy(sheetID, _sheet[i]->sheetID); serial_sheet = 1; Table1->AddRow(); string.Copy(_sheet[i]->sheetID); Table1->UpdateCell(string, 0, nrow1); sprintf(value, "%d", _sheet[i]->numStrands); string.Copy(value); Table1->UpdateCell(string, 2, nrow1); nrow1++; } else serial_sheet++; ch1 = _molecules[0]->GetIndexChain(_sheet[i]->initIndex); Insert_Sheet_Range(Table3, nrow3, ch1, _sheet[i]->sheetID, _sheet[i]->initRes, _sheet[i]->endRes, serial_sheet, cifcategory); if (_sheet[i]->sense == 0) continue; Table2->AddRow(); string.Copy(_sheet[i]->sheetID); Table2->UpdateCell(string, 0, nrow2); sprintf(value, "%d", serial_sheet - 1); string.Copy(value); Table2->UpdateCell(string, 1, nrow2); sprintf(value, "%d", serial_sheet); string.Copy(value); Table2->UpdateCell(string, 2, nrow2); if (_sheet[i]->sense > 0) string.Copy("parallel"); else string.Copy("anti-parallel"); Table2->UpdateCell(string, 4, nrow2); nrow2++; if (_sheet[i]->curIndex < 0 || _sheet[i]->prevIndex < 0) continue; ch1 = _molecules[0]->GetIndexChain(_sheet[i]->curIndex); ch2 = _molecules[0]->GetIndexChain(_sheet[i]->prevIndex); Insert_Sheet_Hbond(Table4, nrow4, ch1, ch2, _sheet[i]->sheetID, _sheet[i]->curAtom, _sheet[i]->curRes, _sheet[i]->prevAtom, _sheet[i]->prevRes, serial_sheet, cifcategory1); } _CifObj->WriteTable(Table1, _StructureId, CifCategory[category_id].category); _CifObj->WriteTable(Table2, _StructureId, "struct_sheet_order"); _CifObj->WriteTable(Table3, _StructureId, "struct_sheet_range"); _CifObj->WriteTable(Table4, _StructureId, "rcsb_struct_sheet_hbond"); } void _MAXIT::ndbcif_process_struct_conn(const int category_id) { int exist_ssbond = 0; int exist_link = 0; int exist_hydbnd = 0; int exist_sltbrg = 0; int exist_mismat = 0; int exist_bspair = 0; int exist_modifb = 0; int exist_modifp = 0; int exist_modifs = 0; int exist_modres = 0; int nrow = 0, i, j, k, l, num1, num2, hydrog = 0; _ATOM **atom1 = NULL, **atom2 = NULL; _CHAIN *fst_chain = NULL; _CHAIN *snd_chain = NULL; _CHAIN *trd_chain = NULL; CifString string; double dist = 10.0; _FIELD *Fst = NULL, *Snd = NULL; ISTable *Table = NULL; _RESIDUE *fstRes = NULL, *sndRes = NULL; if (_num_mol == 0 || _molecules == NULL) return; if (!_n_ssbond && !_n_link && !_n_hydbnd && !_n_sltbrg && !_n_mismat && !_n_bspair && !_n_modifb && !_n_modifp && !_n_modifs && !_n_modres) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); Table = create_new_table(&CifCategory[category_id]); l = 0; for (i = 0; i < _n_ssbond; i++) { fst_chain = _molecules[0]->GetIndexChain(_ssbond[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_ssbond[i]->SndIndex); if (!fst_chain || !fst_chain) continue; Fst = fst_chain->SeqResIndex(_ssbond[i]->FstRes); Snd = snd_chain->SeqResIndex(_ssbond[i]->SndRes); if (!Fst || !Snd) continue; fstRes = Fst->Residue; sndRes = Snd->Residue; atom1 = fstRes->find_atom("SG", num1); atom2 = sndRes->find_atom("SG", num2); for (j = 0; j < num1; j++) { for (k = 0; k < num2; k++) { if (!strcmp(atom1[j]->alt_loc(), atom2[k]->alt_loc()) || !strcmp(atom1[j]->alt_loc(), "") || !strcmp(atom2[k]->alt_loc(), "")) { dist = cal_distance(atom1[j], atom2[k]); if (dist < 3.0) { l++; exist_ssbond = Insert_Struct_Conn(Table, nrow, "disulf", "", "", "", "", "", fst_chain, "SG", atom1[j]->alt_loc(), _ssbond[i]->FstRes, _ssbond[i]->SymOP_1, snd_chain, "SG", atom2[k]->alt_loc(), _ssbond[i]->SndRes, _ssbond[i]->SymOP_2, NULL, "", "", -1, "", category_id, l); } } } } if (atom1) delete [] atom1; atom1 = NULL; if (atom2) delete [] atom2; atom2 = NULL; } for (i = 0; i < _n_link; i++) { fst_chain = _molecules[0]->GetIndexChain(_link[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_link[i]->SndIndex); if (!fst_chain || !fst_chain) continue; Fst = fst_chain->SeqResIndex(_link[i]->FstRes); Snd = snd_chain->SeqResIndex(_link[i]->SndRes); if (!Fst || !Snd) continue; fstRes = Fst->Residue; sndRes = Snd->Residue; if (!fstRes || !sndRes) continue; if (!fstRes->find_atom(_link[i]->FstAtom) || !sndRes->find_atom(_link[i]->SndAtom)) continue; exist_link = Insert_Struct_Conn(Table, nrow, "covale", "", "", "", "", "", fst_chain, _link[i]->FstAtom, _link[i]->altLoc1, _link[i]->FstRes, _link[i]->SymOP_1, snd_chain, _link[i]->SndAtom, _link[i]->altLoc2, _link[i]->SndRes, _link[i]->SymOP_2, NULL, "", "", -1, _link[i]->details, category_id, i + 1); } hydrog = 0; for (i = 0; i < _n_hydbnd; i++) { fst_chain = _molecules[0]->GetIndexChain(_hydbnd[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_hydbnd[i]->SndIndex); trd_chain = _molecules[0]->GetIndexChain(_hydbnd[i]->H_Index); exist_hydbnd = Insert_Struct_Conn(Table, nrow, "hydrog", "", "", "", "", "", fst_chain, _hydbnd[i]->FstAtom, _hydbnd[i]->altLoc1, _hydbnd[i]->FstRes, _hydbnd[i]->SymOP_1, snd_chain, _hydbnd[i]->SndAtom, _hydbnd[i]->altLoc2, _hydbnd[i]->SndRes, _hydbnd[i]->SymOP_2, trd_chain, _hydbnd[i]->H_Atom, _hydbnd[i]->altLocH, _hydbnd[i]->H_Res, "", category_id, ++hydrog); } for (i = 0; i < _n_sltbrg; i++) { fst_chain = _molecules[0]->GetIndexChain(_sltbrg[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_sltbrg[i]->SndIndex); exist_sltbrg = Insert_Struct_Conn(Table, nrow, "saltbr", "", "", "", "", "", fst_chain, _sltbrg[i]->FstAtom, _sltbrg[i]->altLoc1, _sltbrg[i]->FstRes, _sltbrg[i]->SymOP_1, snd_chain, _sltbrg[i]->SndAtom, _sltbrg[i]->altLoc2, _sltbrg[i]->SndRes, _sltbrg[i]->SymOP_2, NULL, "", "", -1, _sltbrg[i]->details, category_id, i + 1); } for (i = 0; i < _n_mismat; i++) { fst_chain = _molecules[0]->GetIndexChain(_mismat[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_mismat[i]->SndIndex); exist_mismat = Insert_Struct_Conn(Table, nrow, "mismat", "", "", "", "", "", fst_chain, "", "", _mismat[i]->FstRes, "", snd_chain, "", "", _mismat[i]->SndRes, "", NULL, "", "", -1, "", category_id, i + 1); } for (i = 0; i < _n_bspair; i++) { fst_chain = _molecules[0]->GetIndexChain(_bspair[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_bspair[i]->SndIndex); exist_bspair = Insert_Struct_Conn(Table, nrow, "hydrog", "", "", "", "", "", fst_chain, _bspair[i]->FstAtom, "", _bspair[i]->FstRes, "", snd_chain, _bspair[i]->SndAtom, "", _bspair[i]->SndRes, _bspair[i]->Asym_or_Gen, NULL, "", "", -1, _bspair[i]->Type, category_id, ++hydrog); } for (i = 0; i < _n_modifb; i++) { fst_chain = _molecules[0]->GetIndexChain(_modifb[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_modifb[i]->SndIndex); exist_modifb = Insert_Struct_Conn(Table, nrow, "covale_base", "", _modifb[i]->Name, "", _modifb[i]->Replaced_Atom, "", fst_chain, _modifb[i]->FstAtom, "", _modifb[i]->FstRes, "", snd_chain, _modifb[i]->SndAtom, "", _modifb[i]->SndRes, "", NULL, "", "", -1, "", category_id, i + 1); } for (i = 0; i < _n_modifp; i++) { fst_chain = _molecules[0]->GetIndexChain(_modifp[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_modifp[i]->SndIndex); exist_modifp = Insert_Struct_Conn(Table, nrow, "covale_phosphate", "", _modifp[i]->Name, "", _modifp[i]->Replaced_Atom, "", fst_chain, _modifp[i]->FstAtom, "", _modifp[i]->FstRes, "", snd_chain, _modifp[i]->SndAtom, "", _modifp[i]->SndRes, "", NULL, "", "", -1, "", category_id, i + 1); } for (i = 0; i < _n_modifs; i++) { fst_chain = _molecules[0]->GetIndexChain(_modifs[i]->FstIndex); snd_chain = _molecules[0]->GetIndexChain(_modifs[i]->SndIndex); exist_modifs = Insert_Struct_Conn(Table, nrow, "covale_sugar", "", _modifs[i]->Name, _modifs[i]->Sugar_Name, _modifs[i]->Replaced_Atom, "", fst_chain, _modifs[i]->FstAtom, "", _modifs[i]->FstRes, "", snd_chain, _modifs[i]->SndAtom, "", _modifs[i]->SndRes, "", NULL, "", "", -1, "", category_id, i + 1); } for (i = 0; i < _n_modres; i++) { fst_chain = _molecules[0]->GetIndexChain(_modres[i]->FstIndex); exist_modres = Insert_Struct_Conn(Table, nrow, "modres", _modres[i]->PDB_ID, "", "", "", _modres[i]->Standard_Name, fst_chain, "", "", _modres[i]->FstRes, "", NULL, "", "", -1, "", NULL, "", "", -1, _modres[i]->details, category_id, i + 1); } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); if (exist_ssbond || exist_link || exist_hydbnd || exist_sltbrg || exist_mismat || exist_bspair || exist_modifb || exist_modifp || exist_modifs || exist_modres) { CIF_CATEGORY *cifcategory = find_category("struct_conn_type"); if (_CifObj->IsTablePresent(_StructureId, cifcategory->category)) _CifObj->DeleteTable(_StructureId, cifcategory->category); Table = create_new_table(cifcategory); nrow = 0; if (exist_ssbond) { Table->AddRow(); string.Copy("disulf"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_link) { Table->AddRow(); string.Copy("covale"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_hydbnd || exist_bspair) { Table->AddRow(); string.Copy("hydrog"); Table->UpdateCell(string, 0, nrow); string.Copy("For hydrogen bonding between nucleic acid bases, donor to acceptor distance of 2.2 -3.5 Angstroms was used."); Table->UpdateCell(string, 1, nrow); nrow++; } if (exist_sltbrg) { Table->AddRow(); string.Copy("saltbr"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_mismat) { Table->AddRow(); string.Copy("mismat"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_modifb) { Table->AddRow(); string.Copy("covale_base"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_modifp) { Table->AddRow(); string.Copy("covale_phosphate"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_modifs) { Table->AddRow(); string.Copy("covale_sugar"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_modres) { Table->AddRow(); string.Copy("modres"); Table->UpdateCell(string, 0, nrow); nrow++; } _CifObj->WriteTable(Table, _StructureId, cifcategory->category); } } void _MAXIT::ndbcif_process_nonstandard_list(const int category_id) { if (_num_mol == 0 || _molecules == NULL) return; if (_n_het == 0 || _het == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); ISTable *Table = create_new_table(&CifCategory[category_id]); _CHAIN *chn = NULL; _FIELD *Fst = NULL; int nrow = 0, i, l; char value[10]; CifString string; for (i = 0; i < _n_het; i++) { chn = _molecules[0]->GetIndexChain(_het[i]->initIndex); if (!chn) continue; Fst = chn->SeqResIndex(_het[i]->initRes); if (!Fst) continue; Table->AddRow(); for (l = 0; l < CifCategory[category_id].nkeywords; l++) { string.Copy(""); if (!strcasecmp(CifCategory[category_id].keywords[l].name, "id")) { string.Copy(Fst->Field[0]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "label_asym_id")) { string.Copy(chn->ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "label_seq_id")) { string.Copy(Fst->Field[2]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ins_code")) { string.Copy(Fst->InsCode); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "auth_asym_id")) { string.Copy(chn->PDB_ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "auth_seq_id")) { string.Copy(Fst->Field[4]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "number_atoms_nh")) { sprintf(value, "%d", _het[i]->numAtoms); string.Copy(value); } Table->UpdateCell(string, l, nrow); } nrow++; } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndbcif_process_struct_conf(const int category_id) { if (_num_mol == 0 || _molecules == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); int exist_helix = 0; int exist_turn = 0; int helix_num = 1; int turn_num = 1; ISTable *Table = create_new_table(&CifCategory[category_id]); int nrow = 0, j = 0; char value[10]; CifString string; _HELIX *helix = NULL; _TURN *turn = NULL; _CHAIN *chain = _molecules[0]->GetFirstChain(); while (chain) { for (j = 0; j < chain->n_helix(); j++) { helix = chain->helix(j); if (!helix) continue; sprintf(value, "%d", helix->helixClass); exist_helix =Insert_Struct_Conf(Table, nrow, chain, "HELX_P", helix->helixID, helix->initRes, helix->endRes, value, helix->comment, category_id, helix_num); helix_num++; } for (j = 0; j < chain->n_turn(); j++) { turn = chain->turn(j); if (!turn) continue; exist_turn = Insert_Struct_Conf(Table, nrow, chain, "TURN_P", turn->turnID, turn->initRes, turn->endRes, "", turn->comment, category_id, turn_num); turn_num++; } chain = _molecules[0]->GetNextChain(); } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); if (exist_helix || exist_turn) { CIF_CATEGORY *cifcategory = find_category("struct_conf_type"); if (_CifObj->IsTablePresent(_StructureId, cifcategory->category)) _CifObj->DeleteTable(_StructureId, cifcategory->category); Table = create_new_table(cifcategory); nrow = 0; if (exist_helix) { Table->AddRow(); string.Copy("HELX_P"); Table->UpdateCell(string, 0, nrow); nrow++; } if (exist_turn) { Table->AddRow(); string.Copy("TURN_P"); Table->UpdateCell(string, 0, nrow); nrow++; } _CifObj->WriteTable(Table, _StructureId, cifcategory->category); } } void _MAXIT::ndbcif_process_stasym(const int id) { if (_num_mol == 0 || _molecules == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[id].category); ISTable *Table = create_new_table(&CifCategory[id]); int nrow = 0, j = 0; CifString string; char value[10]; _CHAIN *chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { Table->AddRow(); for (j = 0; j < CifCategory[id].nkeywords; j++) { string.Copy(""); if (!strcasecmp(CifCategory[id].keywords[j].name, "id")) string.Copy(chain->ChainID()); else if (!strcasecmp(CifCategory[id].keywords[j].name, "ndb_pdb_id")) string.Copy(chain->PDB_ChainID()); else if (!strcasecmp(CifCategory[id].keywords[j].name, "ndb_alt_id")) string.Copy(chain->PUB_ChainID()); else if (!strcasecmp(CifCategory[id].keywords[j].name, "rcsb_blank_PDB_chainid_flag")) { if (!strcmp(chain->PDB_ChainID_Flag(), "")) string.Copy("N"); else string.Copy(chain->PDB_ChainID_Flag()); } else if (!strcasecmp(CifCategory[id].keywords[j].name, "ndb_type")) { string.Copy(NdbToken[chain->chain_type()-1].TokenName); } else if (!strcasecmp(CifCategory[id].keywords[j].name, "ndb_order")) { value[0] = '\0'; if (chain->order() > 0) sprintf(value, "%d", chain->order()); string.Copy(value); } else if (!strcasecmp(CifCategory[id].keywords[j].name, "ndb_modified")) { if (chain->isModified()) string.Copy("Y"); else string.Copy("N"); } else if (!strcasecmp(CifCategory[id].keywords[j].name, "entity_id")) { sprintf(value, "%d", chain->entity_id()); string.Copy(value); } else if (!strcasecmp(CifCategory[id].keywords[j].name, "details")) { One_Card_Info_Format *pCard = _CardInfo[STASYM_TOKEN-1].Head(); while (pCard) { if (!strcmp(pCard->Field(3), chain->ChainID())) break; pCard = pCard->Next(); } if (pCard) string.Copy(pCard->Field(5)); } Table->UpdateCell(string, j, nrow); } nrow++; chain = _molecules[_rep_mol]->GetNextChain(); } _CifObj->WriteTable(Table, _StructureId, CifCategory[id].category); } void _MAXIT::ndbcif_process_entity_poly_seq(const int id, const int no_pdbx_strand_id) { int j = 0, k = 0, irow = 0, last = 0, len = 0, len1 = 0, nrow = 0; int n_entity_id = 0, *entity_id = NULL, len_p = 0, strand_index = -1; int target_index = -1; char value[10], *code = NULL; CifString string, sequence, sequence_p; ConnectFormat *drug = NULL; _FIELD *SeqRes = NULL; _CHAIN *chain = NULL; ISTable *Table = NULL, *Table1 = NULL; One_Card_Info_Format *pCard = NULL; if (_num_mol == 0 || _molecules == NULL) return; entity_id = new int[_molecules[0]->Num_Chain()]; for (j = 0; j < _molecules[0]->Num_Chain(); j++) entity_id[j] = -1; if (_CifObj->IsTablePresent(_StructureId, CifCategory[id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[id].category); if (_CifObj->IsTablePresent(_StructureId, "entity_poly")) _CifObj->DeleteTable(_StructureId, "entity_poly"); Table = create_new_table(&CifCategory[id]); pCard = _CardInfo[TARGET_TOKEN-1].Head(); Table1 = new ISTable("entity_poly"); Table1->AddColumn("entity_id"); Table1->AddColumn("type"); Table1->AddColumn("nstd_linkage"); Table1->AddColumn("nstd_monomer"); Table1->AddColumn("ndb_seq_one_letter_code"); Table1->AddColumn("ndb_seq_one_letter_code_can"); if (!no_pdbx_strand_id) { Table1->AddColumn("ndb_chain_id"); strand_index = 6; } if (pCard) { Table1->AddColumn("pdbx_target_identifier"); if (!no_pdbx_strand_id) target_index = 7; else target_index = 6; } chain = _molecules[0]->GetFirstChain(); while (chain) { if (!chain->has_sequence()) { chain = _molecules[0]->GetNextChain(); continue; } for (j = 0; j < n_entity_id; j++) { if (entity_id[j] == chain->entity_id()) break; } if (j < n_entity_id) { if (!no_pdbx_strand_id) { for (j = 0; j < irow; j++) { Table1->GetCell(string, 0, j); if (atoi(string.Text()) == chain->entity_id()) { Table1->GetCell(string, strand_index, j); if (string == "" || string == "." || string == "?") string.Copy(chain->PDB_ChainID()); else if (strcmp(chain->PDB_ChainID(), "")) { string += ","; string += chain->PDB_ChainID(); } Table1->UpdateCell(string, strand_index, j); break; } } } chain = _molecules[0]->GetNextChain(); continue; } entity_id[j] = chain->entity_id(); n_entity_id++; Table1->AddRow(); sprintf(value, "%d", entity_id[j]); string.Copy(value); Table1->UpdateCell(string, 0, irow); if (chain->chain_type() == ATOMP_TOKEN) string.Copy("polypeptide(L)"); else if (chain->chain_type() == ATOMS_TOKEN) string.Copy("polysaccharide(D)"); else if (chain->chain_type() == ATOMN_TOKEN) { if (chain->na_type() == ATOMN_TYPE_DNA_ONLY) string.Copy("polydeoxyribonucleotide"); else if (chain->na_type() == ATOMN_TYPE_RNA_ONLY || chain->na_type() == ATOMN_TYPE_TRNA) string.Copy("polyribonucleotide"); // else if (chain->na_type() < 0) { else { for (j = 0; j < _n_entity; j++) { if (_entity[j].Entity_ID == chain->entity_id()) break; } if (j < _n_entity && _entity[j].Description && (strstr(_entity[j].Description, "RIBOSOM") || strstr(_entity[j].Description, "ribiosom") || strstr(_entity[j].Description, "RNA") || strstr(_entity[j].Description, "rna"))) string.Copy("polyribonucleotide"); else string.Copy("polydeoxyribonucleotide"); } // else string.Copy("other"); } Table1->UpdateCell(string, 1, irow); string.Copy("no"); Table1->UpdateCell(string, 2, irow); last = 0; sequence.Copy(""); sequence_p.Copy(""); len = 0; len_p = 0; for (j = 0; j < chain->SeqLen(); j++) { SeqRes = chain->SeqRes(j); if (SeqRes->Deleted) continue; Table->AddRow(); code = get_oneletter_code(SeqRes->Field[0]); len1 = strlen(code); if (len1 == 1) { if (len + len1 > 80) { sequence += "\n"; len = 0; } sequence += code; len += len1; if (len_p + len1 > 80) { sequence_p += "\n"; len_p = 0; } sequence_p += code; len_p += len1; } else if (len1 == 2 && code[0] == '+') { if (len + 1 > 80) { sequence += "\n"; len = 0; } sequence += &code[1]; len += 1; if (len_p + 1 > 80) { sequence_p += "\n"; len_p = 0; } sequence_p += &code[1]; len_p += 1; } else { if (len + len1 + 2 > 80) { sequence += "\n"; len = 0; } sequence += "("; sequence += code; sequence += ")"; len += (len1 + 2); drug = find_drug(code); if (drug) { if (drug->parent_residue() && strcmp(drug->parent_residue(), "")) { code = get_oneletter_code(drug->parent_residue()); if (strlen(code) == 1) strcpy(value, code); else strcpy(value, "X"); } else strcpy(value, "X"); } else strcpy(value, "X"); if (len_p + 1 > 80) { sequence_p += "\n"; len_p = 0; } sequence_p += value; len_p += 1; } if ((chain->chain_type() == ATOMP_TOKEN || chain->chain_type() == ATOMN_TOKEN) && (SeqRes->Field[0][0] == '+' || !is_a_standard_residue(SeqRes->Field[0]))) { last = 1; } for (k = 0; k < CifCategory[id].nkeywords; k++) { string.Copy(""); if (!strcasecmp(CifCategory[id].keywords[k].name, "entity_id")) { sprintf(value, "%d", entity_id[n_entity_id-1]); string.Copy(value); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "num")) { sprintf(value, "%d", j + 1); string.Copy(value); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "mon_id")) { string.Copy(SeqRes->Field[0]); } Table->UpdateCell(string, k, nrow); } nrow++; } if (last) string.Copy("yes"); else string.Copy("no"); Table1->UpdateCell(string, 3, irow); Table1->UpdateCell(sequence, 4, irow); Table1->UpdateCell(sequence_p, 5, irow); if (!no_pdbx_strand_id) { string.Copy(chain->PDB_ChainID()); Table1->UpdateCell(string, strand_index, irow); } if (target_index > 0) { pCard = _CardInfo[TARGET_TOKEN-1].Head(); while (pCard) { if (atoi(pCard->Field(1)) == chain->entity_id()) break; pCard = pCard->Next(); } if (pCard) { string.Copy(pCard->Field(2)); Table1->UpdateCell(string, target_index, irow); } } irow++; chain = _molecules[0]->GetNextChain(); } delete [] entity_id; _CifObj->WriteTable(Table, _StructureId, CifCategory[id].category); _CifObj->WriteTable(Table1, _StructureId, "entity_poly"); } void _MAXIT::ndbcif_process_asym_poly_seq_ndb(const int id) { int nrow = 0, j = 0, k = 0; char value[10]; _CHAIN *chain = NULL; CifString string; _FIELD *SeqRes = NULL; ISTable *Table = NULL; if (_num_mol == 0 || _molecules == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[id].category); if (_CifObj->IsTablePresent(_StructureId, "pdbx_nonpoly_scheme")) _CifObj->DeleteTable(_StructureId, "pdbx_nonpoly_scheme"); if (_CifObj->IsTablePresent(_StructureId, "ndb_nonpoly_scheme")) _CifObj->DeleteTable(_StructureId, "ndb_nonpoly_scheme"); Table = create_new_table(&CifCategory[id]); chain = _molecules[0]->GetFirstChain(); while (chain) { if (!chain->has_sequence()) { chain = _molecules[0]->GetNextChain(); continue; } for (j = 0; j < chain->SeqLen(); j++) { SeqRes = chain->SeqRes(j); if (SeqRes->Deleted) continue; Table->AddRow(); for (k = 0; k < CifCategory[id].nkeywords; k++) { string.Copy(""); if (!strcasecmp(CifCategory[id].keywords[k].name, "id")) { string.Copy(chain->ChainID()); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "entity_id")) { sprintf(value, "%d", chain->entity_id()); string.Copy(value); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "seq_id")) { sprintf(value, "%d", j + 1); string.Copy(value); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "mon_id")) { string.Copy(SeqRes->Field[0]); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "ndb_num")) { string.Copy(SeqRes->Field[2]); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "pdb_num")) { if (strcmp(SeqRes->InsCode, "")) { sprintf(value, "%s%s", SeqRes->Field[4], SeqRes->InsCode); string.Copy(value); } else string.Copy(SeqRes->Field[4]); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "pdb_ins_code")) { if (strcmp(SeqRes->InsCode, "")) string.Copy(SeqRes->InsCode); else string.Copy("."); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "auth_num")) { string.Copy(SeqRes->Field[6]); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "pdb_mon_id")) { string.Copy(SeqRes->Field[3]); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "auth_mon_id")) { string.Copy(SeqRes->Field[5]); } else if (!strcasecmp(CifCategory[id].keywords[k].name, "pdb_id")) { string.Copy(chain->PDB_ChainID()); } Table->UpdateCell(string, k, nrow); } nrow++; } chain = _molecules[0]->GetNextChain(); } _CifObj->WriteTable(Table, _StructureId, CifCategory[id].category); Table = new ISTable("ndb_nonpoly_scheme"); for (k = 0; k < NKEYWORDS; k++) { Table->AddColumn(pdbx_nonpoly_scheme[k]); } nrow = 0; chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->has_sequence()) { chain = _molecules[0]->GetNextChain(); continue; } for (j = 0; j < chain->SeqLen(); j++) { SeqRes = chain->SeqRes(j); if (SeqRes->Deleted) continue; Table->AddRow(); for (k = 0; k < NKEYWORDS; k++) { string.Copy(""); if (!strcasecmp(pdbx_nonpoly_scheme[k], "asym_id")) { string.Copy(chain->ChainID()); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "entity_id")) { sprintf(value, "%d", chain->entity_id()); string.Copy(value); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "mon_id")) { string.Copy(SeqRes->Field[0]); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "ndb_num")) { string.Copy(SeqRes->Field[2]); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "pdb_num")) { if (strcmp(SeqRes->InsCode, "")) { sprintf(value, "%s%s", SeqRes->Field[4], SeqRes->InsCode); string.Copy(value); } else string.Copy(SeqRes->Field[4]); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "pdb_ins_code")) { if (strcmp(SeqRes->InsCode, "")) string.Copy(SeqRes->InsCode); else string.Copy("."); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "auth_num")) { string.Copy(SeqRes->Field[6]); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "pdb_mon_id")) { string.Copy(SeqRes->Field[3]); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "auth_mon_id")) { string.Copy(SeqRes->Field[5]); } else if (!strcasecmp(pdbx_nonpoly_scheme[k], "pdb_id")) { string.Copy(chain->PDB_ChainID()); } Table->UpdateCell(string, k, nrow); } nrow++; } chain = _molecules[0]->GetNextChain(); } _CifObj->WriteTable(Table, _StructureId, "ndb_nonpoly_scheme"); } void _MAXIT::processing_r_factor(const double factor) { int i, j, rowNo, item_index, irow; double temp; char value[80]; CifString string; ISTable *Table = NULL; for (i = 0; i < N_R_FACTOR; i++) { if (!_CifObj->IsTablePresent(_StructureId, r_factor[i].catetory)) continue; Table = _CifObj->GetTablePtr(_StructureId, r_factor[i].catetory); rowNo = Table->GetNumRows(); item_index = Table->GetColumnIndex(r_factor[i].item); for (irow = 0; irow < rowNo; irow++) { if (!Table->GetCell(string, item_index, irow)) { if (string != "" && string != "?" && string != ".") { temp = atof(string.Text()) *factor; sprintf(value, "%.7f", temp); for (j = strlen(value) - 1; j >= 0; j--) { if (value[j] == '0') value[j] = '\0'; else break; } string.Copy(value); Table->UpdateCell(string, item_index, irow); } } } _CifObj->WriteTable(Table, _StructureId, r_factor[i].catetory); } } void _MAXIT::ndbcif_postprocessing_molecule_weight() { if (_num_mol == 0 || _molecules == NULL) return; if (!_CifObj->IsTablePresent(_StructureId, "entity")) return; ISTable *Table = _CifObj->GetTablePtr(_StructureId, "entity"); int rowNo = Table->GetNumRows(); int id_index = Table->GetColumnIndex("id"); int wg_index = Table->GetColumnIndex("formula_weight"); int type = Table->GetColumnIndex("rcsb_nonpoly_type"); if (id_index < 0 || wg_index < 0) return; CifString string; char value[20]; _CHAIN *chain = NULL; ConnectFormat *drug = NULL; _RESIDUE *residue = NULL; for (int irow = 0; irow < rowNo; irow++) { Table->GetCell(string, id_index, irow); if (string != "" && string != "?" && string != ".") { chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { if (chain->entity_id() == atoi(string.Text())) { if (chain->weight() > 0) sprintf(value, "%.3f", chain->weight()); else strcpy(value, ""); string.Copy(value); Table->UpdateCell(string, wg_index, irow); if (chain->chain_type() != ATOMP_TOKEN && chain->chain_type() != ATOMN_TOKEN && chain->chain_type() != ATOMS_TOKEN && type >= 0) { residue = chain->GetFirstResidue(); if (residue) { drug = find_drug(residue->ResName()); if (drug) { string.Copy(drug->AtomType()); Table->UpdateCell(string, type, irow); } else if (!strcmp(residue->ResName(), "UNL")) { string.Copy("HETAIN"); Table->UpdateCell(string, type, irow); } } } } chain = _molecules[_rep_mol]->GetNextChain(); } } } _CifObj->WriteTable(Table, _StructureId, "entity"); } void _MAXIT::ndbcif_postprocessing_exptl_crystal() { if (!_CifObj->IsTablePresent(_StructureId, "exptl_crystal")) return; ISTable *Table = _CifObj->GetTablePtr(_StructureId, "exptl_crystal"); int rowNo = Table->GetNumRows(); int id_index = Table->GetColumnIndex("id"); if (id_index < 0) return; CifString string; char value[10]; for (int irow = 0; irow < rowNo; irow++) { sprintf(value, "%d", irow+1); string.Copy(value); Table->UpdateCell(string, id_index, irow); } _CifObj->WriteTable(Table, _StructureId, "exptl_crystal"); } void _MAXIT::ndbcif_postprocessing_wavelength_id() { if (!_CifObj->IsTablePresent(_StructureId, "diffrn_radiation")) return; ISTable *Table = _CifObj->GetTablePtr(_StructureId, "diffrn_radiation"); int rowNo = Table->GetNumRows(); int id_index = Table->GetColumnIndex("wavelength_id"); if (id_index < 0) return; CifString string; for (int irow = 0; irow < rowNo; irow++) { Table->GetCell(string, id_index, irow); if (string == "" || string == "?" || string == ".") { string.Copy("1"); Table->UpdateCell(string, id_index, irow); } } _CifObj->WriteTable(Table, _StructureId, "diffrn_radiation"); } void _MAXIT::ndbcif_postprocessing_ncs_oper() { if (!_CifObj->IsTablePresent(_StructureId, "struct_ncs_oper")) return; ISTable *Table = _CifObj->GetTablePtr(_StructureId, "struct_ncs_oper"); if (is_empty_table(Table)) return; int rowNo = Table->GetNumRows(); int code_index = Table->GetColumnIndex("code"); if (code_index < 0) return; CifString string; for (int irow = 0; irow < rowNo; irow++) { Table->GetCell(string, code_index, irow); if (string == "" || string == "?") string.Copy("generate"); else if (string == "1") string.Copy("given"); Table->UpdateCell(string, code_index, irow); } _CifObj->WriteTable(Table, _StructureId, "struct_ncs_oper"); } void _MAXIT::ndbcif_process_general_category(const int category_id, const int ndb_tokenid) { int irow = 0, i, j, fieldno; CifString string; ISTable *Table = NULL; One_Card_Info_Format *pCard = _CardInfo[ndb_tokenid].Head(); if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); Table = create_new_table(&CifCategory[category_id]); while (pCard) { Table->AddRow(); for (i = 0; i < CifCategory[category_id].nkeywords; i++) { for (j = 0; j < CifCategory[category_id].keywords[i].numNdbInfo; j++) { fieldno = CifCategory[category_id].keywords[i].NdbInfo[j].NdbFieldNo-1; if (fieldno < 0) continue; string.Copy(pCard->Field(fieldno)); Table->UpdateCell(string, i, irow); } } irow++; pCard = pCard->Next(); } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndbcif_process_remark(const int category_id, const int ndb_tokenid) { if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); ISTable *Table = create_new_table(&CifCategory[category_id]); int irow = 0, i, j, fieldno; CifString string(""); CifString id("-1"); One_Card_Info_Format *pCard = _CardInfo[ndb_tokenid].Head(); while (pCard) { if (id != pCard->Field(1)) { if (string != "") { Table->AddRow(); for (i = 0; i < CifCategory[category_id].nkeywords; i++) { for (j = 0; j < CifCategory[category_id].keywords[i].numNdbInfo; j++) { fieldno = CifCategory[category_id].keywords[i].NdbInfo[j].NdbFieldNo-1; if (fieldno == 1) Table->UpdateCell(id, i, irow); else if (fieldno == 2) Table->UpdateCell(string, i, irow); } } irow++; string.Copy(""); } id.Copy(pCard->Field(1)); string += pCard->Field(2); } else { string += '\n'; string += pCard->Field(2); } pCard = pCard->Next(); } if (string != "") { Table->AddRow(); for (i = 0; i < CifCategory[category_id].nkeywords; i++) { for (j = 0; j < CifCategory[category_id].keywords[i].numNdbInfo; j++) { fieldno = CifCategory[category_id].keywords[i].NdbInfo[j].NdbFieldNo-1; if (fieldno == 1) Table->UpdateCell(id, i, irow); else if (fieldno == 2) Table->UpdateCell(string, i, irow); } } irow++; string.Copy(""); } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndbcif_process_database_pdb_rev(const int category_id) { One_Card_Info_Format *pCard = NULL, *qCard = NULL; PDB_REV *pdb_rev = NULL; int n_rev = 0, i, j, len, irow = 0; char buffer[10], *p; CifString string; ISTable *Table = NULL, *Table1 = NULL; CIF_CATEGORY *cifcategory1 = NULL; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); Table = create_new_table(&CifCategory[category_id]); pCard = _CardInfo[REVDAT_TOKEN-1].Head(); while (pCard) { for (i = 0; i < n_rev; i++) if (atoi(pCard->Field(1)) == pdb_rev[i].num) break; if (i == n_rev) { n_rev++; pdb_rev = (PDB_REV *) realloc(pdb_rev, n_rev * sizeof(PDB_REV)); pdb_rev[i].num = atoi(pCard->Field(1)); strcpy(pdb_rev[i].date, pCard->Field(3)); strcpy(pdb_rev[i].replaces, pCard->Field(4)); pdb_rev[i].mod_type = atoi(pCard->Field(5)); pdb_rev[i].record = NULL; } for (j = 6; j < 10; j++) { if (strcmp(pCard->Field(j), "")) { if (pdb_rev[i].record == NULL) { len = strlen(pCard->Field(j))+1; pdb_rev[i].record = (char *) calloc(len, sizeof(char)); strcpy(pdb_rev[i].record, pCard->Field(j)); } else if (!strstr(pdb_rev[i].record, pCard->Field(j))) { len = strlen(pCard->Field(j)) + 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, pCard->Field(j)); } } } pCard = pCard->Next(); } if (n_rev > 1) qsort((void *) pdb_rev, n_rev, sizeof(PDB_REV), pdb_rev_compare); for (i = 0; i < n_rev; i++) { Table->AddRow(); sprintf(buffer, "%d", pdb_rev[i].num); string.Copy(buffer); Table->UpdateCell(string, 0, i); string.Copy(pdb_rev[i].date); Table->UpdateCell(string, 1, i); string.Copy(pdb_rev[i].replaces); Table->UpdateCell(string, 4, i); sprintf(buffer, "%d", pdb_rev[i].mod_type); string.Copy(buffer); Table->UpdateCell(string, 5, i); if (pdb_rev[i].mod_type == 0) { qCard = _CardInfo[HEADER_TOKEN-1].Head(); if (qCard && strcmp(qCard->Field(2), "")) { string.Copy(qCard->Field(2)); Table->UpdateCell(string, 2, i); } } } if (n_rev == 0 && _CardInfo[HEADER_TOKEN-1].Head() && strcmp(_CardInfo[HEADER_TOKEN-1].Head()->Field(2), "")) { Table->AddRow(); CifString string; string.Copy(_CardInfo[HEADER_TOKEN-1].Head()->Field(2)); Table->UpdateCell(string, 2, 0); } if (_CifObj->IsTablePresent(_StructureId, "database_PDB_rev_record")) _CifObj->DeleteTable(_StructureId, "database_PDB_rev_record"); cifcategory1 = find_category("database_PDB_rev_record"); Table1 = create_new_table(cifcategory1); irow = 0; for (i = 0; i < n_rev; i++) { p = pdb_rev[i].record; while (p) { Table1->AddRow(); sprintf(buffer, "%d", pdb_rev[i].num); string.Copy(buffer); Table1->UpdateCell(string, 0, irow); p = get_word(p, buffer); string.Copy(buffer); Table1->UpdateCell(string, 1, irow); irow++; } } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); _CifObj->WriteTable(Table1, _StructureId, cifcategory1->category); for (i = 0; i < n_rev; i++) { if (pdb_rev[i].record) free ((void *) pdb_rev[i].record); } free ((void *) pdb_rev); } void _MAXIT::ndbcif_process_matrix(const int category_id) { int irow = 0, i, j, tokenid, str_len, rowIndex, fieldno, len, serialNo; int index = -1, serial_no = 0; char TokenName[8]; CifString string; ISTable *Table = NULL; One_Card_Info_Format *pCard = NULL; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); Table = create_new_table(&CifCategory[category_id]); Table->AddRow(); for (i = 0; i < CifCategory[category_id].nkeywords; i++) { tokenid = CifCategory[category_id].keywords[i].NdbInfo[0].NdbTokenId-1; if (tokenid < 0 || tokenid > MxTokens) continue; str_len = strlen(CifCategory[category_id].keywords[i].name); pCard = _CardInfo[tokenid].Head(); if (pCard) { rowIndex = 0; fieldno=CifCategory[category_id].keywords[i].NdbInfo[0].NdbFieldNo-1; if (NdbToken[tokenid].MatrixType != 0 && str_len > 9 && !strncmp(&CifCategory[category_id].keywords[i].name[str_len-9], "vector", 6)) { len = strlen(CifCategory[category_id].keywords[i].name) - 2; rowIndex = atoi(&CifCategory[category_id].keywords[i].name[len]); } else if (NdbToken[tokenid].MatrixType != 0) { for (j = 0; j < str_len - 1; j++) if (CifCategory[category_id].keywords[i].name[j] == '[') break; rowIndex = atoi(&CifCategory[category_id].keywords[i].name[j+1]); } strcpy(TokenName, pCard->Field(0)); while (NdbToken[tokenid].MatrixType != 0 && pCard && rowIndex > atoi(&TokenName[strlen(TokenName)-1])) { pCard = pCard->Next(); if (pCard) strcpy(TokenName, pCard->Field(0)); } serialNo = 0; while (pCard) { if (serialNo > irow) { irow++; Table->AddRow(); } if (fieldno < 0 || fieldno > NdbToken[tokenid].NumField) string.Copy(""); else string.Copy(pCard->Field(fieldno)); Table->UpdateCell(string, i, serialNo); serialNo++; if (rowIndex == 0 && NdbToken[tokenid].SeqField == 0) break; do { pCard = pCard->Next(); if (pCard) { strcpy(TokenName, pCard->Field(0)); index = atoi(&TokenName[strlen(TokenName)-1]); if (NdbToken[tokenid].SeqField) { serial_no = atoi(pCard->Field(NdbToken[tokenid]. SeqField-1)); } } } while (pCard && (rowIndex != 0 && rowIndex != index || NdbToken[tokenid].SeqField == 0 || (serialNo+1) > serial_no)); } } } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndbcif_process_name(const int category_id) { int is_Jrnl = 0, id_field = 0, irow = -1, i, j, k, fieldno, tokenid; int str_len, pos; char tmpstring[82]; CifString id, string; ISTable *Table = NULL; One_Card_Info_Format *pCard = NULL; tokenid = CifCategory[category_id].keywords[0].NdbInfo[0].NdbTokenId-1; if (tokenid == JRNL_TOKEN-1) { tokenid = CifCategory[category_id].keywords[0].NdbInfo[0].JrnlTokenId-1; pCard = _JrnlCardInfo[tokenid].Head(); is_Jrnl = 1; } else pCard = _CardInfo[tokenid].Head(); if (pCard == NULL) return; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); Table = create_new_table(&CifCategory[category_id]); while (pCard) { for (i = 0; i < CifCategory[category_id].nkeywords; i++) { if (is_Jrnl && i == id_field) continue; for (j = 0; j Field(1), "") || !strcmp(pCard->Field(1), "0")) id.Copy("primary"); else id.Copy(pCard->Field(1)); } if (!strcmp(pCard->Field(fieldno), "") && irow >= 0) Table->UpdateCell(string, i, irow); else { str_len = strlen(pCard->Field(fieldno)); pos = 0; while (pos < str_len) { memset(tmpstring, 0, 82); for (k = pos; k < str_len; k++) if (pCard->Field(fieldno)[k] == ',') break; strncpy(tmpstring, &pCard->Field(fieldno)[pos], k-pos); if (pCard->Field(fieldno)[k] == ',' && pCard->Field(fieldno)[k+1] == ' ') pos = k+2; else pos = k+1; irow++; Table->AddRow(); if (is_Jrnl) Table->UpdateCell(id, id_field, irow); ndb_name_conversion_last_first(tmpstring); string.Copy(tmpstring); Table->UpdateCell(string, i, irow); } } } } pCard = pCard->Next(); } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::ndb_to_cif_coordinates(const int format, const int remove_hydrogen, const int standardized, const int is_iupac, const int id_option, const int exchange, const int together, const int no_deriv) { if (_num_mol == 0 || _molecules == NULL) return; int atom_id = 0, row = 0, card_id = -1, i, l, n_list = 0, num, remove_q; int label_index, rowNo; char list[100][5], alt_loc[5]; _ATOM *atom = NULL; _CHAIN *chain = NULL; _RESIDUE *residue = NULL; CIF_CATEGORY *cifcategory = NULL, *cifcategory1 = NULL; CifString string, str; ISTable *Table = NULL, *Table1 = NULL; cifcategory = find_category("atom_site"); if (_CifObj->IsTablePresent(_StructureId, cifcategory->category)) _CifObj->DeleteTable(_StructureId, cifcategory->category); Table = create_atom_table(cifcategory, standardized); cifcategory1 = find_category("atom_site_anisotrop"); if (_CifObj->IsTablePresent(_StructureId, cifcategory1->category)) _CifObj->DeleteTable(_StructureId, cifcategory1->category); Table1 = create_new_table(cifcategory1); remove_q = 0; for (l = 0; l < _num_mol; l++) { chain = _molecules[l]->GetFirstChain(); while (chain) { if (is_iupac && chain->chain_type() == ATOMP_TOKEN) chain->labeling_iupac_hydrogen(); card_id = chain->chain_type() - 1; residue = chain->GetFirstResidue(); while (residue) { if (is_iupac) residue->labeling_iupac_hydrogen(); atom = residue->GetFirstAtom(); while (atom) { if (atom->is_hydrogen() && remove_hydrogen == 1) { atom = residue->GetNextAtom(); continue; } if (!strcmp(atom->atom_type(), "Q") && _experiment_type == EXPERIMENT_TYPE_NMR) { remove_q = 1; atom = residue->GetNextAtom(); continue; } atom_id++; atom->set_atnum(atom_id); strcpy(alt_loc, atom->alt_loc()); if (!strcmp(alt_loc, "") || !strcmp(alt_loc, "?")) strcpy(alt_loc, "."); for (i = 0; i < n_list; i++) { if (!strcmp(list[i], alt_loc)) break; } if (i == n_list) { strcpy(list[i], alt_loc); n_list++; } put_atom_to_atom_site(Table, cifcategory, _molecules[l]->Mol_ID(), chain->entity_id(), card_id, format, atom, standardized); if (Table1 && atom->is_anisou()) put_atom_to_atom_site_anisotrop(Table1, cifcategory1, atom, row, card_id); atom = residue->GetNextAtom(); } residue = chain->GetNextResidue(); } chain = _molecules[l]->GetNextChain(); } } if (remove_q) ndb_log_message(NDB_MSG_WARN, "Q atoms have been removed"); if (!Table1->GetNumRows()) { delete Table1; Table1 = NULL; } _CifObj->WriteTable(Table, _StructureId, cifcategory->category); if (standardized) { if (!no_deriv) { if (together) get_derived_features(_CifObj); else { char *p, tmpFile[100], tmpFile1[300], templateFileName[9] = "./XXXXXX"; CifString ids[3]; strcpy(tmpFile, templateFileName); int fd = mkstemp(tmpFile); close (fd); CifFileObj *fobj = new CifFileObj(tmpFile, WRITE_MODE); get_derived_features(fobj); num = get_pdb_ndb_ids(id_option, ids); int order = fobj->GetBlockOrder(_StructureId); if (exchange) { for (l = 0; l < num; l++) { fobj->RenameBlock(ids[l].Text(), order); sprintf(tmpFile1, "%s-deriv.cif", ids[l].Text()); ndb_set_string_to_lower(tmpFile1); fobj->Write(tmpFile1); } } else { if (ids[0] != "") fobj->RenameBlock(ids[0].Text(), order); strcpy(tmpFile1, _input_filename); p = strstr(tmpFile1, "."); if (p) *p = '\0'; strcat(tmpFile1, "-deriv.cif"); fobj->Write(tmpFile1); } sprintf(tmpFile1, "rm -f %s", tmpFile); system(tmpFile1); delete fobj; } } } _CifObj->DeleteTable(_StructureId, "atom_sites_alt"); ISTable *Table2 = new ISTable("atom_sites_alt"); Table2->AddColumn("id"); Table2->AddColumn("details"); for (i = 0; i < n_list; i++) { Table2->AddRow(); string.Copy(list[i]); Table2->UpdateCell(string, 0, i); } _CifObj->WriteTable(Table2, _StructureId, "atom_sites_alt"); if (Table1) { label_index = Table1->GetColumnIndex("ndb_label_alt_id"); rowNo = Table1->GetNumRows(); for (i = 0; i < rowNo; i++) { Table1->GetCell(string, label_index, i); if (string == "?" || string == "") { string.Copy("."); Table1->UpdateCell(string, label_index, i); } } _CifObj->WriteTable(Table1, _StructureId, cifcategory1->category); } } void _MAXIT::open_mmcif_file() { if (_CifObj) delete _CifObj; if (_is_binary) _CifObj = new CifFileObj(_output_filename, WRITE_MODE); else { get_temp_file(); _CifObj = new CifFileObj(_temp_file, WRITE_MODE); } } void _MAXIT::write_mmcif_file(const int standardized, const int id_option, const int exchange) { int id_idx, num, numCategory, i, j, k, rowNo, order, no_find_name = 0; char **categoryName = NULL, buffer[20], Name[100]; ISTable *Table = NULL; CifString string, id, ids[3]; if (!_CifObj || _is_binary) return; if (standardized || exchange) { num = get_pdb_ndb_ids(id_option, ids); if (!num) { no_find_name = 1; num = 1; ids[0].Copy(_StructureId); } if (exchange) { set_exchange_status(INTERNAL_TO_EXCHANGE); _CifObj = dictionary_exchange(_CifObj, _temp_file); } order = _CifObj->GetBlockOrder(_StructureId); categoryName = _CifObj->GetTableNames(numCategory); strcpy(Name, _StructureId); for (k = 0; k < num; k++) { Table = _CifObj->GetTablePtr(Name, "entry"); id_idx = Table->GetColumnIndex("id"); id.Copy(ids[k]); Table->UpdateCell(id, id_idx, 0); for (i = 0; i < numCategory; i++) { Table = _CifObj->GetTablePtr(Name, categoryName[i]); id_idx = Table->GetColumnIndex("entry_id"); if (id_idx >= 0) { rowNo = Table->GetNumRows(); for (j = 0; j < rowNo; j++) { Table->UpdateCell(id, id_idx, j); } } } _CifObj->RenameBlock(ids[k].Text(), order); if (exchange) { if (no_find_name) { _CifObj->Write(_output_filename, 0, 1); } else { sprintf(buffer, "%s.cif.tr", ids[k].Text()); ndb_set_string_to_lower(buffer); _CifObj->Write(buffer, 0, 1); } } strcpy(Name, ids[k].Text()); } for (i = 0; i < numCategory; i++) delete categoryName[i]; delete categoryName; if (exchange) return; } _CifObj->Write(_output_filename, 0, 1); } void _MAXIT::ndbcif_process_refine_ls_restr(const int category_id) { int irow = 0, index = 0, pid, i, j, tokenid, fieldno; char abbreviation = 'o'; CifString string; if (_CifObj->IsTablePresent(_StructureId, CifCategory[category_id].category)) _CifObj->DeleteTable(_StructureId, CifCategory[category_id].category); ISTable *Table = create_new_table(&CifCategory[category_id]); One_Card_Info_Format *pCard = _CardInfo[REFMET_TOKEN-1].Head(); if (pCard) { string.Copy(pCard->Field(3)); string.ToLower(); for (pid = 0; pid < mxPrograms; pid++) { if (strstr(string.Text(), programs[pid].program)) { abbreviation = programs[pid].abbreviation[0]; break; } } } for (i = 0; i < mxRmsRecords; i++) { if (rmsRecords[i].type[0] == abbreviation && rmsRecords[i].type[1] == '_') { string.Copy(rmsRecords[i].type); Table->AddRow(); index = 0; Table->UpdateCell(string, index, irow); index++; for (j = 0; j < NDB_CIF_RMS_ITEMS; j++) { tokenid = rmsRecords[i].tokens[j]; fieldno = rmsRecords[i].fields[j] ; if (tokenid < 0 || tokenid >= MxTokens || fieldno < 0 || fieldno >= NdbToken[tokenid].NumField) string.Copy(""); else { pCard = _CardInfo[tokenid].Head(); if (pCard == NULL) string.Copy(""); else string.Copy(pCard->Field(fieldno)); } Table->UpdateCell(string, index, irow); index++; } irow++; } } _CifObj->WriteTable(Table, _StructureId, CifCategory[category_id].category); } void _MAXIT::cif_process_revdat() { int i, irow, irow1 = 0, revised_index[4], rowNo, num_index; char buffer[20], value[20]; CifString string; ISTable *Table = NULL, *Table1 = NULL; CIF_CATEGORY *cifcategory1 = NULL; Table = _CifObj->GetTablePtr(_StructureId, "database_PDB_rev_record"); if (!is_empty_table(Table)) return; Table = _CifObj->GetTablePtr(_StructureId, "database_PDB_rev"); if (is_empty_table(Table)) return; rowNo = Table->GetNumRows(); num_index = Table->GetColumnIndex("num"); if (num_index < 0) return; 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"); _CifObj->DeleteTable(_StructureId, "database_PDB_rev_record"); cifcategory1 = find_category("database_PDB_rev_record"); Table1 = create_new_table(cifcategory1); for (irow = 0; irow < rowNo; irow++) { get_value(string, Table, num_index, irow); strcpy(buffer, string.Text()); for (i = 0; i < 4; i++) { if (revised_index[i] < 0) continue; get_value(string, Table, revised_index[i], irow); if (string == "") continue; strcpy(value, string.Text()); string.Copy(""); Table->UpdateCell(string, revised_index[i], irow); Table1->AddRow(); string.Copy(buffer); Table1->UpdateCell(string, 0, irow1); string.Copy(value); Table1->UpdateCell(string, 1, irow1); irow1++; } } _CifObj->WriteTable(Table1, _StructureId, "database_PDB_rev_record"); } int _MAXIT::get_pdb_ndb_ids(const int id_option, CifString ids[3]) { int i, id_idx, code_idx, rowNo, count = 0; CifString string, id; ISTable *Table = NULL; for (i = 0; i < 3; i++) ids[i].Clear(); Table = _CifObj->GetTablePtr(_StructureId, "database_2"); if (is_empty_table(Table)) return count; id_idx = Table->GetColumnIndex("database_id"); code_idx = Table->GetColumnIndex("database_code"); rowNo = Table->GetNumRows(); for (i = 0; i < rowNo; i++) { Table->GetCell(string, id_idx, i); if ((id_option & 1) && (string == "PDB") || (id_option & 2) && (string == "NDB") || (id_option & 4) && (string == "RCSB")) { Table->GetCell(id, code_idx, i); ids[count].Copy(id); count++; } } return count; } static ISTable *create_new_table(CIF_CATEGORY *cifcategory) { ISTable *Table = new ISTable(cifcategory->category); for (int i = 0; i < cifcategory->nkeywords; i++) Table->AddColumn(cifcategory->keywords[i].name); return Table; } static ISTable *create_atom_table(CIF_CATEGORY *cifcategory, const int standardized) { ISTable *Table = new ISTable(cifcategory->category); for (int i = 0; i < cifcategory->nkeywords; i++) { if (standardized && (!strcasecmp(cifcategory->keywords[i].name, "ndb_auth_seq_id") || !strcasecmp(cifcategory->keywords[i].name, "ndb_auth_comp_id") || !strcasecmp(cifcategory->keywords[i].name, "ndb_auth_asym_id") || !strcasecmp(cifcategory->keywords[i].name, "ndb_auth_atom_name") || !strcasecmp(cifcategory->keywords[i].name, "footnote_id"))) continue; Table->AddColumn(cifcategory->keywords[i].name); } return Table; } static void put_atom_to_atom_site(ISTable *Table, CIF_CATEGORY *cifcategory, const int model, const int entity_id, const int card_id, const int format, _ATOM *atom, const int standardized) { int i, row, tmp_id, col; char value[80]; CifString string; row = Table->GetNumRows(); Table->AddRow(); col = 0; for (i = 0; i < cifcategory->nkeywords; i++) { string.Copy(""); if (!strcmp(cifcategory->keywords[i].name, "ndb_model")) { sprintf(value, "%d", model); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "group_PDB")) { if (format == NDB_FILE_FORMAT_PDB) { tmp_id = get_atom_card_id(card_id); string.Copy(AtomInfo[tmp_id].PdbTitle); } else string.Copy(NdbToken[card_id].TokenName); } else if (!strcmp(cifcategory->keywords[i].name, "id")) { sprintf(value, "%d", atom->atnum()); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "type_symbol")) string.Copy(atom->atom_type()); else if (!strcmp(cifcategory->keywords[i].name, "label_atom_id")) string.Copy(atom->atmtype()); else if (!strcmp(cifcategory->keywords[i].name, "label_alt_id")) { string.Copy(atom->alt_loc()); if (string == "?" || string == "") string.Copy("."); } else if (!strcmp(cifcategory->keywords[i].name, "label_comp_id")) string.Copy(atom->restype()); else if (!strcmp(cifcategory->keywords[i].name, "label_asym_id")) string.Copy(atom->chnid()); else if (!strcmp(cifcategory->keywords[i].name, "label_entity_id")) { sprintf(value, "%d", entity_id); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "label_seq_id")) { if (card_id == ATOMP_TOKEN-1 || card_id == ATOMN_TOKEN-1) { sprintf(value, "%d", atom->resnum()); string.Copy(value); } else string.Copy("."); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_label_seq_num")) { sprintf(value, "%d", atom->resnum()); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_ins_code")) string.Copy(atom->ins_code()); else if (!strcmp(cifcategory->keywords[i].name, "Cartn_x")) { sprintf(value, "%8.3f", atom->orig().x); ndb_clean_string(value); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "Cartn_y")) { sprintf(value, "%8.3f", atom->orig().y); ndb_clean_string(value); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "Cartn_z")) { sprintf(value, "%8.3f", atom->orig().z); ndb_clean_string(value); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "occupancy")) { sprintf(value, "%6.2f", atom->occ()); ndb_clean_string(value); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "B_iso_or_equiv")) { sprintf(value, "%6.2f", atom->t_fct()); ndb_clean_string(value); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "Cartn_x_esd")) { if (atom->is_sigatm()) { sprintf(value, "%8.3f", atom->sigatm().sig_x); ndb_clean_string(value); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "Cartn_y_esd")) { if (atom->is_sigatm()) { sprintf(value, "%8.3f", atom->sigatm().sig_y); ndb_clean_string(value); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "Cartn_z_esd")) { if (atom->is_sigatm()) { sprintf(value, "%8.3f", atom->sigatm().sig_z); ndb_clean_string(value); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "occupancy_esd")) { if (atom->is_sigatm()) { sprintf(value, "%6.2f", atom->sigatm().sig_o); ndb_clean_string(value); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "B_iso_or_equiv_esd")) { if (atom->is_sigatm()) { sprintf(value, "%6.2f", atom->sigatm().sig_t); ndb_clean_string(value); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "footnote_id")) { if (standardized) continue; if (atom->footnote() != -10000) { sprintf(value, "%d", atom->footnote()); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "ndb_not_in_asym")) string.Copy(atom->not_in_asym()); else if (!strcmp(cifcategory->keywords[i].name, "auth_seq_id")) { if (strcmp(atom->ins_code(), "")) sprintf(value, "%d%s", atom->pdb_resnum(), atom->ins_code()); else sprintf(value, "%d", atom->pdb_resnum()); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "auth_comp_id")) string.Copy(atom->pdb_resnam()); else if (!strcmp(cifcategory->keywords[i].name, "auth_asym_id")) string.Copy(atom->pdb_chnid()); else if (!strcmp(cifcategory->keywords[i].name, "auth_atom_id")) string.Copy(atom->pdb_atmnam()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_seq_id")) { if (standardized) continue; sprintf(value, "%d", atom->pub_resnum()); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_comp_id")) { if (standardized) continue; string.Copy(atom->pub_resnam()); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_asym_id")) { if (standardized) continue; string.Copy(atom->pub_chnid()); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_atom_name")) { if (standardized) continue; string.Copy(atom->pub_atmnam()); } Table->UpdateCell(string, col, row); col++; } } static void put_atom_to_atom_site_anisotrop(ISTable *Table, CIF_CATEGORY *cifcategory, _ATOM *atom, int &row, const int card_id) { int i; char value[80]; CifString string; Table->AddRow(); row++; for (i = 0; i < cifcategory->nkeywords; i++) { string.Copy(""); if (!strcmp(cifcategory->keywords[i].name, "id")) { sprintf(value, "%d", atom->atnum()); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "type_symbol")) string.Copy(atom->atom_type()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_label_atom_id")) string.Copy(atom->atmtype()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_label_alt_id")) string.Copy(atom->alt_loc()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_label_comp_id")) string.Copy(atom->restype()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_label_asym_id")) string.Copy(atom->chnid()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_label_seq_num")) { if (card_id == ATOMP_TOKEN-1 || card_id == ATOMN_TOKEN-1) { sprintf(value, "%d", atom->resnum()); string.Copy(value); } else string.Copy("."); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_label_ins_code")) string.Copy(atom->ins_code()); else if (!strcmp(cifcategory->keywords[i].name, "U[1][1]")) { sprintf(value, "%.4f", atom->anisou().u11 / 10000.0); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "U[1][2]")) { sprintf(value, "%.4f", atom->anisou().u12 / 10000.0); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "U[1][3]")) { sprintf(value, "%.4f", atom->anisou().u13 / 10000.0); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "U[2][2]")) { sprintf(value, "%.4f", atom->anisou().u22 / 10000.0); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "U[2][3]")) { sprintf(value, "%.4f", atom->anisou().u23 / 10000.0); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "U[3][3]")) { sprintf(value, "%.4f", atom->anisou().u33 / 10000.0); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "U[1][1]_esd")) { if (atom->is_siguij()) { sprintf(value, "%.4f", atom->siguij().sig_u11 / 10000.0); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "U[1][2]_esd")) { if (atom->is_siguij()) { sprintf(value, "%.4f", atom->siguij().sig_u12 / 10000.0); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "U[1][3]_esd")) { if (atom->is_siguij()) { sprintf(value, "%.4f", atom->siguij().sig_u13 / 10000.0); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "U[2][2]_esd")) { if (atom->is_siguij()) { sprintf(value, "%.4f", atom->siguij().sig_u22 / 10000.0); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "U[2][3]_esd")) { if (atom->is_siguij()) { sprintf(value, "%.4f", atom->siguij().sig_u23 / 10000.0); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "U[3][3]_esd")) { if (atom->is_siguij()) { sprintf(value, "%.4f", atom->siguij().sig_u33 / 10000.0); string.Copy(value); } } else if (!strcmp(cifcategory->keywords[i].name, "ndb_not_in_asym")) string.Copy(atom->not_in_asym()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_PDB_residue_no")) { if (strcmp(atom->ins_code(), "")) sprintf(value, "%d%s", atom->pdb_resnum(), atom->ins_code()); else sprintf(value, "%d", atom->pdb_resnum()); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_PDB_residue_name")) string.Copy(atom->pdb_resnam()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_PDB_strand_id")) string.Copy(atom->pdb_chnid()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_PDB_atom_name")) string.Copy(atom->pdb_atmnam()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_seq_id")) { sprintf(value, "%d", atom->pub_resnum()); string.Copy(value); } else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_comp_id")) string.Copy(atom->pub_resnam()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_asym_id")) string.Copy(atom->pub_chnid()); else if (!strcmp(cifcategory->keywords[i].name, "ndb_auth_atom_name")) string.Copy(atom->pub_atmnam()); Table->UpdateCell(string, i, row-1); } } static int Insert_Struct_Conf(ISTable *Table, int &nrow, _CHAIN *chain, const char *type, const char *ID, const int fst, const int snd, const char *clas, const char *comment, const int category_id, const int serial_no) { int l; char value[50]; CifString string; _FIELD *Fst = chain->SeqResIndex(fst); _FIELD *Snd = chain->SeqResIndex(snd); if (!Fst || !Snd) return 0; Table->AddRow(); for (l = 0; l < CifCategory[category_id].nkeywords; l++) { string.Copy(""); if (!strcasecmp(CifCategory[category_id].keywords[l].name, "conf_type_id")) { string.Copy(type); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "id")) { sprintf(value, "%s%d", type, serial_no); string.Copy(value); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "pdb_id")) { string.Copy(ID); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "beg_label_comp_id")) { string.Copy(Fst->Field[0]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "beg_label_asym_id")) { string.Copy(chain->ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "beg_label_seq_id")) { string.Copy(Fst->Field[2]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ndb_beg_label_ins_code_pdb")) { string.Copy(Fst->InsCode); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "end_label_comp_id")) { string.Copy(Snd->Field[0]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "end_label_asym_id")) { string.Copy(chain->ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "end_label_seq_id")) { string.Copy(Snd->Field[2]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ndb_end_label_ins_code_pdb")) { string.Copy(Snd->InsCode); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "beg_auth_comp_id")) { string.Copy(Fst->Field[3]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "beg_auth_asym_id")) { string.Copy(chain->PDB_ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "beg_auth_seq_id")) { if (strcmp(Fst->InsCode, "")) { sprintf(value, "%s%s", Fst->Field[4], Fst->InsCode); string.Copy(value); } else string.Copy(Fst->Field[4]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "end_auth_comp_id")) { string.Copy(Snd->Field[3]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "end_auth_asym_id")) { string.Copy(chain->PDB_ChainID()); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "end_auth_seq_id")) { if (strcmp(Snd->InsCode, "")) { sprintf(value, "%s%s", Snd->Field[4], Snd->InsCode); string.Copy(value); } else string.Copy(Snd->Field[4]); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ndb_helix_class_pdb")) { string.Copy(clas); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "details")) { string.Copy(comment); } else if (!strcasecmp(CifCategory[category_id].keywords[l].name, "ndb_length")) { if (!strcmp(type, "HELX_P")) { sprintf(value, "%d", snd - fst + 1); string.Copy(value); } } Table->UpdateCell(string, l, nrow); } nrow++; return 1; } static void Insert_Sheet_Range(ISTable *Table, int &nrow, _CHAIN *chain, const char *sheetID, const int initRes, const int endRes, const int id, CIF_CATEGORY *category) { int l; char value[50]; CifString string; _FIELD *Init = chain->SeqResIndex(initRes); _FIELD *End = chain->SeqResIndex(endRes); if (!Init || !End) return; Table->AddRow(); for (l = 0; l < category->nkeywords; l++) { string.Copy(""); if (!strcasecmp(category->keywords[l].name, "sheet_id")) { string.Copy(sheetID); } else if (!strcasecmp(category->keywords[l].name, "id")) { sprintf(value, "%d", id); string.Copy(value); } else if (!strcasecmp(category->keywords[l].name, "beg_label_comp_id")) { string.Copy(Init->Field[0]); } else if (!strcasecmp(category->keywords[l].name, "beg_label_asym_id")) { string.Copy(chain->ChainID()); } else if (!strcasecmp(category->keywords[l].name, "beg_label_seq_id")) { string.Copy(Init->Field[2]); } else if (!strcasecmp(category->keywords[l].name, "ndb_beg_label_ins_code_pdb")) { string.Copy(Init->InsCode); } else if (!strcasecmp(category->keywords[l].name, "end_label_comp_id")) { string.Copy(End->Field[0]); } else if (!strcasecmp(category->keywords[l].name, "end_label_asym_id")) { string.Copy(chain->ChainID()); } else if (!strcasecmp(category->keywords[l].name, "end_label_seq_id")) { string.Copy(End->Field[2]); } else if (!strcasecmp(category->keywords[l].name, "ndb_end_label_ins_code_pdb")) { string.Copy(End->InsCode); } else if (!strcasecmp(category->keywords[l].name, "beg_auth_comp_id")) { string.Copy(Init->Field[3]); } else if (!strcasecmp(category->keywords[l].name, "beg_auth_asym_id")) { string.Copy(chain->PDB_ChainID()); } else if (!strcasecmp(category->keywords[l].name, "beg_auth_seq_id")) { if (strcmp(Init->InsCode, "")) { sprintf(value, "%s%s", Init->Field[4], Init->InsCode); string.Copy(value); } else string.Copy(Init->Field[4]); } else if (!strcasecmp(category->keywords[l].name, "end_auth_comp_id")) { string.Copy(End->Field[3]); } else if (!strcasecmp(category->keywords[l].name, "end_auth_asym_id")) { string.Copy(chain->PDB_ChainID()); } else if (!strcasecmp(category->keywords[l].name, "end_auth_seq_id")) { if (strcmp(End->InsCode, "")) { sprintf(value, "%s%s", End->Field[4], End->InsCode); string.Copy(value); } else string.Copy(End->Field[4]); } Table->UpdateCell(string, l, nrow); } nrow++; } static void Insert_Sheet_Hbond(ISTable *Table, int &nrow, _CHAIN *curchain, _CHAIN *prevchain, const char *sheetID, const char *curAtom, const int curRes, const char *prevAtom, const int prevRes, const int id, CIF_CATEGORY *ctg) { int l; char value[50]; CifString string; _FIELD *Cur = curchain->SeqResIndex(curRes); _FIELD *Prev = prevchain->SeqResIndex(prevRes); if (!Cur || !Prev || !strcmp(curAtom, "") || !strcmp(prevAtom, "")) return; Table->AddRow(); for (l = 0; l < ctg->nkeywords; l++) { string.Copy(""); if (!strcasecmp(ctg->keywords[l].name, "sheet_id")) { string.Copy(sheetID); } else if (!strcasecmp(ctg->keywords[l].name, "range_id_1")) { sprintf(value, "%d", id-1); string.Copy(value); } else if (!strcasecmp(ctg->keywords[l].name, "range_id_2")) { sprintf(value, "%d", id); string.Copy(value); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_label_atom_id")) { string.Copy(curAtom); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_label_comp_id")) { string.Copy(Cur->Field[0]); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_label_asym_id")) { string.Copy(curchain->ChainID()); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_label_seq_id")) { string.Copy(Cur->Field[2]); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_PDB_ins_code")) { string.Copy(Cur->InsCode); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_auth_atom_id")) { string.Copy(curAtom); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_auth_comp_id")) { string.Copy(Cur->Field[3]); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_auth_asym_id")) { string.Copy(curchain->PDB_ChainID()); } else if (!strcasecmp(ctg->keywords[l].name, "range_2_auth_seq_id")) { if (strcmp(Cur->InsCode, "")) { sprintf(value, "%s%s", Cur->Field[4], Cur->InsCode); string.Copy(value); } else string.Copy(Cur->Field[4]); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_label_atom_id")) { string.Copy(prevAtom); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_label_comp_id")) { string.Copy(Prev->Field[0]); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_label_asym_id")) { string.Copy(prevchain->ChainID()); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_label_seq_id")) { string.Copy(Prev->Field[2]); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_PDB_ins_code")) { string.Copy(Prev->InsCode); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_auth_atom_id")) { string.Copy(prevAtom); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_auth_comp_id")) { string.Copy(Prev->Field[3]); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_auth_asym_id")) { string.Copy(prevchain->PDB_ChainID()); } else if (!strcasecmp(ctg->keywords[l].name, "range_1_auth_seq_id")) { if (strcmp(Prev->InsCode, "")) { sprintf(value, "%s%s", Prev->Field[4], Prev->InsCode); string.Copy(value); } else string.Copy(Prev->Field[4]); } Table->UpdateCell(string, l, nrow); } nrow++; } static int Insert_Struct_Conn(ISTable *Table, int &nrow, const char *type, const char *PDB_id, const char *mod_name, const char *sugar_name, const char *atom_id, const char *standard_id, _CHAIN *fst_chain, const char *fst_atom, const char *fst_loc, const int fst, const char *sym_op1, _CHAIN *snd_chain, const char *snd_atom, const char *snd_loc, const int snd, const char *sym_op2, _CHAIN *trd_chain, const char *trd_atom, const char *trd_loc, const int trd, const char *comment, const int id, const int serial_no) { int l; char value[50]; CifString string; _FIELD *Fst = NULL; _FIELD *Snd = NULL; _FIELD *Trd = NULL; if (fst_chain) Fst = fst_chain->SeqResIndex(fst); if (snd_chain) Snd = snd_chain->SeqResIndex(snd); if (trd_chain) Trd = trd_chain->SeqResIndex(trd); if (!Fst && !Snd && !Trd) return 0; Table->AddRow(); for (l = 0; l < CifCategory[id].nkeywords; l++) { string.Copy(""); if (!strcasecmp(CifCategory[id].keywords[l].name, "conn_type_id")) { string.Copy(type); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "id")) { sprintf(value, "%s%d", type, serial_no); string.Copy(value); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_PDB_id")) { string.Copy(PDB_id); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr1_mod_name")) { string.Copy(mod_name); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr1_sugar_name")) { string.Copy(sugar_name); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr1_replaced_atom")) { string.Copy(atom_id); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_label_comp_id")) { string.Copy(Fst->Field[0]); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_label_asym_id")) { string.Copy(fst_chain->ChainID()); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_label_seq_id")) { if (fst_chain->chain_type() == ATOMP_TOKEN || fst_chain->chain_type() == ATOMN_TOKEN) string.Copy(Fst->Field[2]); else string.Copy("."); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr1_label_ins_code")) { string.Copy(Fst->InsCode); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_label_atom_id")) { string.Copy(fst_atom); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr1_label_alt_loc")) { string.Copy(fst_loc); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_symmetry")) { if (strcmp(sym_op1, "")) string.Copy(sym_op1); else string.Copy("1_555"); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr1_standard_comp_id")) { string.Copy(standard_id); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_label_comp_id")) { if (Snd) string.Copy(Snd->Field[0]); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_label_asym_id")) { if (snd_chain) string.Copy(snd_chain->ChainID()); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_label_seq_id")) { if (Snd) { if (snd_chain->chain_type() == ATOMP_TOKEN || snd_chain->chain_type() == ATOMN_TOKEN) string.Copy(Snd->Field[2]); else string.Copy("."); } } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr2_label_ins_code")) { if (Snd) string.Copy(Snd->InsCode); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_label_atom_id")) { string.Copy(snd_atom); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr2_label_alt_loc")) { string.Copy(snd_loc); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_symmetry")) { if (strcmp(sym_op2, "")) string.Copy(sym_op2); else string.Copy("1_555"); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_auth_comp_id")) { string.Copy(Fst->Field[3]); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_auth_asym_id")) { string.Copy(fst_chain->PDB_ChainID()); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr1_auth_seq_id")) { if (strcmp(Fst->InsCode, "")) { sprintf(value, "%s%s", Fst->Field[4], Fst->InsCode); string.Copy(value); } else string.Copy(Fst->Field[4]); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_auth_comp_id")) { if (Snd) string.Copy(Snd->Field[3]); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_auth_asym_id")) { if (snd_chain) string.Copy(snd_chain->PDB_ChainID()); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ptnr2_auth_seq_id")) { if (Snd) { if (strcmp(Snd->InsCode, "")) { sprintf(value, "%s%s", Snd->Field[4], Snd->InsCode); string.Copy(value); } else string.Copy(Snd->Field[4]); } } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr3_label_atom_id")) { string.Copy(trd_atom); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr3_label_seq_id")) { if (Trd) string.Copy(Trd->Field[2]); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr3_label_asym_id")) { if (trd_chain) string.Copy(trd_chain->ChainID()); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr3_label_alt_loc")) { string.Copy(trd_loc); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "ndb_ptnr3_label_ins_code")) { if (Trd) string.Copy(Trd->InsCode); } else if (!strcasecmp(CifCategory[id].keywords[l].name, "details")) { if (comment) string.Copy(comment); } Table->UpdateCell(string, l, nrow); } nrow++; return 1; } static int pdb_rev_compare(const void *a, const void *b) { return (((PDB_REV *) a)->num - ((PDB_REV *) b)->num); } void _MAXIT::cif_layer1_to_layer2_revdat() { int i, database_id, database_code, rowNo; char PDB_ID[10], value[20]; CifString cifstring; ISTable *Table = NULL, *Table1 = NULL, *tmpTable = NULL; CIF_CATEGORY *cifcategory = NULL; Table = _CifObj->GetTablePtr(_StructureId, "database_PDB_rev"); if (Table == NULL) { cifcategory = find_category("database_PDB_rev"); Table = create_new_table(cifcategory); _CifObj->WriteTable(Table, _StructureId, "database_PDB_rev"); } Table1 = _CifObj->GetTablePtr(_StructureId, "database_PDB_rev_record"); if (Table1 == NULL) { cifcategory = find_category("database_PDB_rev_record"); Table1 = create_new_table(cifcategory); _CifObj->WriteTable(Table1, _StructureId, "database_PDB_rev_record"); } strcpy(PDB_ID, ""); tmpTable = _CifObj->GetTablePtr(_StructureId, "database_2"); if (!is_empty_table(tmpTable)) { database_id = tmpTable->GetColumnIndex("database_id"); database_code = tmpTable->GetColumnIndex("database_code"); rowNo = tmpTable->GetNumRows(); for (i = 0; i < rowNo; i++) { get_value(cifstring, tmpTable, database_id, i); if (cifstring == "PDB") { get_value(cifstring, tmpTable, database_code, i); strcpy(PDB_ID, cifstring.Text()); break; } } } int num = Table->GetNumRows(); int num_index = Table->GetColumnIndex("num"); int date_index = Table->GetColumnIndex("date"); int replaces_index = Table->GetColumnIndex("replaces"); int type_index = Table->GetColumnIndex("mod_type"); Table->AddRow(); sprintf(value, "%d", num+1); cifstring.Copy(value); Table->UpdateCell(cifstring, num_index, num); cifstring.Copy("2000-01-12"); Table->UpdateCell(cifstring, date_index, num); cifstring.Copy(PDB_ID); Table->UpdateCell(cifstring, replaces_index, num); cifstring.Copy("4"); Table->UpdateCell(cifstring, type_index, num); char changes[7][8] = { "HEADER", "COMPND", "REMARK", "JRNL", "ATOM", "SOURCE", "SEQRES" }; int irow = Table1->GetNumRows(); num_index = Table1->GetColumnIndex("rev_num"); type_index = Table1->GetColumnIndex("type"); for (i = 0; i < 7; i++) { Table1->AddRow(); sprintf(value, "%d", num+1); cifstring.Copy(value); Table1->UpdateCell(cifstring, num_index, irow); cifstring.Copy(changes[i]); Table1->UpdateCell(cifstring, type_index, irow); irow++; } Table = _CifObj->GetTablePtr(_StructureId, "ndb_database_status"); if (is_empty_table(Table)) return; int status_code = Table->GetColumnIndex("status_code"); if (status_code < 0) return; get_value(cifstring, Table, status_code, 0); if (cifstring == "" || !strcasecmp(cifstring.Text() , "PROC")) { cifstring.Copy("REL"); Table->UpdateCell(cifstring, status_code, 0); } }