/* FILE: ndb_atlas.C */ /* VERSION: 1.600 */ /* DATE: 2/3/2005 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. The user of this software shall indemnify, hold harmless and defend Rutgers, its governors, trustees, officers, employees, students, agents and the authors against any and all claims, suits, losses, liabilities, damages, costs, fees, and expenses including reasonable attorneys' fees resulting from or arising out of the use of this software. This indemnification shall include, but is not limited to, any and all claims alleging products liability. */ /* PDB SOFTWARE LICENSE AGREEMENT BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS BECOMING A PARTY TO THIS AGREEMENT. IF LICENSEE DOES NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE. 1. LICENSE AGREEMENT This is a license between you ("Licensee") and the Protein Data Bank (PDB) at Rutgers, The State University of New Jersey (hereafter referred to as "RUTGERS"). The software is owned by RUTGERS and protected by copyright laws, and some elements are protected by laws governing trademarks, trade dress and trade secrets, and may be protected by patent laws. 2. LICENSE GRANT RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, and distribute in binary and source code format, or any derivative work thereof, together with any associated media, printed materials, and on-line or electronic documentation (if any) provided by RUTGERS (collectively, the "SOFTWARE"), subject to the following terms and conditions: (i) any distribution of the SOFTWARE shall bind the receiver to the terms and conditions of this Agreement; (ii) any distribution of the SOFTWARE in modified form shall clearly state that the SOFTWARE has been modified from the version originally obtained from RUTGERS. 2. COPYRIGHT; RETENTION OF RIGHTS. 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Title and related rights in the content accessed through the SOFTWARE is the property of the applicable content owner and is protected by applicable law. The license granted under this Agreement gives Licensee no rights to such content. 7. DISCLAIMER OF WARRANTY. THE SOFTWARE IS PROVIDED FREE OF CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE. SHOULD THE SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS AGREEMENT. NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER. 8. LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. */ #include #include #include #include #include #include #include "_validation.h" #include "erf_util.h" #include "util.h" #include "ndb_atlas.h" #include "ndb_misclib.h" static void write_text_part(FILE *fp, ATLAS_TEXT *text, const int is_prev_check, const int experiment_type); static void get_citation_val(CifString &buff, One_Card_Info_Format *Head, const int serial_no, const int field_no); static int get_multiple_rows(One_Card_Info_Format *Head, const int field_no, const int serial_no, const int value, CifString &res); static void add_superscripts(char *modifier_st, char *buff, const int isindex); static void correct_string(char *string); static REFN *get_refn(CifString &authors, CifString &title, CifString &jrnl, CifString &volume, CifString &first_page, CifString &last_page, CifString &year); static CRYS *get_crys(CifString &method, CifString &drop, CifString &reservoir, CifString &soaking); void _VALIDATION::ndb_write_atlas_entries(char *File_ID, const int is_prev_check) { char fname[160]; char small_sid[160]; strcpy(small_sid, _StructureId); ndb_clean_string(small_sid); lowercased(small_sid); char pdb_id[20]; pdb_id[0] = '\0'; if (_CardInfo[PDBFIL_TOKEN-1].Head() && strcmp(_CardInfo[PDBFIL_TOKEN-1].Head()->Field(1), "")) strcpy(pdb_id, _CardInfo[PDBFIL_TOKEN-1].Head()->Field(1)); ATLAS_TEXT *atlas_text = get_atlas_text(_StructureId, pdb_id); sprintf(fname, "%s.html", File_ID); FILE *fp_entry = fopen(fname, "w"); sprintf(fname, "RCSB Atlas Entry for Structure %s", small_sid); html_atlas_preamble(fp_entry, fname); write_text_part(fp_entry, atlas_text, is_prev_check, _experiment_type); // html_atlas_trailer(fp_entry); fclose(fp_entry); delete [] atlas_text->struct_features; delete [] atlas_text->compound_name; for (int i = 0; i < atlas_text->Num_seqs; i++) delete [] atlas_text->seqs[i]; delete [] atlas_text->seqs; if (atlas_text->refn) { if (atlas_text->refn->author) delete [] atlas_text->refn->author; if (atlas_text->refn->title) delete [] atlas_text->refn->title; if (atlas_text->refn->refn) delete [] atlas_text->refn->refn; delete atlas_text->refn; } if (atlas_text->crys) { if (atlas_text->crys->method) delete [] atlas_text->crys->method; if (atlas_text->crys->drop) delete [] atlas_text->crys->drop; if (atlas_text->crys->reservoir) delete [] atlas_text->crys->reservoir; if (atlas_text->crys->soaking) delete [] atlas_text->crys->soaking; delete atlas_text->crys; } delete [] atlas_text->refinement; delete atlas_text; } ATLAS_TEXT* _VALIDATION::get_atlas_text(const char *sid, const char *pdb_id) { int len, i, j, commas, index, jrnl_id, name_index, Serial_No; char buffer[BIGSTRING], *stmpt = NULL; CifString buff, tmp_buff, authors, title, jrnl, volume, first_page, year; CifString last_page, program, rvalue, reflections, high, low, sigmaF; FILE *fp = NULL; One_Card_Info_Format *pJrnlCard = NULL; ISTable *Table = NULL; ATLAS_TEXT *atlas_text = new ATLAS_TEXT; atlas_text->struct_features = NULL; atlas_text->compound_name = NULL; atlas_text->Num_seqs = 0; atlas_text->isComplex = 0; atlas_text->seqs = NULL; atlas_text->refn = NULL; atlas_text->crys = NULL; atlas_text->refinement = NULL; atlas_text->struct_id[0] = '\0'; atlas_text->spacegroup[0] = '\0'; atlas_text->cell[0] = '\0'; if (pdb_id[0] != '\0') sprintf(atlas_text->struct_id, "RCSB ID: %s PDB ID: %s", sid, pdb_id); else sprintf(atlas_text->struct_id, "RCSB ID: %s", sid); get_classification_st(buff, atlas_text->isComplex); if (buff != "") { atlas_text->struct_features = new char[strlen(buff.Text())+1]; strcpy(atlas_text->struct_features, buff.Text()); } get_name_st(buff, tmp_buff); if (buff != "") { if (tmp_buff != "") { len = strlen(buff.Text()) + strlen(tmp_buff.Text()) + 20; atlas_text->compound_name = new char[len]; commas = get_ncommas(tmp_buff.Text()); sprintf(atlas_text->compound_name, "%s\n
\nModifier%s: %s\n", buff.Text(), commas ? "s" : "", tmp_buff.Text()); } else { len = strlen(buff.Text()) + 5; atlas_text->compound_name = new char[len]; sprintf(atlas_text->compound_name, "%s\n", buff.Text()); } } if (_Num_Seqs) { fp = fopen("SEQUENCE.DAT", "w"); atlas_text->Num_seqs = _Num_Seqs; atlas_text->seqs = new char*[_Num_Seqs]; for (i = 0; i < _Num_Seqs; i++) { buff.Copy("Chain "); buff += _Seqs[i]->ChainId; buff += ": "; tmp_buff.Copy(_Seqs[i]->ChainId); tmp_buff += " "; len = strlen(buff.Text()); for (j = 0; j < _Seqs[i]->SeqLen; j++) { stmpt = get_oneletter_code(_Seqs[i]->res[j]->name); if (strlen(_Seqs[i]->res[j]->name) == 3 && strlen(stmpt) == 1) tmp_buff += stmpt; if (len >= 54) { if (strlen(stmpt) == 1) { buff += stmpt; buff += "
\n"; } else { buff += "("; buff += stmpt; buff += ")
\n"; } len = 0; } else { if (strlen(stmpt) == 1) buff += stmpt; else { buff += "("; buff += stmpt; buff += ")"; } len += strlen(stmpt); } } if (strlen(tmp_buff.Text()) > 4) fprintf(fp, "%s\n", tmp_buff.Text()); atlas_text->seqs[i] = new char[strlen(buff.Text())+1]; strcpy(atlas_text->seqs[i], buff.Text()); } fclose (fp); } jrnl_id = find_jrnl_id("TITL"); pJrnlCard = _JrnlCardInfo[jrnl_id].Head(); Serial_No = 0; while (pJrnlCard) { if (strcmp(pJrnlCard->Field(4), "")) { Serial_No = atoi(pJrnlCard->Field(1)); break; } pJrnlCard = pJrnlCard->Next(); } authors.Clear(); title.Clear(); jrnl.Clear(); volume.Clear(); first_page.Clear(); last_page.Clear(); year.Clear(); if (pJrnlCard) { jrnl_id = find_jrnl_id("AUTH"); get_citation_val(authors, _JrnlCardInfo[jrnl_id].Head(), Serial_No, 5); jrnl_id = find_jrnl_id("TITL"); get_citation_val(title, _JrnlCardInfo[jrnl_id].Head(), Serial_No, 5); jrnl_id = find_jrnl_id("REF"); get_citation_val(jrnl, _JrnlCardInfo[jrnl_id].Head(), Serial_No, 5); get_citation_val(volume, _JrnlCardInfo[jrnl_id].Head(), Serial_No, 7); get_citation_val(first_page, _JrnlCardInfo[jrnl_id].Head(), Serial_No, 8); get_citation_val(last_page, _JrnlCardInfo[jrnl_id].Head(), Serial_No, 10); get_citation_val(year, _JrnlCardInfo[jrnl_id].Head(), Serial_No, 9); } else if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "citation"); if (!is_empty_table(Table)) { jrnl_id = Table->GetColumnIndex("title"); get_value(title, Table, jrnl_id, 0); jrnl_id = Table->GetColumnIndex("journal_abbrev"); get_value(jrnl, Table, jrnl_id, 0); jrnl_id = Table->GetColumnIndex("journal_volume"); get_value(volume, Table, jrnl_id, 0); jrnl_id = Table->GetColumnIndex("page_first"); get_value(first_page, Table, jrnl_id, 0); jrnl_id = Table->GetColumnIndex("page_last"); get_value(last_page, Table, jrnl_id, 0); jrnl_id = Table->GetColumnIndex("year"); get_value(year, Table, jrnl_id, 0); jrnl_id = Table->GetColumnIndex("id"); get_value(tmp_buff, Table, jrnl_id, 0); authors.Clear(); Table = _CifObj->GetTablePtr(_StructureId, "citation_author"); if (!is_empty_table(Table)) { name_index = Table->GetColumnIndex("name"); jrnl_id = Table->GetColumnIndex("citation_id"); len = Table->GetNumRows(); for (i = 0; i < len; i++) { Table->GetCell(buff, jrnl_id, i); if (buff != tmp_buff) continue; get_value(buff, Table, name_index, i); if (buff == "") continue; strcpy(buffer, buff.Text()); ndb_name_conversion_first_last(buffer); if (authors != "") authors += ", "; authors += buffer; } } } } atlas_text->refn = get_refn(authors, title, jrnl, volume, first_page, last_page, year); if (_cell && !_cell->is_artifical) { strcpy(buffer, _cell->space_group); if (buffer[0] != '\0') strcpy(atlas_text->spacegroup, map_space_group(buffer)); sprintf(atlas_text->cell, "
\n%6s = %7.2lf %6s = %7.2lf %6s = %7.2lf (Ångstroms)\n",
                "A", _cell->a, "B", _cell->b, "C", _cell->c);
            int len = strlen(atlas_text->cell);
            sprintf(&atlas_text->cell[len],
                "%6s = %7.2lf %6s = %7.2lf %6s = %7.2lf (degrees)\n
\n", "alpha", _cell->alpha, "beta", _cell->beta, "gamma", _cell->gamma); } authors.Clear(); title.Clear(); jrnl.Clear(); volume.Clear(); if (_CardInfo[CRMETH_TOKEN-1].Head() || _CardInfo[CRSOLU_TOKEN-1].Head()) { if (_CardInfo[CRMETH_TOKEN-1].Head() && strcmp(_CardInfo[CRMETH_TOKEN-1].Head()->Field(2), "")) { sprintf(buffer, "METHOD: %s", _CardInfo[CRMETH_TOKEN-1].Head()->Field(2)); ndb_set_string_to_mixed(buffer); authors.Copy(buffer); } if (_CardInfo[CRSOLU_TOKEN-1].Head()) { get_multiple_rows(_CardInfo[CRSOLU_TOKEN-1].Head(), 4, 3, 1, title); get_multiple_rows(_CardInfo[CRSOLU_TOKEN-1].Head(), 4, 3, 2, jrnl); get_multiple_rows(_CardInfo[CRSOLU_TOKEN-1].Head(), 4, 3, 3, volume); } } else if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "exptl_crystal_grow"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("method"); get_value(authors, Table, index, 0); if (authors != "") { sprintf(buffer, "METHOD: %s", authors.Text()); ndb_set_string_to_mixed(buffer); authors.Copy(buffer); } } Table = _CifObj->GetTablePtr(_StructureId, "exptl_crystal_grow_comp"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("sol_id"); name_index = Table->GetColumnIndex("name"); len = Table->GetNumRows(); for (i = 0; i < len; i++) { get_value(buff, Table, index, i); get_value(tmp_buff, Table, name_index, i); if (tmp_buff != "") { tmp_buff.ToLower(); strcpy(buffer, tmp_buff.Text()); map_solution_case(buffer); if (buff == "1") { title += buffer; title += ", "; } else if (buff == "2") { jrnl += buffer; jrnl += ", "; } else if (buff == "3") { volume += buffer; volume += ", "; } } } if (title != "") { strcpy(buffer, title.Text()); correct_string(buffer); title.Copy(buffer); } if (jrnl != "") { strcpy(buffer, jrnl.Text()); correct_string(buffer); jrnl.Copy(buffer); } if (volume != "") { strcpy(buffer, volume.Text()); correct_string(buffer); volume.Copy(buffer); } } } atlas_text->crys = get_crys(authors, title, jrnl, volume); if (!(_experiment_type & EXPERIMENT_TYPE_NMR)) { program.Clear(); rvalue.Clear(); reflections.Clear(); high.Clear(); low.Clear(); sigmaF.Clear(); if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "refine"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("ls_R_factor_obs"); get_value(rvalue, Table, index, 0); if (rvalue == "") { index = Table->GetColumnIndex("ls_R_factor_R_work"); get_value(rvalue, Table, index, 0); } if (rvalue == "") { index = Table->GetColumnIndex("ls_R_factor_all"); get_value(rvalue, Table, index, 0); } if (rvalue != "") { float r = atof(rvalue.Text()); sprintf(buffer, "%.3f", r * 100.0); rvalue.Copy(buffer); } index = Table->GetColumnIndex("ls_number_reflns_obs"); get_value(reflections, Table, index, 0); index = Table->GetColumnIndex("ls_d_res_low"); get_value(low, Table, index, 0); index = Table->GetColumnIndex("ls_d_res_high"); get_value(high, Table, index, 0); index = Table->GetColumnIndex("ndb_ls_sigma_F"); get_value(sigmaF, Table, index, 0); } Table = _CifObj->GetTablePtr(_StructureId, "computing"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("structure_refinement"); get_value(program, Table, index, 0); } } else { if (_CardInfo[REFMET_TOKEN-1].Head() && strcmp(_CardInfo[REFMET_TOKEN-1].Head()->Field(3), "")) program.Copy(_CardInfo[REFMET_TOKEN-1].Head()->Field(3)); if (_CardInfo[RFACTR_TOKEN-1].Head()) { if (strcmp(_CardInfo[RFACTR_TOKEN-1].Head()->Field(7), "")) rvalue.Copy(_CardInfo[RFACTR_TOKEN-1].Head()->Field(7)); else if (strcmp(_CardInfo[RFACTR_TOKEN-1].Head()->Field(10), "")) rvalue.Copy(_CardInfo[RFACTR_TOKEN-1].Head()->Field(10)); else if (strcmp(_CardInfo[RFACTR_TOKEN-1].Head()->Field(8), "")) rvalue.Copy(_CardInfo[RFACTR_TOKEN-1].Head()->Field(8)); if (strcmp(_CardInfo[RFACTR_TOKEN-1].Head()->Field(2), "")) reflections.Copy(_CardInfo[RFACTR_TOKEN-1].Head()->Field(2)); if (strcmp(_CardInfo[RFACTR_TOKEN-1].Head()->Field(5), "")) low.Copy(_CardInfo[RFACTR_TOKEN-1].Head()->Field(5)); if (strcmp(_CardInfo[RFACTR_TOKEN-1].Head()->Field(6), "")) high.Copy(_CardInfo[RFACTR_TOKEN-1].Head()->Field(6)); if (strcmp(_CardInfo[RFACTR_TOKEN-1].Head()->Field(4), "")) sigmaF.Copy(_CardInfo[RFACTR_TOKEN-1].Head()->Field(4)); } } buff.Clear(); if (program != "") { buff += "The structure was refined using the "; buff += program; buff += " program. "; } len = 0; if (rvalue != "") { buff += "The R value is "; buff += rvalue; len = 1; } if (reflections != "") { buff += " for "; buff += reflections; buff += " reflections"; len = 1; } if (low != "" && high != "") { if (len) buff += "\n"; buff += " in the resolution range "; buff += low; buff += " to "; buff += high; buff += " Å"; len = 1; } else if (high != "") { if (len) buff += "\n"; buff += "to a resolution of "; buff += high; buff += " Å"; len = 1; } if (sigmaF != "") { buff += " with Fobs > "; buff += sigmaF; buff += " sigma (Fobs)"; len = 1; } if (len) buff += "."; if (buff != "") { atlas_text->refinement = new char[strlen(buff.Text())+1]; strcpy(atlas_text->refinement, buff.Text()); } } return atlas_text; } void _VALIDATION::get_name_st(CifString &name, CifString &modifier_st) { int i, j, hit = 0, drugsYN, modifiedYN, index, rowNo, STRUCT_TOKEN; char st1[25], ch, st2[25], buff[BIGSTRING], *stpt = NULL; char conformation_type[BIGSTRING], buffer[BIGSTRING]; CifString cifstring; ISTable *Table = NULL; name.Clear(); modifier_st.Clear(); memset(buff, '\0', BIGSTRING); memset(buffer, '\0', BIGSTRING); memset(conformation_type, '\0', BIGSTRING); STRUCT_TOKEN = find_card_id("STRUCT"); if (_CardInfo[STRUCT_TOKEN].Head()) strcpy(conformation_type, _CardInfo[STRUCT_TOKEN].Head()->Field(1)); else if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "ndb_na_struct_keywds"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("conformation_type"); get_value(cifstring, Table, index, 0); if (cifstring != "") strcpy(conformation_type, cifstring.Text()); } } drugsYN = (_CardInfo[DCHEM_TOKEN-1].Head() != NULL); if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "ndb_drug_info"); if (!is_empty_table(Table)) drugsYN = 1; } buff[0] = '\0'; if (_CardInfo[COMPND_TOKEN-1].Head() && strcmp(_CardInfo[COMPND_TOKEN-1].Head()->Field(2), "")) { strcpy(buff, _CardInfo[COMPND_TOKEN-1].Head()->Field(2)); } modifiedYN = 0; if (_CardInfo[MODIFB_TOKEN-1].Head() || _CardInfo[MODIFP_TOKEN-1].Head() || _CardInfo[MODIFS_TOKEN-1].Head()) modifiedYN = 1; else if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "struct_conn_type"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("id"); rowNo = Table->GetNumRows(); for (i = 0; i < rowNo; i++) { Table->GetCell(cifstring, index, i); if (!strcasecmp(cifstring.Text(), "covale_base") || !strcasecmp(cifstring.Text(), "covale_sugar") || !strcasecmp(cifstring.Text(), "covale_phosphate")) { modifiedYN = 1; break; } } } } if (strcmp(buff, "")) { if (!strncmp(buff, "5'-", 3)) { lowercased((char *) buff); if (modifiedYN || drugsYN) { add_superscripts(buffer, buff, 0); modifier_st.Copy(buffer); } repl_subst(buff, "A", "*a"); repl_subst(buff, "G", "*g"); repl_subst(buff, "C", "*c"); repl_subst(buff, "T", "*t"); repl_subst(buff, "U", "*u"); repl_subst(buff, "I", "*i"); repl_subst(buff, "+A", "+a"); repl_subst(buff, "+G", "+g"); repl_subst(buff, "+C", "+c"); repl_subst(buff, "+T", "+t"); repl_subst(buff, "+U", "+u"); repl_subst(buff, "+I", "+i"); repl_subst(buff, ")A", ")a"); repl_subst(buff, ")G", ")g"); repl_subst(buff, ")C", ")c"); repl_subst(buff, ")T", ")t"); repl_subst(buff, ")U", ")u"); repl_subst(buff, ")I", ")I"); repl_subst(buff, "", "*"); map_descriptor_case(buff); } strcpy(st1, "0k"); strcpy(st2, "0K"); for (ch = '0'; (!hit && (ch <= '9')); ch++) { st1[0] = ch; st2[0] = ch; hit = repl_subst(buff, st2, st1); } strcpy(st1, "0 k,"); strcpy(st2, "0K"); for (ch = '0'; (!hit && (ch <= '9')); ch++) { st1[0] = ch; st2[0] = ch; hit = repl_subst(buff, st2, st1); } strcpy(st1, "0 k"); strcpy(st2, "0K"); for (ch = '0'; (!hit && (ch <= '9')); ch++) { st1[0] = ch; st2[0] = ch; hit = repl_subst_last(buff, st2, st1); } strcpy(st1, "0c"); strcpy(st2, "0C"); for (ch = '0'; (!hit && (ch <= '9')); ch++) { st1[0] = ch; st2[0] = ch; hit = repl_subst(buff, st2, st1); } strcpy(st1, "0 c,"); strcpy(st2, "0C"); for (ch = '0'; (!hit && (ch <= '9')); ch++) { st1[0] = ch; st2[0] = ch; hit = repl_subst(buff, st2, st1); } strcpy(st1, "0 c,"); strcpy(st2, "0C"); for (ch = '0'; (!hit && (ch <= '9')); ch++) { st1[0] = ch; st2[0] = ch; hit = repl_subst_last(buff, st2, st1); } i = 0; for (stpt = buff; *stpt != '\0'; stpt++) { if (strncmp(buff, "5'-", 3) || strncmp(conformation_type, "P", 1)) { if (isalpha(stpt[0]) && isdigit(stpt[1])) { j = i; while ((j > 0) && isalpha(buff[j])) { buff[j] = toupper(buff[j]); j--; } } } if (((stpt[0] == ' ') || (stpt[0] == ',') || (stpt[0] == '(')) && (isalpha(stpt[1])) && ((stpt[2] == '\0') || (stpt[2] == '-') || (stpt[2] == ' ') || (stpt[2] ==')'))) stpt[1] = toupper(stpt[1]); else if ((stpt[0] == 'n') && (stpt[1] == ',') && (stpt[2] == 'n') && !(isalpha(stpt[3]))) { stpt[0] = 'N'; stpt[2] = 'N'; } i++; } repl_subst(buff, "DNA", "dna"); repl_subst(buff, "RNA", "rna"); repl_subst(buff, "(pH ", "(ph "); repl_subst(buff, "( pH ", " ph "); repl_subst(buff, "Hoechst", "hoechst"); repl_subst(buff, "(II)", "(ii)"); repl_subst(buff, "(III)", "(iii)"); repl_subst(buff, "-O-","-o-"); repl_subst(buff, " HCHO", " hcho"); repl_subst(buff, "N-","n-"); if (drugsYN) { repl_subst(buff, "actinomycin D", "actinomycin d"); repl_subst(buff, "triostin A", "triostin a"); repl_subst(buff, "distamycin A", "distamycin a"); } } name.Copy(buff); } void _VALIDATION::get_classification_st(CifString &Classification, int& isComplex) { int drugsYN = 0, mismatch_YN = 0, modified_YN = 0, i, index, rowNo; int STRUCT_TOKEN, STRKEY_TOKEN; char helix_type[BIGSTRING], classification[BIGSTRING]; char conformation_type[BIGSTRING], tmp_buff[BIGSTRING]; static char buff[BIGSTRING]; CifString cifstring; ISTable *Table = NULL; isComplex = 0; memset(buff, '\0', BIGSTRING); memset(tmp_buff, '\0', BIGSTRING); memset(helix_type, '\0', BIGSTRING); memset(classification, '\0', BIGSTRING); memset(conformation_type, '\0', BIGSTRING); if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "struct_conn_type"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("id"); rowNo = Table->GetNumRows(); for (i = 0; i < rowNo; i++) { Table->GetCell(cifstring, index, i); if (!strcasecmp(cifstring.Text(), "covale_base") || !strcasecmp(cifstring.Text(), "covale_sugar") || !strcasecmp(cifstring.Text(), "covale_phosphate")) { modified_YN = 1; } else if (!strcasecmp(cifstring.Text(), "mismat")) mismatch_YN = 1; } } Table = _CifObj->GetTablePtr(_StructureId, "ndb_na_struct_keywds"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("conformation_type"); get_value(cifstring, Table, index, 0); strcpy(conformation_type, cifstring.Text()); index = Table->GetColumnIndex("strand_description"); get_value(cifstring, Table, index, 0); strcpy(helix_type, cifstring.Text()); } Table = _CifObj->GetTablePtr(_StructureId, "struct_keywords"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("ndb_keywords"); get_value(cifstring, Table, index, 0); strcpy(classification, cifstring.Text()); } } else { drugsYN = (_CardInfo[DCHEM_TOKEN-1].Head() != NULL); mismatch_YN = (_CardInfo[MISMAT_TOKEN-1].Head() != NULL); modified_YN = (_CardInfo[MODIFB_TOKEN-1].Head() != NULL || _CardInfo[MODIFP_TOKEN-1].Head() != NULL || _CardInfo[MODIFS_TOKEN-1].Head() != NULL); STRUCT_TOKEN = find_card_id("STRUCT"); if (_CardInfo[STRUCT_TOKEN].Head()) { strcpy(conformation_type, _CardInfo[STRUCT_TOKEN].Head()->Field(1)); strcpy(helix_type, _CardInfo[STRUCT_TOKEN].Head()->Field(2)); } if (_CardInfo[HEADER_TOKEN-1].Head()) strcpy(classification, _CardInfo[HEADER_TOKEN-1].Head()->Field(1)); } ndb_set_string_to_upper(conformation_type); if (!strncmp("A", conformation_type, 1) || !strncmp("B", conformation_type, 1) || !strncmp("Z", conformation_type, 1)) { strcat(buff, conformation_type); strcat(buff, "-"); } else if (!strncmp("RH", conformation_type, 2)) { strcat(buff, (strlen(buff)) ? " right handed" : " Right handed "); } else if (!strncmp("U", conformation_type, 1)) { strcat(buff, (strlen(buff) == 0) ? "Unusual " : "unusual "); } if ((!strncmp("DNA/RNA", classification, 7)) || (!strncmp("DEOXYRIBONUCLEIC ACID/RIBONUCLEIC ACID", classification, 38))) strcat(buff, "Form nucleic acid hybrid"); else if (strstr(classification, "COMPLEX") && strstr(classification, "DNA")) strcat(buff, "DNA"); else if (strstr(classification, "COMPLEX") && strstr(classification, "RNA")) strcat(buff, "RNA"); else if (!strcmp(classification, "DNA")) strcat(buff, "DNA"); else if (!strcmp(classification, "RNA")) strcat(buff, "RNA"); else strcat(buff, ""); if (strstr(classification, "COMPLEX") && (strstr(classification, "DNA") && strcmp(classification, "DNA-BINDING PROTEIN") || strstr(classification, "RNA") && strcmp(classification, "RNA-BINDING PROTEIN"))) isComplex = 1; if (strcmp(helix_type, "")) { strcat(buff, " "); strcpy(tmp_buff, helix_type); lowercased(tmp_buff); strcat(buff, tmp_buff); } if (!strcmp("T", conformation_type)) strcpy(buff, "tRNA"); else if (!strcmp("P", conformation_type)) strcpy(buff, "Protein-nucleic acid complex"); else if (!strncmp("RIBONUCL", classification, 8) || !strncmp("HIV-1RT", classification, 7)) strcpy(buff, "Ribonuclease"); else if (!strncmp("KIN", classification, 3)) strcpy(buff, "Kinase"); memset(tmp_buff, '\0', BIGSTRING); STRKEY_TOKEN = find_card_id("STRKEY"); if (_input_format == NDB_FILE_FORMAT_MIX || _input_format == NDB_FILE_FORMAT_MMCIF) { Table = _CifObj->GetTablePtr(_StructureId, "ndb_na_struct_keywds"); if (!is_empty_table(Table)) { index = Table->GetColumnIndex("special_feature"); get_value(cifstring, Table, index, 0); if (cifstring != "") strcpy(tmp_buff, cifstring.Text()); } } else if (_CardInfo[STRKEY_TOKEN].Head() && strcmp(_CardInfo[STRKEY_TOKEN].Head()->Field(2), "")) { strcpy(tmp_buff, _CardInfo[STRKEY_TOKEN].Head()->Field(2)); } if (strcmp(tmp_buff, "")) { strcat(buff, ", "); lowercased(tmp_buff); repl_subst(tmp_buff, " DNA", " dna"); repl_subst(tmp_buff, "-DNA", "-dna"); repl_subst(tmp_buff, "DNA-", "-dna"); repl_subst(tmp_buff, "/DNA", "/dna"); repl_subst(tmp_buff, "DNA/", "/dna"); repl_subst(tmp_buff, " RNA", " rna"); repl_subst(tmp_buff, "-RNA", "-rna"); repl_subst(tmp_buff, "RNA-", "rna-"); repl_subst(tmp_buff, "RNA/", "rna/"); repl_subst(tmp_buff, "/RNA", "/rna"); strcat(buff, tmp_buff); } if (modified_YN ) { if (strcmp(buff, "")) strcat(buff, ", modified"); else strcpy(buff, "modified"); } if (mismatch_YN ) { if (strcmp(buff, "")) strcat(buff, ", mismatch"); else strcpy(buff, "mismatch"); } if (drugsYN) { if (strcmp(buff, "")) strcat(buff, ", bound to drug"); else strcpy(buff, "bound to drug"); } Classification.Copy(buff); } static void write_text_part(FILE *fp, ATLAS_TEXT *text, const int is_prev_check, const int experiment_type) { if (strcmp(text->struct_id, "")) atlas_head(fp, 1, text->struct_id); atlas_par(fp); if (text->struct_features && !is_prev_check) { if (text->isComplex) atlas_head(fp, 2, "Nucleic acid features"); else atlas_head(fp, 2, "Features"); atlas_par(fp); atlas_line(fp, text->struct_features); atlas_par(fp); } if (text->compound_name && !is_prev_check) { atlas_head(fp, 2, "Compound name"); atlas_line(fp, text->compound_name); atlas_par(fp); } if (text->Num_seqs) { if (experiment_type & EXPERIMENT_TYPE_NMR || experiment_type & EXPERIMENT_TYPE_MODEL) atlas_head(fp, 2, "Sequence"); else atlas_head(fp, 2, "Sequence in asymmetric unit"); atlas_begin(fp, "itemize"); for (int i = 0; i < text->Num_seqs; i++) atlas_item(fp, "", text->seqs[i]); atlas_end(fp, "itemize"); } if (text->refn) { atlas_head(fp, 2, "Citation"); if (text->refn->author) { atlas_line(fp, text->refn->author); atlas_line_break(fp); } if (text->refn->title) { atlas_line(fp, text->refn->title); atlas_line_break(fp); } if (text->refn->refn) atlas_line(fp, text->refn->refn); atlas_par(fp); } if (strcmp(text->spacegroup, "") && !(experiment_type & EXPERIMENT_TYPE_NMR) && !(experiment_type & EXPERIMENT_TYPE_MODEL)) { atlas_head(fp, 2, "Space group"); atlas_line(fp, "\n"); atlas_line(fp, text->spacegroup); atlas_line(fp, "\n"); atlas_par(fp); } if (strcmp(text->cell, "") && !(experiment_type & EXPERIMENT_TYPE_NMR) && !(experiment_type & EXPERIMENT_TYPE_MODEL)) { atlas_head(fp, 2, "Cell constants"); html_begin(fp, "pre"); atlas_line(fp, text->cell); html_end(fp, "pre"); atlas_par(fp); } if (text->crys && !(experiment_type & EXPERIMENT_TYPE_NMR) && !(experiment_type & EXPERIMENT_TYPE_MODEL)) { atlas_head(fp, 2, "Crystallization conditions"); atlas_line(fp,""); atlas_line(fp,""); atlas_begin(fp,"itemize"); if (text->crys->method) atlas_item(fp, NULL, text->crys->method); if (text->crys->drop) atlas_item(fp, NULL, text->crys->drop); if (text->crys->reservoir) atlas_item(fp, NULL, text->crys->reservoir); if (text->crys->soaking) atlas_item(fp, NULL, text->crys->soaking); atlas_end(fp, "itemize"); atlas_line(fp,"\n"); } if (text->refinement && !(experiment_type & EXPERIMENT_TYPE_NMR)) { atlas_head(fp, 2, "Refinement"); atlas_line(fp, "\n"); atlas_line(fp, text->refinement); atlas_par(fp); } atlas_par(fp); } static void get_citation_val(CifString &buff, One_Card_Info_Format *Head, const int serial_no, const int field_no) { One_Card_Info_Format *pJrnlCard = Head; buff.Clear(); while (pJrnlCard) { if (atoi(pJrnlCard->Field(1)) == serial_no) break; pJrnlCard = pJrnlCard->Next(); } if (pJrnlCard) buff.Copy(pJrnlCard->Field(field_no-1)); } static int get_multiple_rows(One_Card_Info_Format *Head, const int field_no, const int serial_no, const int value, CifString &res) { char buff[BIGSTRING]; int first = 1, nrow = 0; memset(buff, 0, BIGSTRING); One_Card_Info_Format *pCard = Head; while (pCard) { strcpy(buff, pCard->Field(field_no)); lowercased(buff); if (atoi(pCard->Field(serial_no)) == value) { map_solution_case(buff); } else buff[0] = '\0'; if (strcmp(buff, "")) { if (first) first = 0; else if (serial_no < 0 && pCard->Next() && pCard->Next()->Next() == NULL) res += " and "; else res += ", "; res += buff; } nrow++; pCard = pCard->Next(); } return nrow; } static void add_superscripts(char *modifier_st, char *buff, const int isindex) { const char *html_syms[11] = {"+", "^","++","^^","+", "^","++","^^","+", "^","++"}; int maxsyms = 11; int nmods = 0; int len, i, j; int found_mod = 0; int at_5_prime = 0; char mod_substring[160]; char old_st[160]; char new_st[160]; char buffer[BIGSTRING]; char modifier_tmp[MxStrLen]; strcpy(modifier_st, ""); strcpy(buffer, buff); len = strlen(buff); for (i = 0; i < len; i++) { strcpy(modifier_tmp, ""); if (!strncmp(buff + i, "5'-", 3)) if (at_5_prime) { ndb_log_message(NDB_MSG_DEBUG4, "Something's wrong, two consecutive 5'-.\n"); ndb_log_message(NDB_MSG_DEBUG4, "String %s in add_superscripts.\n", buff); exit(1); } else at_5_prime = 1; else if (!strncmp(buff + i, "-3'", 3)) if (at_5_prime) at_5_prime = 0; if (at_5_prime) { if (buff[i+1] == '(') { if ((buff[i] == '*') || (buff[i] == '(')) found_mod = 1; else if (buff[i] == 'p') found_mod = 2; else if (buff[i] == '-') found_mod = 3; if (found_mod) { i++; j = i; while ((j < len) && (buff[j] != ')')) j++; if (j >= BIGSTRING) { ndb_log_message(NDB_MSG_DEBUG4, "String \"%s\" ended while searching for modifier end in "); ndb_log_message(NDB_MSG_DEBUG4, "add_superscripts.\n"); exit(1); } strncpy(mod_substring, buff + i + 1, j -i -1); mod_substring[j -i -1] = '\0'; strcpy(old_st, "("); strcat(old_st, mod_substring); strcat(old_st, ")"); if ((found_mod == 1) || (found_mod == 3)) strncat(old_st, buff + j + 1, 1); if ((found_mod == 1) || (found_mod == 3)) { strncpy(new_st, buff + j + 1, 1); new_st[1] = '\0'; if (found_mod == 1) new_st[0] = toupper(new_st[0]); } else strcpy(new_st, ""); if (isindex) { strcat(new_st,"+"); repl_subst_one(buffer, new_st, old_st); } else { if (nmods >= maxsyms) { ndb_log_message(NDB_MSG_DEBUG4, "Error: too many modifiers in compound name.\n"); exit(1); } strcat(new_st,""); strcat(new_st, html_syms[nmods]); strcat(new_st,""); strcat(modifier_tmp, (nmods > 0) ? ", " : " "); strcat(modifier_tmp, ""); strcat(modifier_tmp, html_syms[nmods]); strcat(modifier_tmp, ""); strcat(modifier_tmp, " = "); strcat(modifier_tmp, replace_mod(mod_substring)); if (!strstr(modifier_st, modifier_tmp)) { strcat(modifier_st, modifier_tmp); } } found_mod = 0; repl_subst_one(buffer, new_st, old_st); } } } } strcpy(buff, buffer); } static void correct_string(char *string) { int i, len; char *buffer = NULL; if (string[0] == '\0') return; len = strlen(string); buffer = new char[len + 20]; for (i = len - 1; i >= 0; i--) { if (string[i] == ',') { string[i] = '\0'; break; } } strcpy(buffer, string); len = strlen(string); for (i = len - 1; i >= 0; i--) { if (buffer[i] == ',') { buffer[i] = '\0'; break; } } if (i > 0) { strcat(buffer, " and"); strcat(buffer, &string[i+1]); strcpy(string, buffer); } delete [] buffer; } static REFN *get_refn(CifString &authors, CifString &title, CifString &jrnl, CifString &volume, CifString &first_page, CifString &last_page, CifString &year) { int i, len; char *stmpt = NULL; CifString buff; REFN *refn = new REFN; refn->author = NULL; refn->title = NULL; refn->refn = NULL; if (authors != "") { stmpt = authors.Text(); len = strlen(stmpt); buff.Clear(); for (i = 0; i < len; i++) { buff += stmpt[i]; if (stmpt[i] == ',' && (i + 1) < len && stmpt[i + 1] != ' ') buff += " "; else if (stmpt[i] == '.' && (i + 2) < len && stmpt[i + 1] != ' ' && stmpt[i + 2] != '.') buff += " "; } refn->author = new char[strlen(buff.Text())+1]; strcpy(refn->author, buff.Text()); } if (title != "") { refn->title = new char[strlen(title.Text())+1]; strcpy(refn->title, title.Text()); } buff.Clear(); if (jrnl != "" && strncasecmp(jrnl.Text(), "To Be Published", 15)) { stmpt = jrnl.Text(); len = strlen(stmpt); i = 0; buff.Copy(""); while (i < len) { buff += stmpt[i]; if (stmpt[i] == '.' && (i + 1) < len) buff += " "; i++; } buff += ",\n"; if (volume != "") { buff += ""; buff += volume; buff += ", "; } if (first_page != "") { if (last_page != "") { buff += "pp. "; buff += first_page; buff += "-"; buff += last_page; } else { buff += "p. "; buff += first_page; } } if (year != "") { buff += ", "; buff += year; buff += "."; } } else buff.Copy("To Be Published."); refn->refn = new char[strlen(buff.Text())+1]; strcpy(refn->refn, buff.Text()); return refn; } static CRYS *get_crys(CifString &method, CifString &drop, CifString &reservoir, CifString &soaking) { if (method == "" && drop == "" && reservoir == "" && soaking == "") return NULL; CRYS *crys = new CRYS; crys->method = NULL; crys->drop = NULL; crys->reservoir = NULL; crys->soaking = NULL; if (method != "") { crys->method = new char[strlen(method.Text())+1]; strcpy(crys->method, method.Text()); } if (drop != "") { crys->drop = new char[strlen(drop.Text())+7]; sprintf(crys->drop, "Drop: %s", drop.Text()); } if (reservoir != "") { crys->reservoir = new char[strlen(reservoir.Text())+12]; sprintf(crys->reservoir, "Reservoir: %s", reservoir.Text()); } if (soaking != "") { crys->soaking = new char[strlen(soaking.Text())+19]; sprintf(crys->soaking, "Soaking solution: %s", soaking.Text()); } return crys; }