/* FILE: ndb_to_pdb.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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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 "_maxit.h" #include "util.h" #include "erf_category.h" #include "erf_util.h" #include "ndb_misclib.h" typedef struct { int oper_id; int num_chain; char chain[50][3]; } NCS_COR; typedef struct { char biol_id[4]; } _BIOL_ID; #define NUM_TML 6 static const char *tml_token[NUM_TML] = { "RFTPOS", "RFMPOS", "RFLPOS", "RFTTHR", "RFMTHR", "RFLTHR" }; static const char *tml_type[NUM_TML] = { "tight positional", "medium positional", "loose positional", "tight thermal", "medium thermal", "loose thermal"}; static void print_null_remark_value(One_Card_Info_Format *newCard, const int fieldLength, const int fieldJustification); static void print_space_between_remark_field(One_Card_Info_Format *newCard, REMARKS *Remark, const int field_no); static void get_remark_field_format(char *FieldFormat, REMARKS *Remark, const int field_no); static void clean_descriptor(char *string, char *ec); static void delete_space_between_string(char *string); static float cal_min_distance(_MOLECULE *mol, _ATOM *atom); static float cal_dist(_ATOM *atom_a, _ATOM *atom_b); static int check_align(const int Remark_No, REMARK_FIELD *FieldList); #ifdef SUN_OS #ifdef __cplusplus extern "C" { #endif #endif static int biol_id_compare(const void *biol1, const void *biol2); #ifdef SUN_OS #ifdef __cplusplus } #endif #endif void _MAXIT::ndb_to_pdb_general(const int remark) { int i, j, k, len, Auth_Token, token_id[6], sym1[4], sym2[4]; char buff1[12], buff2[12]; One_Card_Info_Format *pCard = NULL, *qCard = NULL; token_id[0] = find_card_id("TLSGRO"); token_id[1] = find_card_id("TLSRNG"); j = 0; pCard = _CardInfo[token_id[0]].Head(); while (pCard) { i = 0; qCard = _CardInfo[token_id[1]].Head(); while (qCard) { if (!strcmp(qCard->Field(1), pCard->Field(1))) i++; qCard = qCard->Next(); } pCard->AddElementToField(i, 2); j++; pCard = pCard->Next(); } token_id[0] = find_card_id("NCSGRO"); token_id[1] = find_card_id("CCPNCS"); k = 0; pCard = _CardInfo[token_id[0]].Head(); while (pCard) { i = 0; qCard = _CardInfo[token_id[1]].Head(); while (qCard) { if (!strcmp(qCard->Field(1), pCard->Field(1))) { if (atoi(qCard->Field(6)) > i) i = atoi(qCard->Field(6)); } qCard = qCard->Next(); } pCard->AddElementToField(i, 2); k++; pCard = pCard->Next(); } token_id[0] = find_card_id("NCSTLS"); pCard = _CardInfo[token_id[0]].Head(); if (!pCard) pCard = _CardInfo[token_id[0]].add_a_new_card(NdbToken[token_id[0]], 0); pCard->AddElementToField(k, 1); pCard->AddElementToField(j, 2); Auth_Token = find_card_id("TMLPTL"); if (Auth_Token >= 0 && _CardInfo[Auth_Token].Head()) { for (i = 0; i < NUM_TML; i++) { token_id[i] = find_card_id(tml_token[i]); if (token_id[i] < 0) continue; pCard = _CardInfo[token_id[i]].Head(); while (pCard) pCard = _CardInfo[token_id[i]].delete_a_card(pCard); } pCard = _CardInfo[Auth_Token].Head(); while (pCard) { pCard->CleanStringField(6); for (i = 0; i < NUM_TML; i++) { if (!strcmp(pCard->Field(6), tml_type[i])) break; } if (i < NUM_TML) { qCard = _CardInfo[token_id[i]].add_a_new_card(NdbToken[token_id[i]], 0); for (j = 1; j < qCard->NumField(); j++) { if (j == 2 && !strcmp(pCard->Field(j), "")) qCard->AddElementToField(" ", j); else qCard->AddElementToField(pCard->Field(j), j); } } pCard = pCard->Next(); } } Auth_Token = find_card_id("TLSRNG"); if (Auth_Token >= 0 && _CardInfo[Auth_Token].Head()) { pCard = _CardInfo[Auth_Token].Head(); while (pCard) { if (!strcmp(pCard->Field(2), "")) pCard->AddElementToField(" ", 2); if (!strcmp(pCard->Field(4), "")) pCard->AddElementToField(" ", 4); pCard = pCard->Next(); } } Auth_Token = find_card_id("CCPNCS"); if (Auth_Token >= 0 && _CardInfo[Auth_Token].Head()) { pCard = _CardInfo[Auth_Token].Head(); while (pCard) { if (!strcmp(pCard->Field(2), "")) pCard->AddElementToField(" ", 2); if (!strcmp(pCard->Field(4), "")) pCard->AddElementToField(" ", 4); pCard = pCard->Next(); } } Auth_Token = find_card_id("SITELS"); if (Auth_Token >= 0 && _CardInfo[Auth_Token].Head()) { pCard = _CardInfo[Auth_Token].Head(); while (pCard) { if (!strcmp(pCard->Field(3), "")) pCard = _CardInfo[Auth_Token].delete_a_card(pCard); else pCard = pCard->Next(); } } ndb_to_pdb_processing_authors(); ndb_to_pdb_processing_shelx_and_tnt(); ndb_to_pdb_processing_synchrotron(); ndb_to_pdb_proc_header(); replace_pdb_compnd_source_card(); ndb_to_pdb_get_remarks(remark); get_cispep_cards(); token_id[0] = SSBOND_TOKEN-1; sym1[0] = 10; sym2[0] = 11; token_id[1] = LINK_TOKEN-1; sym1[1] = 13; sym2[1] = 14; token_id[2] = HYDBND_TOKEN-1; sym1[2] = 18; sym2[2] = 19; token_id[3] = SLTBRG_TOKEN-1; sym1[3] = 13; sym2[3] = 14; for (i = 0; i < 4; i++) { pCard = _CardInfo[token_id[i]].Head(); while (pCard) { strcpy(buff1, pCard->Field(sym1[i])); if (strcmp(buff1, "")) { k = 0; len = strlen(buff1); for (j = 0; j < len; j++) { if (buff1[j] == '_') continue; buff2[k] = buff1[j]; k++; } buff2[k] = '\0'; pCard->AddElementToField(buff2, sym1[i]); } strcpy(buff1, pCard->Field(sym2[i])); if (strcmp(buff1, "")) { k = 0; len = strlen(buff1); for (j = 0; j < len; j++) { if (buff1[j] == '_') continue; buff2[k] = buff1[j]; k++; } buff2[k] = '\0'; pCard->AddElementToField(buff2, sym2[i]); } pCard = pCard->Next(); } } Auth_Token = find_card_id("CAVEAT"); pCard = _CardInfo[Auth_Token].Head(); if (pCard && _CardInfo[PDBFIL_TOKEN-1].Head()) { while (pCard) { pCard->AddElementToField(_CardInfo[PDBFIL_TOKEN-1].Head()->Field(1), 2); pCard = pCard->Next(); } } } void _MAXIT::ndb_to_pdb_processing_authors() { int Author_Token = find_card_id("AUTHOR"); int Auth_Token = find_jrnl_id("AUTH"); char buffer[1000]; One_Card_Info_Format *pCard = _JrnlCardInfo[Auth_Token].Head(); while (pCard) { strcpy(buffer, pCard->Field(4)); delete_space_between_string(buffer); pCard->AddElementToField(buffer, 4); pCard = pCard->Next(); } pCard = _CardInfo[Author_Token].Head(); while (pCard) { strcpy(buffer, pCard->Field(2)); delete_space_between_string(buffer); pCard->AddElementToField(buffer, 2); pCard = pCard->Next(); } if (_JrnlCardInfo[Auth_Token].Head() && !_CardInfo[Author_Token].Head() && strcmp(_JrnlCardInfo[Auth_Token].Head()->Field(4), "")) { pCard = _CardInfo[Author_Token].add_a_new_card(NdbToken[Author_Token], 0); pCard->AddElementToField(_JrnlCardInfo[Auth_Token].Head()->Field(4), 2); } } void _MAXIT::ndb_to_pdb_processing_shelx_and_tnt() { One_Card_Info_Format *pCard = NULL, *qCard = NULL, *rCard = NULL, *tCard = NULL; int RNOCUT_TOKEN = find_card_id("RNOCUT"); pCard = _CardInfo[REFMET_TOKEN-1].Head(); if (pCard) { if (!strncasecmp(pCard->Field(3), "SHELX", 5)) { qCard = _CardInfo[RFACTR_TOKEN-1].Head(); if (qCard) { rCard = _CardInfo[RNOCUT_TOKEN].Head(); if (rCard) { if (!strcmp(rCard->Field(1), "")) rCard->AddElementToField(qCard->Field(8), 1); if (!strcmp(rCard->Field(2), "")) rCard->AddElementToField(qCard->Field(7), 2); } else { rCard = _CardInfo[RNOCUT_TOKEN]. add_a_new_card(NdbToken[RNOCUT_TOKEN], 0); rCard->AddElementToField(qCard->Field(8), 1); rCard->AddElementToField(qCard->Field(7), 2); } } tCard = _CardInfo[FREERF_TOKEN-1].Head(); if (qCard && tCard) { rCard = _CardInfo[RNOCUT_TOKEN].Head(); if (rCard) { if (!strcmp(rCard->Field(3), "")) rCard->AddElementToField(tCard->Field(1), 3); if (!strcmp(rCard->Field(4), "")) rCard->AddElementToField(tCard->Field(3), 4); if (!strcmp(rCard->Field(5), "")) rCard->AddElementToField(tCard->Field(4), 5); } else { rCard = _CardInfo[RNOCUT_TOKEN]. add_a_new_card(NdbToken[RNOCUT_TOKEN], 0); rCard->AddElementToField(tCard->Field(1), 3); rCard->AddElementToField(tCard->Field(3), 4); rCard->AddElementToField(tCard->Field(4), 5); } } } else if (!strncasecmp(pCard->Field(3), "TNT", 3) || !strncasecmp(pCard->Field(3), "NUCLSQ", 6) || !strncasecmp(pCard->Field(3), "PROLSQ", 6)) { qCard = _CardInfo[RFACTR_TOKEN-1].Head(); if (qCard) { if (!strcmp(qCard->Field(4), "") || fabs(atof(qCard->Field(4))) < 0.1) { rCard = _CardInfo[RNOCUT_TOKEN].Head(); if (rCard) { if (!strcmp(rCard->Field(1), "")) rCard->AddElementToField(qCard->Field(8), 1); } else { rCard = _CardInfo[RNOCUT_TOKEN]. add_a_new_card(NdbToken[RNOCUT_TOKEN], 0); rCard->AddElementToField(qCard->Field(8), 1); } } } } } } void _MAXIT::ndb_to_pdb_processing_synchrotron() { char site[100], beamline[1000]; One_Card_Info_Format *pCard = NULL, *qCard = NULL; pCard = _CardInfo[DTMETH_TOKEN-1].Head(); while (pCard) { if (!strcasecmp(pCard->Field(4), "SYNCHROTRON")) { strcpy(pCard->Field(1), "Y"); qCard = _CardInfo[RADIAT_TOKEN-1].Head(); while (qCard) { if (!strcmp(pCard->Field(NdbToken[DTMETH_TOKEN-1].SeqField-1), qCard->Field(NdbToken[RADIAT_TOKEN-1].SeqField-1))) break; qCard = qCard->Next(); } site[0] = '\0'; beamline[0] = '\0'; if (qCard) { qCard->UpperCaseField(5); separation_string_base_word(qCard->Field(5), site, beamline, "BEAMLINE"); } if (strcmp(site, "") || strcmp(beamline, "")) { qCard = _CardInfo[DTMEAS_TOKEN-1].Head(); while (qCard) { if (!strcmp(pCard->Field(NdbToken[DTMETH_TOKEN-1].SeqField-1), qCard->Field(NdbToken[DTMEAS_TOKEN-1].SeqField-1))) break; qCard = qCard->Next(); } if (qCard == NULL) { qCard = _CardInfo[DTMEAS_TOKEN-1]. add_a_new_card(NdbToken[DTMEAS_TOKEN-1], 0); qCard->AddElementToField( pCard->Field(NdbToken[DTMETH_TOKEN-1].SeqField-1), NdbToken[DTMEAS_TOKEN-1].SeqField-1); } qCard->AddElementToField(site, 2); qCard->AddElementToField(beamline, 3); } } else pCard->AddElementToField("N", 1); pCard = pCard->Next(); } pCard = _CardInfo[DTMETH_TOKEN-1].Head(); while (pCard) { if (!strcasecmp(pCard->Field(4), "SYNCHROTRON")) { qCard = _CardInfo[DTMEAS_TOKEN-1].Head(); while (qCard) { if (!strcmp(qCard->Field(6), pCard->Field(6))) break; qCard = qCard->Next(); } if (qCard) pCard->AddElementToField(qCard->Field(2), 4); else pCard->AddElementToField("", 4); qCard = _CardInfo[RADIAT_TOKEN-1].Head(); while (qCard) { if (!strcmp(qCard->Field(1), pCard->Field(6))) break; qCard = qCard->Next(); } if (qCard) qCard->AddElementToField("", 5); } pCard = pCard->Next(); } pCard = _CardInfo[DTWAVE_TOKEN-1].Head(); if (_CardInfo[WAVLEN_TOKEN-1].Head() == NULL && pCard) { beamline[0] = '\0'; while (pCard) { strcat(beamline, pCard->Field(3)); if (pCard->Next()) strcat(beamline, ", "); pCard = pCard->Next(); } if (strcmp(beamline, "")) { qCard = _CardInfo[WAVLEN_TOKEN-1]. add_a_new_card(NdbToken[WAVLEN_TOKEN-1], 0); qCard->AddElementToField(beamline, 3); } } pCard = _CardInfo[WAVLEN_TOKEN-1].Head(); while (pCard) { if (!strcmp(pCard->Field(2), "") && strcmp(pCard->Field(3), "")) pCard->AddElementToField(pCard->Field(3), 2); pCard = pCard->Next(); } } void _MAXIT::ndb_to_pdb_proc_header() { One_Card_Info_Format *pCard = NULL, *qCard = NULL; pCard = _CardInfo[HEADER_TOKEN-1].Head(); if (pCard == NULL) return; qCard = _CardInfo[PDBFIL_TOKEN-1].Head(); if (qCard) pCard->AddElementToField(qCard->Field(1), 3); else { qCard = _CardInfo[NDBFIL_TOKEN-1].Head(); if (qCard) pCard->AddElementToField(qCard->Field(1), 3); } if (!strcmp(pCard->Field(1), NDB_DNA_TEXT)) pCard->AddElementToField("DEOXYRIBONUCLEIC ACID", 1); else if (!strcmp(pCard->Field(1), NDB_RNA_TEXT)) pCard->AddElementToField("RIBONUCLEIC ACID", 1); else if (!strcmp(pCard->Field(1), NDB_T_RNA_TEXT)) pCard->AddElementToField("AMINO-ACID TRANSPORT", 1); } void _MAXIT::replace_pdb_compnd_source_card() { int i, found, entity_to_serialno[100]; int SerialNo = 0; int compndSerialNo = 0; int sourceSerialNo = 0; int nsource_Nat = 0; int nsource_Gen = 0; int nsource_Syn = 0; int isSynthetic = GEN; char ec_number[800], buffer[800], buffer1[800]; One_Card_Info_Format *pCard = NULL, *qCard = NULL, *rCard = NULL; One_Card_Info_Format *compndCard = NULL, *sourceCard = NULL; for (i = 0; i < 100; i++) entity_to_serialno[i] = 0; pCard = _CardInfo[SOURCE_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[SOURCE_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[COMPND_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[COMPND_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[SEQIFO_TOKEN-1].Head(); while (pCard) { qCard = _CardInfo[STBIOL_TOKEN-1].Head(); if (qCard) { while (qCard) { if (!strcmp(pCard->Field(2), qCard->Field(12))) { if (strcmp(qCard->Field(15), "")) pCard->AddElementToField(qCard->Field(15), 1); else pCard->AddElementToField(qCard->Field(1), 1); break; } qCard = qCard->Next(); } } else { for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; if (_stbiol[i]->NDB_Strand_ID == pCard->Field(2)) { pCard->AddElementToField(_stbiol[i]->order, 1); break; } } } pCard = pCard->Next(); } _CardInfo[SEQIFO_TOKEN-1].reorder_cards(1, INTEGER_COMPARE, ASCENT); while (PdbSource_Nat[nsource_Nat].pdbname && strcmp(PdbSource_Nat[nsource_Nat].pdbname, "")) { if (PdbSource_Nat[nsource_Nat].NdbTokenId <= 0) PdbSource_Nat[nsource_Nat].NdbTokenId = find_card_id(PdbSource_Nat[nsource_Nat].NdbTokenName)+1; nsource_Nat++; } while (PdbSource_Gen[nsource_Gen].pdbname && strcmp(PdbSource_Gen[nsource_Gen].pdbname, "")) { if (PdbSource_Gen[nsource_Gen].NdbTokenId <= 0) PdbSource_Gen[nsource_Gen].NdbTokenId = find_card_id(PdbSource_Gen[nsource_Gen].NdbTokenName)+1; nsource_Gen++; } while (PdbSource_Syn[nsource_Syn].pdbname && strcmp(PdbSource_Syn[nsource_Syn].pdbname, "")) { if (PdbSource_Syn[nsource_Syn].NdbTokenId <= 0) PdbSource_Syn[nsource_Syn].NdbTokenId = find_card_id(PdbSource_Syn[nsource_Syn].NdbTokenName)+1; nsource_Syn++; } pCard = _CardInfo[SEQIFO_TOKEN-1].Head(); while (pCard) { qCard = _CardInfo[ENTITY_TOKEN-1].Head(); while (qCard && strcmp(qCard->Field(1), pCard->Field(9))) qCard = qCard->Next(); if (!qCard || strcasecmp(qCard->Field(2), "POLYMER")) { pCard = pCard->Next(); continue; } ec_number[0] = '\0'; if (!entity_to_serialno[atoi(qCard->Field(1))]) { sprintf(buffer, "MOL_ID: %d", ++SerialNo); add_compnd_card(buffer, ++compndSerialNo); entity_to_serialno[atoi(qCard->Field(1))] = SerialNo; found = FALSE; rCard = _CardInfo[ENTDES_TOKEN-1].Head(); while (rCard && strcmp(rCard->Field(1), qCard->Field(1))) rCard = rCard->Next(); if (rCard && strcmp(rCard->Field(3), "")) { found = TRUE; if (!strncasecmp(rCard->Field(3), "PROTEIN", 7)) { strcpy(buffer1, rCard->Field(3)); clean_descriptor(buffer1, ec_number); sprintf(buffer, "MOLECULE: %s", buffer1); } else sprintf(buffer, "MOLECULE: %s", rCard->Field(3)); } if (!found) { rCard = _CardInfo[PROTEI_TOKEN-1].Head(); while (rCard && strcmp(rCard->Field(1), qCard->Field(1))) rCard = rCard->Next(); if (rCard) { found = TRUE; sprintf(buffer, "MOLECULE: %s", rCard->Field(3)); } } if (!found) strcpy(buffer, "MOLECULE: "); ndb_set_string_to_upper(buffer); add_compnd_card(buffer, ++compndSerialNo); if (strcmp(pCard->Field(3), "")) sprintf(buffer, "CHAIN: %s", pCard->Field(3)); else sprintf(buffer, "CHAIN: %s", "NULL"); add_compnd_card(buffer, ++compndSerialNo); rCard = _CardInfo[FRAGMT_TOKEN-1].Head(); while (rCard && strcmp(rCard->Field(1), qCard->Field(1))) rCard = rCard->Next(); if (rCard && strcmp(rCard->Field(3), "")) { sprintf(buffer, "FRAGMENT: %s", rCard->Field(3)); ndb_set_string_to_upper(buffer); add_compnd_card(buffer, ++compndSerialNo); } rCard = _CardInfo[ENTNAM_TOKEN-1].Head(); while (rCard && strcmp(rCard->Field(1), qCard->Field(1))) rCard = rCard->Next(); if (rCard && strcmp(rCard->Field(3), "")) { sprintf(buffer, "SYNONYM: %s", rCard->Field(3)); ndb_set_string_to_upper(buffer); add_compnd_card(buffer, ++compndSerialNo); } found = FALSE; rCard = _CardInfo[ECNUM_TOKEN-1].Head(); while (rCard && strcmp(rCard->Field(1), qCard->Field(1))) rCard = rCard->Next(); if (rCard && strcmp(rCard->Field(2), "")) { sprintf(buffer, "EC: %s", rCard->Field(2)); add_compnd_card(buffer, ++compndSerialNo); found = TRUE; } if (!found && strcmp(ec_number, "")) { sprintf(buffer, "EC: %s", ec_number); add_compnd_card(buffer, ++compndSerialNo); } if (!strcasecmp(qCard->Field(3), "NAT")) { isSynthetic = NAT; } else { add_compnd_card("ENGINEERED: YES", ++compndSerialNo); isSynthetic = GEN; if (!strcasecmp(qCard->Field(3), "SYN")) isSynthetic = SYN; } found = FALSE; rCard = _CardInfo[ENTMUT_TOKEN-1].Head(); while (rCard && strcmp(rCard->Field(1), qCard->Field(1))) rCard = rCard->Next(); if (rCard && strcmp(rCard->Field(3), "")) { add_compnd_card("MUTATION: YES", ++compndSerialNo); found = TRUE; } rCard = _CardInfo[ENTAIL_TOKEN-1].Head(); while (rCard && strcmp(rCard->Field(1), qCard->Field(1))) rCard = rCard->Next(); if (rCard && strcmp(rCard->Field(3), "")) { sprintf(buffer, "OTHER_DETAILS: %s", rCard->Field(3)); ndb_set_string_to_upper(buffer); add_compnd_card(buffer, ++compndSerialNo); } if (isSynthetic == GEN) ndb_to_pdb_get_source_card(SerialNo, atoi(qCard->Field(1)), isSynthetic, &sourceSerialNo, nsource_Gen, PdbSource_Gen); else if (isSynthetic == SYN) ndb_to_pdb_get_source_card(SerialNo, atoi(qCard->Field(1)), isSynthetic, &sourceSerialNo, nsource_Syn, PdbSource_Syn); else if (isSynthetic == NAT) ndb_to_pdb_get_source_card(SerialNo, atoi(qCard->Field(1)), isSynthetic, &sourceSerialNo, nsource_Nat, PdbSource_Nat); } else { compndCard = _CardInfo[COMPND_TOKEN-1].Head(); while (compndCard) { if (strstr(compndCard->Field(2), "MOL_ID:") && atoi(&compndCard->Field(2)[8]) == entity_to_serialno[atoi(pCard->Field(9))] && compndCard->Next() && compndCard->Next()->Next() && !strncmp(compndCard->Next()->Next()->Field(2), "CHAIN", 5)) break; compndCard = compndCard->Next(); } if (compndCard && compndCard->Next()) { compndCard = compndCard->Next()->Next(); if (compndCard != NULL) { compndCard->AttachToField(", ", 2); compndCard->AttachToField(pCard->Field(3), 2); } } } pCard = pCard->Next(); } compndCard = _CardInfo[COMPND_TOKEN-1].Head(); while (compndCard && compndCard != _CardInfo[COMPND_TOKEN-1].Tail()) { strcpy(buffer, compndCard->Field(2)); for (i = strlen(buffer) - 1; i >= 0; i--) if (buffer[i] != ' ') break; if (buffer[i] != ';') sprintf(&buffer[i+1], ";"); compndCard->AddElementToField(buffer, 2); compndCard = compndCard->Next(); } sourceCard = _CardInfo[SOURCE_TOKEN-1].Head(); while (sourceCard && sourceCard != _CardInfo[SOURCE_TOKEN-1].Tail()) { strcpy(buffer, sourceCard->Field(2)); for (i = strlen(buffer) - 1; i >= 0; i--) if (buffer[i] != ' ') break; if (buffer[i] != ';') sprintf(&buffer[i+1], ";"); sourceCard->AddElementToField(buffer, 2); sourceCard = sourceCard->Next(); } compndCard = _CardInfo[COMPND_TOKEN-1].Head(); if (compndCard == NULL) { compndCard = _CardInfo[COMPND_TOKEN-1]. add_a_new_card(NdbToken[COMPND_TOKEN-1], 0); compndCard->AddElementToField("NULL", 2); } sourceCard = _CardInfo[SOURCE_TOKEN-1].Head(); if (sourceCard == NULL) { sourceCard = _CardInfo[SOURCE_TOKEN-1]. add_a_new_card(NdbToken[SOURCE_TOKEN-1], 0); sourceCard->AddElementToField("NULL", 2); } } void _MAXIT::add_compnd_card(const char *value, const int serialNo) { One_Card_Info_Format *compndCard = _CardInfo[COMPND_TOKEN-1].add_a_new_card(NdbToken[COMPND_TOKEN-1], 0); compndCard->AddElementToField(value, 2); compndCard->AddElementToField(serialNo, 3); } void _MAXIT::ndb_to_pdb_get_source_card(const int serialno, const int entityId, const int isSynthetic, int *sourceSerialNo, const int nsource, PDB_Source_Format *PdbSource) { One_Card_Info_Format *sourceCard = _CardInfo[SOURCE_TOKEN-1].add_a_new_card(NdbToken[SOURCE_TOKEN-1], 0); char buffer[800]; sprintf(buffer, "MOL_ID: %d", serialno); sourceCard->AddElementToField(buffer, 2); sourceCard->AddElementToField(++(*sourceSerialNo), 3); if (isSynthetic == SYN) { sourceCard = _CardInfo[SOURCE_TOKEN-1]. add_a_new_card(NdbToken[SOURCE_TOKEN-1], 0); sourceCard->AddElementToField("SYNTHETIC: YES", 2); sourceCard->AddElementToField(++(*sourceSerialNo), 3); } for (int i = 0; i < nsource; i++) { if (PdbSource[i].NdbTokenId != 0 && PdbSource[i].NdbTokenId <= MxTokens) { One_Card_Info_Format *pCard = _CardInfo[PdbSource[i].NdbTokenId-1].Head(); while (pCard) { if (strcmp(pCard->Field(PdbSource[i].NdbFieldNo-1), "") && atoi(pCard->Field(1)) == entityId) break; pCard = pCard->Next(); } if (pCard) { sourceCard = _CardInfo[SOURCE_TOKEN-1]. add_a_new_card(NdbToken[SOURCE_TOKEN-1], 0); sprintf(buffer, "%s: %s", PdbSource[i].pdbname, pCard->Field(PdbSource[i].NdbFieldNo-1)); sourceCard->AddElementToField(buffer, 2); sourceCard->AddElementToField(++(*sourceSerialNo), 3); } } } } void _MAXIT::add_remark_90() { One_Card_Info_Format *pCard = _CardInfo[REMARK_TOKEN-1].Head(); while (pCard) { One_Card_Info_Format *pRemarkCard = _CardInfo[PREMRK_TOKEN-1]. add_a_new_card(NdbToken[PREMRK_TOKEN-1], 0); pRemarkCard->AddElementToField(pCard->Field(1), 1); pRemarkCard->AddElementToField(pCard->Field(2), 2); pCard = _CardInfo[REMARK_TOKEN-1].delete_a_card(pCard); } for (int remark_no = 2; remark_no <= 999; remark_no++) { if (remark_no == 90) ndb_to_pdb_get_general_remark(Num_Remark_90, Remark_90, 0, 0, 0, 0); else ndb_to_pdb_get_remark_from_premark(remark_no); } } void _MAXIT::ndb_to_pdb_get_remarks(const int remark) { int Num_RemarkNo = 0, RemarkNo[20], RMKSKP_TOKEN, i, j, len; int is_electron_microscopy = 0; int is_powder_diffration = 0; int exist_DNA = 0, CMRNST_TOKEN, RCSBID_TOKEN; int IsInosine = 0, is_skip, exist, remark_no, card_id, SOLEXP_TOKEN; char buff[82], buff1[10], *p; _CHAIN *chain = NULL; One_Card_Info_Format *pCard = NULL, *qCard = NULL; if (_molecules && _num_mol) { chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() == ATOMN_TOKEN) { exist_DNA = 1; if (chain->na_type() != ATOMN_TYPE_DNA_ONLY) { exist_DNA = 0; break; } } chain = _molecules[0]->GetNextChain(); } } SOLEXP_TOKEN = find_card_id("SOLEXP"); CMRNST_TOKEN = find_card_id("CMRNST"); RCSBID_TOKEN = find_card_id("RCSBID"); for (i = 0; i < 20; i++) RemarkNo[i] = 0; pCard = _CardInfo[PROCES_TOKEN-1].Head(); if (pCard && !strcasecmp(pCard->Field(5), "OSAKA")) { pCard->AddElementToField("PDBJ", 5); } if (_CardInfo[PROCES_TOKEN-1].Head() && (_CardInfo[PROCES_TOKEN-1].Head()->Field(7)[0] == 'Y' || _CardInfo[PROCES_TOKEN-1].Head()->Field(7)[0] == 'y')) { RemarkNo[0] = 500; RemarkNo[1] = 525; Num_RemarkNo = 2; } RMKSKP_TOKEN = find_card_id("RMKSKP"); if (_CardInfo[RMKSKP_TOKEN].Head() && strcmp(_CardInfo[RMKSKP_TOKEN].Head()->Field(1), "")) { strcpy(buff, _CardInfo[RMKSKP_TOKEN].Head()->Field(1)); if (buff[0] == 'Y' || buff[0] == 'y') { RemarkNo[0] = 500; RemarkNo[1] = 525; Num_RemarkNo = 2; } else { len = strlen(buff); for (i = 0; i < len; i++) { if (buff[i] == ',') buff[i] = ' '; } ndb_clean_string(buff); p = get_word(buff, buff1); RemarkNo[Num_RemarkNo++] = atoi(buff1); while (p) { p = get_word(p, buff1); RemarkNo[Num_RemarkNo++] = atoi(buff1); } } } 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 (_experiment_type & EXPERIMENT_TYPE_NMR || _experiment_type & EXPERIMENT_TYPE_MODEL) ndb_to_pdb_processing_nmr_remarks(); if ((_experiment_type & EXPERIMENT_TYPE_NMR) || (_experiment_type & EXPERIMENT_TYPE_MODEL)) { pCard = _CardInfo[REFMET_TOKEN-1].Head(); while (pCard) { if (!strcmp(pCard->Field(4), "")) { pCard->UpperCaseField(3); for (i = 0; i < Max_Refinement_Programs; i++) if (strstr(pCard->Field(3), Refinement_programs[i].Program)) break; if (i != Max_Refinement_Programs) pCard->AddElementToField(Refinement_programs[i].Author, 4); } pCard = pCard->Next(); } } pCard = _CardInfo[EXPDTA_TOKEN-1].Head(); if (pCard) { if (strstr(pCard->Field(2), "ELECTRON MICROSCOPY") || strstr(pCard->Field(2), "CRYO-EM RECONSTRUCTION")) is_electron_microscopy = 1; if (strstr(pCard->Field(2), "POWDER DIFFRACTION")) is_powder_diffration = 1; } for (remark_no = 2; remark_no <= 999; remark_no++) { is_skip = 0; for (i = 0; i < Num_RemarkNo; i++) { if (remark_no == RemarkNo[i]) { is_skip = 1; break; } } if (is_skip) continue; if (find_user_defined_remark(remark_no)) continue; if (remark_no == 2) { if ((_experiment_type & EXPERIMENT_TYPE_XRAY) || (_experiment_type & EXPERIMENT_TYPE_NEUTRON) || (_experiment_type & EXPERIMENT_TYPE_CRYO_EM) || (_experiment_type & EXPERIMENT_TYPE_FIBER) || (_experiment_type & EXPERIMENT_TYPE_ELECTRON)) { pCard = _CardInfo[RFACTR_TOKEN-1].Head(); if (!pCard) pCard = _CardInfo[RFACTR_TOKEN-1]. add_a_new_card(NdbToken[RFACTR_TOKEN-1], 0); qCard = _CardInfo[CMRNST_TOKEN].Head(); if (qCard && strcmp(qCard->Field(3), "") && !strcmp(pCard->Field(6), "")) pCard->AddElementToField(qCard->Field(3), 6); ndb_to_pdb_get_general_remark(1, &Remark_2, 0, 0, 0, 0); } else ndb_to_pdb_get_general_remark(1, &Remark_2_NMR, 0, 0, 0, 0); } else if (remark_no == 3) { if ((_experiment_type & EXPERIMENT_TYPE_NMR) || (_experiment_type & EXPERIMENT_TYPE_MODEL)) ndb_to_pdb_get_general_remark(Num_Remark_3_NMR, Remark_3_NMR, 0, 0, 0, 0); else if (_experiment_type & EXPERIMENT_TYPE_CRYO_EM) ndb_to_pdb_get_general_remark(Num_Remark_3_Cryo_Em, Remark_3_Cryo_Em, 0, 0, 0, 0); else if (_experiment_type & EXPERIMENT_TYPE_SOLN_SCT) { for (i = 0; i < Remark_3_Solution.Remarks_No; i++) { ndb_to_pdb_get_general_remark(Remark_3_Solution.num_remarks[i], Remark_3_Solution.remarks[i], 0, 0, 0, 0); } } else if (_experiment_type != EXPERIMENT_TYPE_BASIC) { ndb_to_pdb_get_group_remarks(); } } else if (remark_no == 4) { ndb_to_pdb_get_general_remark(Num_Remark_4, Remark_4, 0, 0, 0, 0); } else if (remark_no == 100) { if (_CardInfo[NDBPRO_TOKEN-1].Head() && strcmp(_CardInfo[NDBPRO_TOKEN-1].Head()->Field(4), "")) { if (!strcmp(_CardInfo[NDBFIL_TOKEN-1].Head()->Field(1), _CardInfo[PDBFIL_TOKEN-1].Head()->Field(1)) && strcmp(_CardInfo[RCSBID_TOKEN].Head()->Field(1), "") && strcmp(_CardInfo[RCSBID_TOKEN].Head()->Field(1), _CardInfo[NDBFIL_TOKEN-1].Head()->Field(1))) { _CardInfo[NDBFIL_TOKEN-1].Head()->AddElementToField( _CardInfo[RCSBID_TOKEN].Head()->Field(1), 1); } if (!strncmp(_CardInfo[NDBFIL_TOKEN-1].Head()->Field(1), "RCSB", 4)) ndb_to_pdb_get_general_remark(Num_Remark_100_RCSB, Remark_100_RCSB, 0, 0, 0, 0); else ndb_to_pdb_get_general_remark(Num_Remark_100, Remark_100, 0, 0, 0, 0); } else ndb_to_pdb_get_remark_from_premark(100); } else if (remark_no == 101) { exist = ndb_to_pdb_get_remark_from_premark(101); if (!exist) { /* pCard = _CardInfo[MODIFB_TOKEN-1].Head(); while (pCard) { if (pCard->Field(9)[0] != '+' && strcmp(pCard->Field(9), "I")) { sprintf(buff, "+%s", pCard->Field(9)); pCard->AddElementToField(buff, 9); strcpy(pCard->Field(9), buff); } pCard = pCard->Next(); } */ pCard = _CardInfo[MODIFB_TOKEN-1].Head(); if (pCard) ndb_to_pdb_get_general_remark(1, &Remark_101, 0, 0, 0, 0); } } else if (remark_no == 102) { if (exist_DNA) { if (_CardInfo[MISMAT_TOKEN-1].Head()) { ndb_to_pdb_get_general_remark(1, &Remark_102, 0, 0, 0, 0); } else ndb_to_pdb_get_remark_from_premark(102); } } else if (remark_no == 103) { IsInosine = 0; pCard = _CardInfo[MODIFB_TOKEN-1].Head(); while (pCard) { if (!res_name_cmp(pCard->Field(5), "I")) { IsInosine = 1; break; } pCard = pCard->Next(); } if (exist_DNA || IsInosine) ndb_to_pdb_get_general_remark(Num_Remark_103, Remark_103, 1, 0, 1, 0); } else if (remark_no == 104) { if (IsInosine) ndb_to_pdb_get_general_remark(1, &Remark_104, 0, 0, 1, 0); } else if (remark_no == 105) { exist = 0; pCard = _CardInfo[SEQIFO_TOKEN-1].Head(); while (pCard != NULL) { if (!strcmp(pCard->Field(5), "NA")) { exist = 1; break; } pCard = pCard->Next(); } if (exist) { exist = ndb_to_pdb_get_remark_from_premark(105); if (!exist) ndb_to_pdb_get_general_remark(Num_Remark_105, Remark_105, 0, 0, 0, 0); } } else if (remark_no == 106) { #if 0 exist = ndb_to_pdb_get_remark_from_premark(106); if (!exist /* && IsInosine == FALSE && _CardInfo[MISMAT_TOKEN-1].Head() == NULL */ ) { pCard = _CardInfo[BSPAIR_TOKEN-1].Head(); while (pCard) { if (!strcmp(pCard->Field(11), "WATSON-CRICK")) break; pCard = pCard->Next(); } if (pCard) ndb_to_pdb_get_general_remark(Num_Remark_106, Remark_106, 0, 0, 0, 0); } #endif } else if (remark_no == 200) { if (_experiment_type & EXPERIMENT_TYPE_XRAY && !is_powder_diffration) ndb_to_pdb_get_general_remark(Num_Remark_200, Remark_200, 0, 0, 0, 0); } else if (remark_no == 210) { if (_experiment_type & EXPERIMENT_TYPE_NMR) ndb_to_pdb_get_general_remark(Num_Remark_210, Remark_210, 0, 0, 0, 0); } else if (remark_no == 215 ) { if (_experiment_type & EXPERIMENT_TYPE_NMR) ndb_to_pdb_get_general_remark(Num_Remark_215, Remark_215, 0, 0, 0, 0); } else if (remark_no == 220) { if (_experiment_type & EXPERIMENT_TYPE_MODEL) ndb_to_pdb_get_general_remark(Num_Remark_220, Remark_220, 0, 0, 0, 0); } else if (remark_no == 225) { if (_experiment_type & EXPERIMENT_TYPE_MODEL) ndb_to_pdb_get_general_remark(Num_Remark_225, Remark_225, 0, 0, 0, 0); } else if (remark_no == 230) { if (_experiment_type & EXPERIMENT_TYPE_NEUTRON) ndb_to_pdb_get_general_remark(Num_Remark_230, Remark_230, 0, 0, 0, 0); } else if (remark_no == 240) { if (_experiment_type & EXPERIMENT_TYPE_ELECTRON) ndb_to_pdb_get_general_remark(Num_Remark_240, Remark_240, 0, 0, 0, 0); } else if (remark_no == 245) { if (_experiment_type & EXPERIMENT_TYPE_CRYO_EM) ndb_to_pdb_get_general_remark(Num_Remark_245, Remark_245, 0, 0, 0, 0); } else if (remark_no == 247) { if (_experiment_type & EXPERIMENT_TYPE_CRYO_EM) ndb_to_pdb_get_general_remark(Num_Remark_247, Remark_247, 0, 0, 0, 0); } else if (remark_no == 250) { if (is_electron_microscopy || is_powder_diffration) ndb_to_pdb_get_remark_from_premark(250); else if ((_experiment_type & EXPERIMENT_TYPE_BASIC) || (_experiment_type & EXPERIMENT_TYPE_FIBER)) ndb_to_pdb_get_general_remark(Num_Remark_250, Remark_250, 0, 0, 0, 0); } else if (remark_no == 265) { if (_experiment_type & EXPERIMENT_TYPE_SOLN_SCT) { if (SOLEXP_TOKEN >= 0) { pCard = _CardInfo[SOLEXP_TOKEN].Head(); while (pCard) { if (!strcmp(pCard->Field(2), "THEORETICAL MODELLING")) pCard = _CardInfo[SOLEXP_TOKEN].delete_a_card(pCard); else pCard = pCard->Next(); } } for (i = 0; i < Remark_265.Remarks_No; i++) { if (strcmp(Remark_265.TokenName[i], "")) { card_id = find_card_id(Remark_265.TokenName[i]); if (card_id == -1) continue; pCard = _CardInfo[card_id].Head(); if (!pCard) continue; } j = 0; if (Remark_265.repeat[i]) j = 1; ndb_to_pdb_get_general_remark(Remark_265.num_remarks[i], Remark_265.remarks[i], j, 0, 0, 1); } } } else if (remark_no == 280) { if (_experiment_type & EXPERIMENT_TYPE_XRAY || _experiment_type & EXPERIMENT_TYPE_NEUTRON) ndb_to_pdb_get_remark_280_crystal(); } else if (remark_no == 290) { if (_experiment_type & EXPERIMENT_TYPE_XRAY || _experiment_type & EXPERIMENT_TYPE_NEUTRON || is_electron_microscopy) ndb_to_pdb_get_remark_290(); } else if (remark_no == 300) { if (is_electron_microscopy) { if (!ndb_to_pdb_get_remark_from_premark(300)) { if (_experiment_type & EXPERIMENT_TYPE_CRYO_EM) { ndb_to_pdb_get_remark_300(); for (i = 0; i < Remark_Cryo_Em_300.Remarks_No; i++) { j = 0; if (Remark_Cryo_Em_300.repeat[i]) j = 1; ndb_to_pdb_get_general_remark(Remark_Cryo_Em_300.num_remarks[i], Remark_Cryo_Em_300.remarks[i], j, 0, 0, 0); } } } } else if (_experiment_type & EXPERIMENT_TYPE_XRAY || _experiment_type & EXPERIMENT_TYPE_NEUTRON || _experiment_type & EXPERIMENT_TYPE_ELECTRON) { if (!ndb_to_pdb_get_remark_300()) ndb_to_pdb_get_remark_from_premark(300); } else if (_experiment_type & EXPERIMENT_TYPE_CRYO_EM) { ndb_to_pdb_get_remark_300(); for (i = 0; i < Remark_Cryo_Em_300.Remarks_No; i++) { j = 0; if (Remark_Cryo_Em_300.repeat[i]) j = 1; ndb_to_pdb_get_general_remark(Remark_Cryo_Em_300.num_remarks[i], Remark_Cryo_Em_300.remarks[i], j, 0, 0, 0); } } } else if (remark_no == 350) { if (is_electron_microscopy) { exist = ndb_to_pdb_get_remark_from_premark(350); if (!exist) ndb_to_pdb_get_remark_350(); } else if (_experiment_type & EXPERIMENT_TYPE_XRAY || _experiment_type & EXPERIMENT_TYPE_NEUTRON || _experiment_type & EXPERIMENT_TYPE_ELECTRON) { if (!ndb_to_pdb_get_remark_350()) ndb_to_pdb_get_remark_from_premark(350); } } else if (remark_no == 375) { if (_experiment_type & EXPERIMENT_TYPE_XRAY || _experiment_type & EXPERIMENT_TYPE_NEUTRON) ndb_to_pdb_get_remark_375(); } else if (remark_no == 465) ndb_to_pdb_get_remark_465(); else if (remark_no == 470) ndb_to_pdb_get_remark_470(); else if (remark_no == 500) { ndb_to_pdb_get_remark_500(remark); rms_deviation_of_bonds(); rms_deviation_of_angles(); outside_torsions(); non_cis_trans_torsions(); } else if (remark_no == 525) { ndb_to_pdb_get_remark_525(); } else if (remark_no == 800) { exist = ndb_to_pdb_get_remark_from_premark(800); if (!exist) ndb_to_pdb_get_general_remark(Num_Remark_800, Remark_800, 1, 0, 0, 0); } else if (remark_no == 900) { if (_CardInfo[RENTRY_TOKEN-1].Head()) { construct_remark_900(); } else ndb_to_pdb_get_remark_from_premark(900); } else ndb_to_pdb_get_remark_from_premark(remark_no); } } int _MAXIT::find_user_defined_remark(const int remark_no) { char buffer[61], *p; int found = 0; int PDBRMK_TOKEN = find_card_id("PDBRMK"); if (PDBRMK_TOKEN < 0) return found; One_Card_Info_Format *pCard = _CardInfo[PDBRMK_TOKEN].Head(); while (pCard) { if (atoi(pCard->Field(1)) == remark_no) { found = 1; p = pCard->Field(3); while (p) { p = get_max_length_word(p, buffer, 60); One_Card_Info_Format *newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(remark_no, 1); newCard->AddElementToField(buffer, 2); } } pCard = pCard->Next(); } return found; } void _MAXIT::ndb_to_pdb_get_group_remarks() { int card_id, ContNo = 1, one_flag = 1, i; int program = 0; char buffer[80], buff[80], *p; GROUP_REMARKS *group_remark = NULL; One_Card_Info_Format *pCard = NULL, *newCard = NULL; pCard = _CardInfo[REFMET_TOKEN-1].Head(); if (pCard) { if (strlen(pCard->Field(3)) < 80) { strcpy(buffer, pCard->Field(3)); ndb_set_string_to_upper(buffer); if (strstr(buffer, "CNS") || strstr(buffer, "CNX")) program = 1; else if (strstr(buffer, "NUCLSQ")) program = 2; else if (strstr(buffer, "PROLSQ") || strstr(buffer, "PROFFT") || strstr(buffer, "CCP4") || strstr(buffer, "PROTEIN") || strstr(buffer, "RESTRAIN") || strstr(buffer, "GPRLSA")) program = 3; else if (strstr(buffer, "REFMAC 5")) program = 5; else if (strstr(buffer, "REFMAC")) program = 4; else if (strstr(buffer,"TNT")) program = 6; else if (strstr(buffer,"SHELX")) program = 7; } if (pCard->Next()) { one_flag = 0; ContNo = 1; } else one_flag = 1; newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(3, 1); newCard->AddElementToField("REFINEMENT.", 2); while (pCard) { if (strcmp(pCard->Field(3), "") && strlen(pCard->Field(3)) < 63) { pCard->UpperCaseField(3); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(3, 1); if (one_flag) sprintf(buffer, " %s : %s", "PROGRAM", pCard->Field(3)); else sprintf(buffer, " %s %-3d : %s", "PROGRAM", ContNo, pCard->Field(3)); newCard->AddElementToField(buffer, 2); for (i = 0; i < Max_Refinement_Programs; i++) { if (strstr(pCard->Field(3), Refinement_programs[i].Program)) { if (!strcmp(Refinement_programs[i].Program, "O")) { if (!strcmp(pCard->Field(3), "O")) break; } else break; } } if (i != Max_Refinement_Programs) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(3, 1); p = get_max_length_word(Refinement_programs[i].Author, buff, 42); if (!strcmp(buff, "?")) strcpy(buff, "NULL"); if (one_flag) sprintf(buffer, " %s : %s", "AUTHORS", buff); else sprintf(buffer, " %s %-3d : %s", "AUTHORS", ContNo, buff); newCard->AddElementToField(buffer, 2); while (p) { p = get_max_length_word(p, buff, 42); if (!strcmp(buff, "?")) strcpy(buff, "NULL"); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(3, 1); sprintf(buffer, " %s : %s", " ", buff); newCard->AddElementToField(buffer, 2); } } } ContNo++; pCard = pCard->Next(); } } if (!program || program == 1) { pCard = _CardInfo[RFACTR_TOKEN-1].Head(); if (pCard && !strcmp(pCard->Field(10), "")) pCard->AddElementToField(pCard->Field(7), 10); pCard = _CardInfo[NCSMOD_TOKEN-1].Head(); if (!pCard) { pCard = _CardInfo[NCSMOD_TOKEN-1]. add_a_new_card(NdbToken[NCSMOD_TOKEN-1], 0); pCard->AddElementToField(1, 1); } pCard = _CardInfo[XFILES_TOKEN-1].Tail(); if (!pCard) { pCard = _CardInfo[XFILES_TOKEN-1]. add_a_new_card(NdbToken[XFILES_TOKEN-1], 0); pCard->AddElementToField(1, 1); } else { for (i = 1; i < pCard->NumField(); i++) { if (strcmp(pCard->Field(i), "")) break; } if (i < pCard->NumField()) { i = atoi(pCard->Field(1)) + 1; pCard = _CardInfo[XFILES_TOKEN-1]. add_a_new_card(NdbToken[XFILES_TOKEN-1], 0); pCard->AddElementToField(i, 1); } } } group_remark = group_remarks[program]; for (i = 0; i < group_remark->Remarks_No; i++) { if (strcmp(group_remark->TokenName[i], "")) { card_id = find_card_id(group_remark->TokenName[i]); if (card_id == -1) continue; pCard = _CardInfo[card_id].Head(); while (pCard) { ndb_to_pdb_get_general_remark(group_remark->num_remarks[i], group_remark->remarks[i], 0, atoi(pCard->Field(group_remark->repeat[i]-1)), 0, 0); pCard = pCard->Next(); } } else if (group_remark->repeat[i] < 0) ndb_to_pdb_get_general_remark(group_remark->num_remarks[i], group_remark->remarks[i], 1, 0, 0, 0); else ndb_to_pdb_get_general_remark(group_remark->num_remarks[i], group_remark->remarks[i], 0, 0, 0, 0); } } void _MAXIT::ndb_to_pdb_get_general_remark(const int num_remarks, REMARKS *Remarks, const int repeat, const int index, const int IsInosine, const int space) { int i, j, card_id = -1, found, *single = NULL; One_Card_Info_Format *pCard = NULL, *newCard = NULL; for (i = 0; i < num_remarks; i++) { card_id = -1; for (j = 0; j < Remarks[i].NumField; j++) { if (!strcmp(Remarks[i].FieldList[j].TokenName, "") && Remarks[i].FieldList[j].FieldId == 0 && Remarks[i].FieldList[j].FieldWidth == 0) Remarks[i].FieldList[j].FieldWidth = strlen(Remarks[i].FieldList[j].Text); if (strcmp(Remarks[i].FieldList[j].TokenName, "") && card_id == -1) card_id = find_card_id(Remarks[i].FieldList[j].TokenName); } } if (repeat && card_id != -1) { found = 0; pCard = _CardInfo[card_id].Head(); while (pCard) { if (IsInosine && (card_id == BSPAIR_TOKEN-1 && (!strcmp(pCard->Field(11), "WATSON-CRICK") || !strcmp(pCard->Field(5), "") || !strcmp(pCard->Field(9), "")) || card_id == MODIFB_TOKEN-1 && res_name_cmp(pCard->Field(5), "I")) || !IsInosine && card_id == MODIFB_TOKEN-1 && !res_name_cmp(pCard->Field(5), "I")) { pCard = pCard->Next(); continue; } found = 1; break; } if (found) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remarks->Remark_No, 1); } single = new int[num_remarks]; for (i = 0; i < num_remarks; i++) single[i] = 1; pCard = _CardInfo[card_id].Head(); while (pCard) { if (IsInosine && (card_id == BSPAIR_TOKEN-1 && (!strcmp(pCard->Field(11), "WATSON-CRICK") || !strcmp(pCard->Field(5), "") || !strcmp(pCard->Field(9), "")) || card_id == MODIFB_TOKEN-1 && res_name_cmp(pCard->Field(5), "I")) || !IsInosine && card_id == MODIFB_TOKEN-1 && !res_name_cmp(pCard->Field(5), "I")) { pCard = pCard->Next(); continue; } if (space && pCard != _CardInfo[card_id].Head()) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remarks->Remark_No, 1); } for (i = 0; i < num_remarks; i++) { if (Remarks[i].NumField == 1) { if (single[i]) { ndb_to_pdb_get_general_remark(&Remarks[i], pCard); single[i] = 0; } } else ndb_to_pdb_get_general_remark(&Remarks[i], pCard); } pCard = pCard->Next(); } delete [] single; single = NULL; } else { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remarks->Remark_No, 1); for (i = 0; i < num_remarks; i++) { card_id = -1; for (j = 0; j < Remarks[i].NumField; j++) { if (strcmp(Remarks[i].FieldList[j].TokenName, "")) card_id = find_card_id(Remarks[i].FieldList[j].TokenName); if (card_id != -1) break; } if ((Remarks[i].Multiple_Treatment || index) && card_id != -1) { pCard = _CardInfo[card_id].Head(); while (pCard) { if (IsInosine && (card_id == BSPAIR_TOKEN-1 && (!strcmp(pCard->Field(11), "WATSON-CRICK") || !strcmp(pCard->Field(5), "") || !strcmp(pCard->Field(9), "")) || card_id == MODIFB_TOKEN-1 && res_name_cmp(pCard->Field(5), "I")) || !IsInosine && card_id == MODIFB_TOKEN-1 && !res_name_cmp(pCard->Field(5), "I")) { pCard = pCard->Next(); continue; } if (!index || index && atoi(pCard->Field(1)) == index) { ndb_to_pdb_get_general_remark(&Remarks[i], pCard); } pCard = pCard->Next(); } } else ndb_to_pdb_get_general_remark(&Remarks[i]); } } } void _MAXIT::ndb_to_pdb_get_general_remark(REMARKS *Remark) { int i, card_id, field_no, align, serial_no_field; char bigstring[100000], FieldFormat[80]; double temp_double; One_Card_Info_Format *newCard = NULL, *pCard = NULL; newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remark->Remark_No, 1); for (i = 0; i < Remark->NumField; i++) { if (!strcmp(Remark->FieldList[i].TokenName, "") && !strcmp(Remark->FieldList[i].Text, "")) continue; align = check_align(Remark->Remark_No, &(Remark->FieldList[i])); get_remark_field_format(FieldFormat, Remark, i); memset(bigstring, 0, 10000); if (strcmp(Remark->FieldList[i].TokenName, "") && Remark->FieldList[i].FieldId) { card_id = find_card_id(Remark->FieldList[i].TokenName); field_no = Remark->FieldList[i].FieldId-1; pCard = NULL; if (card_id != -1) pCard = _CardInfo[card_id].Head(); if (pCard) { if (pCard->Next() && (card_id == EXPDTA_TOKEN-1 || card_id == XFILES_TOKEN-1 || card_id == find_card_id("DIFPTL") || card_id == DTMEAS_TOKEN-1 || card_id == PHVAL_TOKEN-1 || card_id == CRMETH_TOKEN-1 || card_id == DTMETH_TOKEN-1 || card_id == RADIAT_TOKEN-1 || card_id == DTWAVE_TOKEN-1 || card_id == WAVLEN_TOKEN-1 || card_id == DTTEMP_TOKEN-1)) { serial_no_field = NdbToken[card_id].SeqField - 1; if (card_id == find_card_id("DTWAVE")) serial_no_field = 2; while (pCard) { if (strcmp(pCard->Field(field_no), "")) strcat(bigstring, pCard->Field(field_no)); else if (!strcmp(bigstring, "")) strcat(bigstring, "NULL"); if (pCard->Next() && strcmp(pCard->Next()->Field(field_no), "")) { if (serial_no_field > 0 && !strcmp(pCard->Field(serial_no_field), pCard->Next()->Field(serial_no_field))) strcat(bigstring, ", "); else strcat(bigstring, "; "); } pCard = pCard->Next(); } } else if (strcmp(pCard->Field(field_no), "")) { if (Remark->FieldList[i].FieldType < 3) { temp_double = atof(pCard->Field(field_no)); if (Remark->Special_Treatment == PDB_REMARK_R_VALUE) temp_double = temp_double / 100.0; sprintf(bigstring, FieldFormat, temp_double); } else { if (card_id != HEADER_TOKEN-1 || (field_no+1) != 2) sprintf(bigstring, FieldFormat, pCard->Field(field_no)); } } } } else sprintf(bigstring, FieldFormat, Remark->FieldList[i].Text); ndb_to_pdb_print_remark_value(bigstring, newCard, Remark, i, align); } } void _MAXIT::ndb_to_pdb_get_general_remark(REMARKS *Remark, One_Card_Info_Format *pCard) { int i, field_no, align; char bigstring[10000], FieldFormat[80]; double temp_double; One_Card_Info_Format *newCard = NULL; newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remark->Remark_No, 1); for (i = 0; i < Remark->NumField; i++) { get_remark_field_format(FieldFormat, Remark, i); memset(bigstring, 0, 10000); align = check_align(Remark->Remark_No, &(Remark->FieldList[i])); if (strcmp(Remark->FieldList[i].TokenName, "") && Remark->FieldList[i].FieldId) { field_no = Remark->FieldList[i].FieldId-1; if (strcmp(pCard->Field(field_no), "")) { if (Remark->FieldList[i].FieldType < 3) { temp_double = atof(pCard->Field(field_no)); sprintf(bigstring, FieldFormat, temp_double); } else sprintf(bigstring, FieldFormat, pCard->Field(field_no)); } } else sprintf(bigstring, FieldFormat, Remark->FieldList[i].Text); ndb_to_pdb_print_remark_value(bigstring, newCard, Remark, i, align); } } void _MAXIT::ndb_to_pdb_print_remark_value(char *value, One_Card_Info_Format *newCard, REMARKS *Remark, const int field_no, const int align) { int str_len, FieldLen, length, max_length, k, align_tmp, tmp_len; char *p = NULL, buffer[80], *tmp;; print_space_between_remark_field(newCard, Remark, field_no); str_len = strlen(newCard->Field(2)); FieldLen = NdbToken[REMARK_TOKEN-1].FieldList[2].FieldWidth + 1; if (strcmp(value, "")) { if (FieldLen > ((int) strlen(value) + str_len + 1)) newCard->AttachToField(value, 2); else { max_length = FieldLen - (str_len + 2); p = get_max_length_word(value, buffer, max_length); newCard->AttachToField(buffer, 2); length = strlen(Remark->FieldList[0].Text) + Remark->FieldList[0].FieldStCol; align_tmp = 0; if (align) { max_length = FieldLen - length - 1; align_tmp = 1; tmp = p; tmp_len = 0; while (tmp) { tmp = get_word(tmp, buffer); if ((int) strlen(buffer) > tmp_len) tmp_len = strlen(buffer); } if (tmp_len > (max_length - 1)) { max_length = FieldLen - 3; align_tmp = 0; } } else max_length = FieldLen - 3; while (p) { p = get_max_length_word(p, buffer, max_length); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remark->Remark_No, 1); if (align_tmp) { for (k = 0; k < length; k++) newCard->AttachToField(" ", 2); newCard->AttachToField(buffer, 2); } else { newCard->AddElementToField(" ", 2); newCard->AttachToField(buffer, 2); } } } } else print_null_remark_value(newCard, Remark->FieldList[field_no].FieldWidth, Remark->FieldList[field_no].FieldJustification); if (Remark->Remark_No > 100 && Remark->Remark_No != 103 && Remark->Remark_No != 105 && Remark->Remark_No != 106 && field_no == Remark->NumField-1 && Remark->Remark_No != 200 && Remark->Remark_No != 210 && Remark->Remark_No != 215 && Remark->Remark_No != 220 && Remark->Remark_No != 225 && Remark->Remark_No != 230 && Remark->Remark_No != 240 && Remark->Remark_No != 245 && Remark->Remark_No != 247 && Remark->Remark_No != 265 && Remark->Remark_No != 280 && Remark->Remark_No != 300 && Remark->Remark_No != 350 && Remark->Remark_No != 375 && Remark->Remark_No != 465 && Remark->Remark_No != 470 && Remark->Remark_No != 500 && Remark->Remark_No != 525 && Remark->Remark_No != 800 && Remark->Remark_No != 900) { strcpy(buffer, newCard->Field(2)); ndb_strip_trailing_blanks(buffer); strcat(buffer, "."); newCard->AddElementToField(buffer, 2); } } int _MAXIT::ndb_to_pdb_get_remark_from_premark(const int remarkNo) { int exist; char line[100], *p; One_Card_Info_Format *pCard = NULL, *newCard = NULL; if (remarkNo == 550) return 0; pCard = _CardInfo[PREMRK_TOKEN-1].Head(); while (pCard) { if (atoi(pCard->Field(1)) == remarkNo) break; pCard = pCard->Next(); } if (pCard == NULL) return 0; if (remarkNo == 5) { newCard = pCard; exist = 0; while (newCard && atoi(newCard->Field(1)) == remarkNo) { if (strstr(newCard->Field(2), "LAYER 1 RELEASE")) { exist = 1; break; } newCard = newCard->Next(); } if (exist) return 0; } while (pCard) { if (atoi(pCard->Field(1)) == remarkNo) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(remarkNo, 1); strcpy(line, pCard->Field(2)); p = strstr(line, "N/A"); if (p) sprintf(p, "%s", "NULL"); p = strstr(line, " NONE"); if (p) sprintf(p, "%s", " NULL"); p = strstr(line, ":NONE"); if (p) sprintf(p, "%s", ": NULL"); newCard->AddElementToField(line, 2); } pCard = pCard->Next(); } return 1; } void _MAXIT::ndb_to_pdb_get_remark_280_crystal() { int card_id, len; char buffer[5000]; One_Card_Info_Format *pCard = NULL, *qCard = NULL; card_id = find_card_id("CRDTLS"); if (_CardInfo[card_id].Head() == NULL && _CardInfo[CRSOLU_TOKEN-1].Head()) { pCard = _CardInfo[CRSOLU_TOKEN-1].Head(); memset(buffer, 0, 5000); while (pCard) { if (!strcmp(pCard->Field(3), "1") && strcasecmp(pCard->Field(4), "WATER")) { len = strlen(buffer); if (len) sprintf(&buffer[len], ", %s", pCard->Field(4)); else strcpy(buffer, pCard->Field(4)); } pCard = pCard->Next(); } if (strcmp(buffer, "")) { pCard = _CardInfo[card_id].add_a_new_card(NdbToken[card_id], 0); pCard->AddElementToField(buffer, 2); } } pCard = _CardInfo[card_id].Head(); if (pCard) { qCard = pCard->Next(); while (qCard) { if (strcmp(qCard->Field(2), "")) { if (strcmp(pCard->Field(2), "")) { len = strlen(pCard->Field(2)); if (pCard->Field(2)[len - 1] == '.') pCard->AttachToField(" ", 2); else pCard->AttachToField(". ", 2); } pCard->AttachToField(qCard->Field(2), 2); } qCard = qCard->Next(); } } ndb_to_pdb_get_general_remark(Num_Remark_280, Remark_280, 0, 0, 0, 0); } void _MAXIT::ndb_to_pdb_get_remark_290() { int i, j, k, lineNo, card_id, field_no; double result[3][3], tr[3]; char FieldFormat[80], tmpString[80], buffer[80]; One_Card_Info_Format *newCard = NULL, *pCard = NULL; NDBCELLCONST *cell = _cell; if (cell == NULL) return; for (j = 0; j < Num_Remark_290; j++) { for (i = 0; i < Remark_290[j].NumField; i++) if (!strcmp(Remark_290[j].FieldList[i].TokenName, "") && Remark_290[j].FieldList[i].FieldId == 0 && Remark_290[j].FieldList[i].FieldWidth == 0) Remark_290[j].FieldList[i].FieldWidth = strlen(Remark_290[j].FieldList[i].Text); lineNo = 1; if (Remark_290[j].Special_Treatment == PDB_REMARK_NNNMMM_SYMOP) lineNo = cell->nop; else if (Remark_290[j].Special_Treatment == PDB_REMARK_XYZT) lineNo = cell->nop * 3; for (k = 0; k < lineNo; k++) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remark_290[j].Remark_No, 1); if (Remark_290[j].Special_Treatment == PDB_REMARK_XYZT && k % 3 == 0) ndb_get_symmetry_matrix(cell, k/3, 0, 0, 0, result, tr); for (i = 0; i < Remark_290[j].NumField; i++) { print_space_between_remark_field(newCard, &Remark_290[j], i); get_remark_field_format(FieldFormat, &Remark_290[j], i); if (strcmp(Remark_290[j].FieldList[i].TokenName,"") || Remark_290[j].FieldList[i].FieldId != 0) { card_id = find_card_id(Remark_290[j].FieldList[i].TokenName); field_no = Remark_290[j].FieldList[i].FieldId-1; if (!strcmp(Remark_290[j].FieldList[i].Text,"NNNMMM")) { sprintf(tmpString, "%d%d%d%d", k+1, 5, 5, 5); sprintf(buffer, FieldFormat, tmpString); newCard->AttachToField(buffer, 2); } else if (!strcmp(Remark_290[j].FieldList[i].Text, "SYMOP")) { memset(tmpString, 0, MxStrLen); ndb_get_symmetry_operation_name(cell, k, 0, 0, 0, tmpString); newCard->AttachToField(tmpString, 2); } else if (!strcmp(Remark_290[j].FieldList[i].Text, "SMTRY")) { sprintf(tmpString, "%s%d", Remark_290[j].FieldList[i].Text, k % 3 + 1); sprintf(buffer, FieldFormat, tmpString); newCard->AttachToField(buffer, 2); } else if (!strcmp(Remark_290[j].FieldList[i].Text, "Serial_No")) { sprintf(buffer, FieldFormat, (double) (k / 3 + 1)); newCard->AttachToField(buffer, 2); } else if (!strcmp(Remark_290[j].FieldList[i].Text, "X")) { sprintf(buffer, FieldFormat, result[k%3][0]); newCard->AttachToField(buffer, 2); } else if (!strcmp(Remark_290[j].FieldList[i].Text, "Y")) { sprintf(buffer, FieldFormat, result[k%3][1]); newCard->AttachToField(buffer, 2); } else if (!strcmp(Remark_290[j].FieldList[i].Text, "Z")) { sprintf(buffer, FieldFormat, result[k%3][2]); newCard->AttachToField(buffer, 2); } else if (!strcmp(Remark_290[j].FieldList[i].Text, "T")) { sprintf(buffer, FieldFormat, tr[k%3]); newCard->AttachToField(buffer, 2); } else if (card_id == -1 || card_id > MxTokens || field_no < 0 || field_no > NdbToken[card_id].NumField) print_null_remark_value(newCard, Remark_290[j].FieldList[i].FieldWidth, Remark_290[j].FieldList[i].FieldJustification); else { pCard = _CardInfo[card_id].Head(); if (pCard && (strcmp(pCard->Field(field_no), "") || !strcmp(Remark_290[j].FieldList[i].TokenName, "CRYST1") && strcmp(pCard->Field(7), ""))) { if (!strcmp(pCard->Field(field_no), "") && !strcmp(Remark_290[j].FieldList[i].TokenName, "CRYST1") && strcmp(pCard->Field(7), "")) field_no = 7; sprintf(buffer, FieldFormat, pCard->Field(field_no)); newCard->AttachToField(buffer, 2); } else print_null_remark_value(newCard, Remark_290[j].FieldList[i].FieldWidth, Remark_290[j].FieldList[i].FieldJustification); } } else { sprintf(buffer, FieldFormat, Remark_290[j].FieldList[i].Text); newCard->AttachToField(buffer, 2); } } } } } int _MAXIT::ndb_to_pdb_get_remark_300() { int num_chn = 0, card_id, n_biol = 0, i = 0; _BIOL_ID BIOL[200]; _CHAIN *chain = NULL; One_Card_Info_Format *pCard = NULL, *stBiolCard = NULL; NDBCELLCONST *cell = _cell; if (_num_mol == 0 || _molecules == NULL) return 0; if (cell == NULL) return 0; card_id = find_card_id("CHAINS"); pCard = _CardInfo[card_id].add_a_new_card(NdbToken[card_id], 0); chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() == ATOMP_TOKEN || chain->chain_type() == ATOMN_TOKEN) num_chn++; chain = _molecules[0]->GetNextChain(); } if (num_chn) pCard->AddElementToField(num_chn, 2); if (check_virus_ncs_remark_300()) { pCard = _CardInfo[card_id].Head(); while (pCard) pCard = _CardInfo[card_id].delete_a_card(pCard); return 1; } stBiolCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (stBiolCard) { for (i = 0; i < n_biol; i++) { if (!strcmp(BIOL[i].biol_id, stBiolCard->Field(2))) break; } if (i == n_biol) { strcpy(BIOL[i].biol_id, stBiolCard->Field(2)); n_biol++; } stBiolCard = stBiolCard->Next(); } if (n_biol > 1) qsort((void *) BIOL, n_biol, sizeof(_BIOL_ID), biol_id_compare); for (i = 0; i < n_biol; i++) { if (i == 0) pCard->AddElementToField(BIOL[i].biol_id, 3); else { pCard->AttachToField(", ", 3); pCard->AttachToField(BIOL[i].biol_id, 3); } } if (_experiment_type & EXPERIMENT_TYPE_XRAY || _experiment_type & EXPERIMENT_TYPE_NEUTRON) ndb_to_pdb_get_general_remark(Num_Remark_300, Remark_300, 0, 0, 0, 0); else ndb_to_pdb_get_general_remark(Num_Remark_300_NMR, Remark_300_NMR, 0, 0, 0, 0); pCard = _CardInfo[card_id].Head(); while (pCard) pCard = _CardInfo[card_id].delete_a_card(pCard); return 1; } int _MAXIT::ndb_to_pdb_get_remark_350() { typedef struct { char asym_id[3]; char pdb_id[500]; int n_symmetry; char symmetry[100][10]; int label; } BIOL_UNIT; BIOL_UNIT biol_unit[500]; int n_biol = 0, i, j, k, l, t, len, serialNo, n_unit; int op1, op2, opno, lx, ly, lz, field_no; char FieldFormat[80], buffer[100], *p; _BIOL_ID BIOL[200]; double result[3][3], tr[3]; One_Card_Info_Format *stBiolCard = NULL, *pCard = NULL, *newCard = NULL; NDBCELLCONST *cell = _cell; if (_num_mol == 0 || _molecules == NULL) return 0; if (cell == NULL) return 0; if (check_virus_ncs_remark_350()) return 1; stBiolCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (stBiolCard) { for (i = 0; i < n_biol; i++) { if (!strcmp(BIOL[i].biol_id, stBiolCard->Field(2))) break; } if (i == n_biol) { strcpy(BIOL[i].biol_id, stBiolCard->Field(2)); n_biol++; } stBiolCard = stBiolCard->Next(); } if (n_biol > 1) qsort((void *) BIOL, n_biol, sizeof(_BIOL_ID), biol_id_compare); ndb_to_pdb_get_general_remark(Num_Remark_350, Remark_350, 0, 0, 0, 0); serialNo = 0; for (l = 0; l < n_biol; l++) { n_unit = 0; stBiolCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (stBiolCard) { if (!strcmp(stBiolCard->Field(2), BIOL[l].biol_id)) { if (!strcmp(stBiolCard->Field(4), NDB_BASE_SYMMETRY) && strcmp(stBiolCard->Field(13), "")) { strcpy(biol_unit[n_unit].asym_id, stBiolCard->Field(3)); strcpy(biol_unit[n_unit].pdb_id, stBiolCard->Field(13)); strcpy(biol_unit[n_unit].symmetry[0], stBiolCard->Field(4)); biol_unit[n_unit].n_symmetry = 1; biol_unit[n_unit].label = 1; pCard = stBiolCard->Next(); while (pCard) { if (strcmp(pCard->Field(4), NDB_BASE_SYMMETRY) && !strcmp(pCard->Field(3), stBiolCard->Field(3))) { for (i = 0; i < biol_unit[n_unit].n_symmetry; i++) if (!strcmp(biol_unit[n_unit].symmetry[i], pCard->Field(4))) break; if (i == biol_unit[n_unit].n_symmetry) { op1 = atoi(pCard->Field(4)); for (i = biol_unit[n_unit].n_symmetry - 1; i >= 0; i--) { op2 = atoi(biol_unit[n_unit].symmetry[i]); if (op1 > op2) break; } for (j = biol_unit[n_unit].n_symmetry - 1; j >= (i + 1); j--) { strcpy(biol_unit[n_unit].symmetry[j+1], biol_unit[n_unit].symmetry[j]); } strcpy(biol_unit[n_unit].symmetry[i+1], pCard->Field(4)); biol_unit[n_unit].n_symmetry++; } } pCard = pCard->Next(); } n_unit++; } } stBiolCard = stBiolCard->Next(); } for (i = 0; i < n_unit - 1; i++) { if (!biol_unit[i].label) continue; for (j = i + 1; j < n_unit; j++) { if (!biol_unit[j].label) continue; if (biol_unit[i].n_symmetry != biol_unit[j].n_symmetry) continue; for (k = 0; k < biol_unit[i].n_symmetry; k++) { if (strcmp(biol_unit[i].symmetry[k], biol_unit[j].symmetry[k])) break; } if (k == biol_unit[i].n_symmetry) { biol_unit[j].label = 0; if (!strstr(biol_unit[i].pdb_id, biol_unit[j].pdb_id)) { strcat(biol_unit[i].pdb_id, ", "); strcat(biol_unit[i].pdb_id, biol_unit[j].pdb_id); } } } } newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(350, 1); sprintf(buffer, "BIOMOLECULE: %s", BIOL[l].biol_id); newCard->AddElementToField(buffer, 2); for (i = 0; i < n_unit; i++) { if (!biol_unit[i].label) continue; p = get_max_length_word(biol_unit[i].pdb_id, FieldFormat, 28); sprintf(buffer, "APPLY THE FOLLOWING TO CHAINS: %s", FieldFormat); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(350, 1); newCard->AddElementToField(buffer, 2); while (p) { p = get_max_length_word(p, buffer, 58); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(350, 1); newCard->AddElementToField(buffer, 2); } for (t = 0; t < biol_unit[i].n_symmetry; t++) { serialNo++; opno = atoi(biol_unit[i].symmetry[t])-1; len = strlen(biol_unit[i].symmetry[t]); for (j = 0; j < len; j++) { if (biol_unit[i].symmetry[t][j] == '_') break; } lx = biol_unit[i].symmetry[t][j+1] - '5'; ly = biol_unit[i].symmetry[t][j+2] - '5'; lz = biol_unit[i].symmetry[t][j+3] - '5'; ndb_get_symmetry_matrix(cell, opno, lx, ly, lz, result, tr); for (k = 0; k < 3; k++) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remark_SYMMA.Remark_No, 1); for (j = 0; j < Remark_SYMMA.NumField; j++) { print_space_between_remark_field(newCard, &Remark_SYMMA, j); get_remark_field_format(FieldFormat, &Remark_SYMMA, j); field_no = Remark_SYMMA.FieldList[j].FieldId-1; if (!strcmp("BIOMT", Remark_SYMMA.FieldList[j].Text)) sprintf(buffer, "%s%d", Remark_SYMMA.FieldList[j].Text, k + 1); else if (field_no == 1) sprintf(buffer, FieldFormat, (double) serialNo); else if (j != Remark_SYMMA.NumField - 1) sprintf(buffer, FieldFormat, result[k][j-2]); else sprintf(buffer, FieldFormat, tr[k]); newCard->AttachToField(buffer, 2); } } } } } return 1; } void _MAXIT::ndb_to_pdb_get_remark_375() { int i = 0, num = 0, len = 0; char buffer[70], chnid[5]; _ATOM **atom = NULL; One_Card_Info_Format *newCard = NULL; if (_n_speical == 0 || _speical == NULL) return; ndb_to_pdb_get_general_remark(Num_Remark_375, Remark_375, 0, 0, 0, 0); for (i = 0; i < _n_speical; i++) { atom = _molecules[0]->find_ndb_atom(_speical[i]->a_atomtyp, _speical[i]->a_chnid, _speical[i]->a_resnam, _speical[i]->a_resnum, "", num); if (!atom) continue; newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(375, 1); if (!strcmp(atom[0]->pdb_resnam(), "HOH")) sprintf(buffer, "%-4s ", " "); else sprintf(buffer, "%-4s ", atom[0]->pdb_atmnam()); len = strlen(buffer); sprintf(&buffer[len], "%3s ", atom[0]->pdb_resnam()); len = strlen(buffer); strcpy(chnid, " "); if (strcmp(atom[0]->pdb_chnid(), "")) strcpy(chnid, atom[0]->pdb_chnid()); sprintf(&buffer[len], "%c", chnid[0]); len = strlen(buffer); sprintf(&buffer[len], "%4d", atom[0]->pdb_resnum()); len = strlen(buffer); strcpy(chnid, " "); if (strcmp(atom[0]->ins_code(), "")) strcpy(chnid, atom[0]->ins_code()); sprintf(&buffer[len], "%c", chnid[0]); len = strlen(buffer); sprintf(&buffer[len], " %s", " LIES ON A SPECIAL POSITION."); newCard->AddElementToField(buffer, 2); delete [] atom; } } void _MAXIT::ndb_to_pdb_get_remark_465() { char mol_id[4], chain_id[2], insert_code[2], buffer[80]; One_Card_Info_Format *pCard = NULL, *newCard = NULL; pCard = _CardInfo[MISRES_TOKEN-1].Head(); if (pCard) ndb_to_pdb_get_general_remark(Num_Remark_465, Remark_465, 0, 0, 0, 0); while (pCard) { newCard = _CardInfo[REMARK_TOKEN-1].add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(465, 1); if (strcmp(pCard->Field(2), "")) strcpy(mol_id, pCard->Field(2)); else strcpy(mol_id, " "); if (strcmp(pCard->Field(3), "")) strcpy(chain_id, pCard->Field(3)); else strcpy(chain_id, " "); if (strcmp(pCard->Field(6), "")) strcpy(insert_code, pCard->Field(6)); else strcpy(insert_code, " "); sprintf(buffer, "%3s %3s %c %5s%c", mol_id, pCard->Field(4), chain_id[0], pCard->Field(5), insert_code[0]); newCard->AddElementToField(buffer, 2); pCard = pCard->Next(); } } void _MAXIT::ndb_to_pdb_get_remark_470() { int first = TRUE, first_residue = 0, num = 0; char head[20], model[5], buff[10], buffer[10], chnid = ' ', *p = NULL; char ins = ' '; One_Card_Info_Format *newCard = NULL; _CHAIN *chain = NULL; _RESIDUE *residue = NULL; for (int i = 0; i < _num_mol; i++) { chain = _molecules[i]->GetFirstChain(); while (chain) { if (chain->chain_type() != ATOMN_TOKEN && chain->chain_type() != ATOMP_TOKEN) { chain = _molecules[i]->GetNextChain(); continue; } first_residue = 0; residue = chain->GetFirstResidue(); while (residue) { residue->find_missing_or_extra_atoms(chain->chain_type(), !first_residue, 0); first_residue = 1; if (!strcmp(residue->missing().Text(), "")) { residue = chain->GetNextResidue(); continue; } if (first) { first = FALSE; ndb_to_pdb_get_general_remark(Num_Remark_470, Remark_470, 0, 0, 0, 0); } head[0] = '\0'; model[0] = '\0'; if (_num_mol > 1) sprintf(model, "%3d", _molecules[i]->Mol_ID()); else strcpy(model, " "); ins = residue->GetFirstAtom()->ins_code()[0]; if (ins == '\0') ins = ' '; chnid = chain->PDB_ChainID()[0]; if (chnid == '\0') chnid = ' '; sprintf(head, "%3s %3s %c%4d%c ", model, residue->ResName(), chnid, residue->pdb_res_no(), ins); num = 0; newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(470, 1); newCard->AddElementToField(head, 2); p = residue->missing().Text(); if (p) ndb_clean_string(p); while (p && strcmp(p, "")) { if (num == 7) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(470, 1); newCard->AddElementToField(head, 2); num = 0; } p = get_word(p, buff); sprintf(buffer, "%-6s", buff); newCard->AttachToField(buffer, 2); num++; } residue = chain->GetNextResidue(); } chain = _molecules[i]->GetNextChain(); } } } void _MAXIT::ndb_to_pdb_get_remark_500(const int remark) { int i, rowNo, exist_asym_close_contact = 0, exist_sym_close_contact = 0; int symmetry_op_2, dist_index; BTreeObj<_DIndex> _Index; CifString string; _DIndex _idx; ISTable *Table = NULL; if (!_CifObj) return; Table = _CifObj->GetTablePtr(_StructureId, "ebi_validate_contact"); if (is_empty_table(Table)) return; rowNo = Table->GetNumRows(); symmetry_op_2 = Table->GetColumnIndex("symmetry_op_2"); dist_index = Table->GetColumnIndex("dist"); _Index.Clear(); for (i = 0; i < rowNo; i++) { Table->GetCell(string, symmetry_op_2, i); if (!strcasecmp(string.Text(), "1_555")) exist_asym_close_contact = 1; if (strcasecmp(string.Text(), "1_555")) exist_sym_close_contact = 1; Table->GetCell(string, dist_index, i); _idx.set_value(atof(string.Text())); _idx.set_pos(i); _Index.Add(_idx); } if (exist_asym_close_contact) { if (_experiment_type & EXPERIMENT_TYPE_MODEL || _experiment_type & EXPERIMENT_TYPE_NMR) ndb_to_pdb_get_general_remark(Num_Remark_500_NMR, Remark_500_NMR, 0, 0, 0, 0); else ndb_to_pdb_get_general_remark(Num_Remark_500_A, Remark_500_A, 0, 0, 0, 0); output_close_contact(Table, _Index, 0); } if (!remark && exist_sym_close_contact) { ndb_to_pdb_get_general_remark(Num_Remark_500_S, Remark_500_S, 0, 0, 0, 0); output_close_contact(Table, _Index, 1); } } void _MAXIT::ndb_to_pdb_get_remark_525() { if (_n_waters == 0 || _waters == NULL) return; ndb_to_pdb_get_general_remark(Num_Remark_525, Remark_525, 0, 0, 0, 0); int num = 0, len = 0, i;; double dist = 0; _ATOM **atom = NULL; char buffer[70], chnid[5], ins_code[5]; One_Card_Info_Format *newCard = NULL; for (i = 0; i < _n_waters; i++) { atom = _molecules[0]->find_ndb_atom(_waters[i]->a_atomtyp, _waters[i]->a_chnid, _waters[i]->a_resnam, _waters[i]->a_resnum, "", num); if (!atom) continue; newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(525, 1); strcpy(chnid, " "); strcpy(ins_code, " "); if (strcmp(atom[0]->pdb_chnid(), "")) strcpy(chnid, atom[0]->pdb_chnid()); if (strcmp(atom[0]->ins_code(), "")) strcpy(ins_code, atom[0]->ins_code()); sprintf(buffer, " %3s %c%4d%c", atom[0]->pdb_resnam(), chnid[0], atom[0]->pdb_resnum(), ins_code[0]); dist = cal_min_distance(_molecules[0], atom[0]); delete [] atom; len = strlen(buffer); sprintf(&buffer[len], " DISTANCE = %5.2f ANGSTROMS", dist); newCard->AddElementToField(buffer, 2); } } void _MAXIT::ndb_to_pdb_processing_nmr_remarks() { int count = 0, i = 0; char buff[1000], program[1000], authors[1000]; char maker[100], model[100], strengh[100], *p; One_Card_Info_Format *pCard = NULL, *qCard = NULL; pCard = _CardInfo[REFMET_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[REFMET_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[NMRECD_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[NMRECD_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[NMRSFT_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[NMRSFT_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[SFTWAR_TOKEN-1].Head(); while (pCard) { if (!strcasecmp(pCard->Field(2), "refinement")) count++; pCard = pCard->Next(); } program[0] = '\0'; authors[0] = '\0'; i = 0; pCard = _CardInfo[SFTWAR_TOKEN-1].Head(); while (pCard) { if (!strcasecmp(pCard->Field(2), "refinement")) { i++; if (strcmp(pCard->Field(4), "")) sprintf(buff, "%s %s", pCard->Field(3), pCard->Field(4)); else sprintf(buff, "%s", pCard->Field(3)); if (strcmp(program, "")) strcat(program, ", "); strcat(program, buff); if (count > 1) sprintf(buff, "%s (%s)", pCard->Field(5), pCard->Field(3)); else strcpy(buff, pCard->Field(5)); if (strcmp(authors, "")) strcat(authors, ", "); strcat(authors, buff); } pCard = pCard->Next(); } pCard = _CardInfo[REFMET_TOKEN-1].add_a_new_card(NdbToken[REFMET_TOKEN-1], 0); pCard->AddElementToField(program, 3); pCard->AddElementToField(authors, 4); count = 0; pCard = _CardInfo[SFTWAR_TOKEN-1].Head(); while (pCard) { if (strcasecmp(pCard->Field(2), "refinement")) count++; pCard = pCard->Next(); } program[0] = '\0'; i = 0; pCard = _CardInfo[SFTWAR_TOKEN-1].Head(); while (pCard) { if (strcasecmp(pCard->Field(2), "refinement")) { i++; if (strcmp(pCard->Field(4), "")) sprintf(buff, "%s %s", pCard->Field(3), pCard->Field(4)); else sprintf(buff, "%s", pCard->Field(3)); if (!strstr(program, buff)) { if (strcmp(program, "")) strcat(program, ", "); strcat(program, buff); } } pCard = pCard->Next(); } pCard = _CardInfo[NMRSFT_TOKEN-1].add_a_new_card(NdbToken[NMRSFT_TOKEN-1], 0); pCard->AddElementToField(program, 2); pCard = _CardInfo[NMREXP_TOKEN-1].Head(); program[0] = '\0'; while (pCard) { if (!strstr(program, pCard->Field(3))) { if (!strcmp(program, "")) strcpy(program, pCard->Field(3)); else { strcat(program, ", "); strcat(program, pCard->Field(3)); } } pCard = pCard->Next(); } pCard = _CardInfo[NMRECD_TOKEN-1].add_a_new_card(NdbToken[NMRECD_TOKEN-1], 0); pCard->AddElementToField(program, 2); pCard = _CardInfo[NMRSPM_TOKEN-1].Head(); if (pCard) { maker[0] = model[0] = strengh[0] = '\0'; while (pCard) { p = strstr(pCard->Field(4), "MHZ"); if (p == NULL) { sprintf(buff, "%s MHZ", pCard->Field(4)); pCard->AddElementToField(buff, 4); } if (strcmp(pCard->Field(2), "") && !strstr(model, pCard->Field(2))) { if (strcmp(model, "")) { strcat(model, ", "); strcat(model, pCard->Field(2)); } else strcpy(model, pCard->Field(2)); } if (strcmp(pCard->Field(3), "") && !strstr(maker, pCard->Field(3))) { if (strcmp(maker, "")) { strcat(maker, ", "); strcat(maker, pCard->Field(3)); } else strcpy(maker, pCard->Field(3)); } if (strcmp(pCard->Field(4), "") && !strstr(strengh, pCard->Field(4))) { if (strcmp(strengh, "")) { strcat(strengh, ", "); strcat(strengh, pCard->Field(4)); } else strcpy(strengh, pCard->Field(4)); } pCard = pCard->Next(); } pCard = _CardInfo[NMRSPM_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[NMRSPM_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[NMRSPM_TOKEN-1].add_a_new_card(NdbToken[NMRSPM_TOKEN-1], 0); pCard->AddElementToField(model, 2); pCard->AddElementToField(maker, 3); pCard->AddElementToField(strengh, 4); } pCard = _CardInfo[NMRSMP_TOKEN-1].Head(); while (pCard) { if (strcmp(pCard->Field(7), "")) { pCard->AttachToField(" ", 4); pCard->AttachToField(pCard->Field(7), 4); } pCard = pCard->Next(); } pCard = _CardInfo[NMRSMP_TOKEN-1].Head(); if (pCard) { qCard = pCard->Next(); if (qCard) { for (i = 3; i < 7; i++) { if (!strcmp(pCard->Field(i), "")) pCard->AddElementToField("NULL", i); } } while (qCard) { for (i = 3; i < 7; i++) { pCard->AttachToField("; ", i); if (strcmp(qCard->Field(i), "")) pCard->AttachToField(qCard->Field(i), i); else pCard->AttachToField("NULL", i); } qCard = qCard->Next(); } } int NMRSDT_TOKEN = find_card_id("NMRSDT"); pCard = _CardInfo[NMRSDT_TOKEN].Head(); if (pCard) { qCard = pCard->Next(); if (qCard) { if (!strcmp(pCard->Field(2), "")) pCard->AddElementToField("NULL", 2); } while (qCard) { pCard->AttachToField("; ", 2); if (strcmp(qCard->Field(2), "")) pCard->AttachToField(qCard->Field(2), 2); else pCard->AttachToField("NULL", 2); qCard = qCard->Next(); } } } int _MAXIT::check_virus_ncs_remark_300() { int n_ncs = 0, card_id, i; NCS_COR *ncs = NULL; card_id = find_card_id("NCSRMK"); if (card_id < 0) return 0; One_Card_Info_Format *pCard = _CardInfo[card_id].Head(); if (pCard == NULL) return 0; while (pCard) { for (i = 0; i < n_ncs; i++) { if (ncs[i].oper_id == atoi(pCard->Field(2))) break; } if (i == n_ncs) { n_ncs++; ncs = (NCS_COR *) realloc(ncs, n_ncs * sizeof(NCS_COR)); ncs[i].oper_id = atoi(pCard->Field(2)); strcpy(ncs[i].chain[0], pCard->Field(4)); ncs[i].num_chain = 1; } else { strcpy(ncs[i].chain[ncs[i].num_chain], pCard->Field(4)); ncs[i].num_chain++; } pCard = pCard->Next(); } if (!n_ncs) return 0; ndb_to_pdb_get_general_remark(Num_Remark_300_VIRUS, Remark_300_VIRUS, 0, 0, 0, 0); if (ncs) free ((void *) ncs); return 1; } int _MAXIT::check_virus_ncs_remark_350() { int n_ncs = 0, card_id, i, j, k, n, field_no, str_len; char FieldFormat[82], buffer[60]; NCS_COR *ncs = NULL; One_Card_Info_Format *pCard = NULL, *newCard = NULL; card_id = find_card_id("NCSRMK"); if (card_id < 0) return 0; pCard = _CardInfo[card_id].Head(); if (pCard == NULL) return 0; while (pCard) { for (i = 0; i < n_ncs; i++) { if (ncs[i].oper_id == atoi(pCard->Field(2))) break; } if (i == n_ncs) { n_ncs++; ncs = (NCS_COR *) realloc(ncs, n_ncs * sizeof(NCS_COR)); ncs[i].oper_id = atoi(pCard->Field(2)); strcpy(ncs[i].chain[0], pCard->Field(4)); ncs[i].num_chain = 1; } else { strcpy(ncs[i].chain[ncs[i].num_chain], pCard->Field(4)); ncs[i].num_chain++; } pCard = pCard->Next(); } if (!n_ncs) return 0; ndb_to_pdb_get_general_remark(Num_Remark_350, Remark_350, 0, 0, 0, 0); for (n = 0; n < n_ncs; n++) { if (!n) { for (i = 0; i < 2; i++) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remark_SYMMA_CHAIN[i].Remark_No, 1); strcpy(buffer, ""); for (j = 0; j < Remark_SYMMA_CHAIN[i].NumField; j++) { get_remark_field_format(FieldFormat, &Remark_SYMMA_CHAIN[i], j); field_no = Remark_SYMMA_CHAIN[i].FieldList[j].FieldId-1; str_len = strlen(buffer); if (strcmp(Remark_SYMMA_CHAIN[i].FieldList[j].TokenName, "SYMMA") || field_no == 0) { sprintf(&buffer[str_len], "%s", Remark_SYMMA_CHAIN[i].FieldList[j].Text); } else { for (k = 0; k < ncs[n].num_chain; k++) { str_len = strlen(buffer); if (k) sprintf(&buffer[str_len], ", %s", ncs[n].chain[k]); else sprintf(&buffer[str_len], " %s", ncs[n].chain[k]); } } } newCard->AddElementToField(buffer, 2); } } double result[3][4]; if (!get_matrix(result, ncs[n].oper_id)) continue; for (k = 0; k < 3; k++) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(Remark_SYMMA.Remark_No, 1); for (j = 0; j < Remark_SYMMA.NumField; j++) { print_space_between_remark_field(newCard, &Remark_SYMMA, j); get_remark_field_format(FieldFormat, &Remark_SYMMA, j); field_no = Remark_SYMMA.FieldList[j].FieldId-1; if (!strcmp("BIOMT", Remark_SYMMA.FieldList[j].Text)) sprintf(buffer, "%s%d", Remark_SYMMA.FieldList[j].Text, k + 1); else if (field_no == 1) sprintf(buffer, FieldFormat, (double) (n+1)); else if (j != Remark_SYMMA.NumField - 1) sprintf(buffer, FieldFormat, result[k][j-2]); else sprintf(buffer, FieldFormat, result[k][3]); newCard->AttachToField(buffer, 2); } } } if (ncs) free ((void *) ncs); return 1; } void _MAXIT::rms_deviation_of_bonds() { int i, len, rowNo, auth_atom_id_1, auth_asym_id_1, auth_comp_id_1, auth_seq_id_1; int insert_id_1, auth_atom_id_2, auth_asym_id_2, auth_comp_id_2, auth_seq_id_2; int insert_id_2, bond_deviation, a_resnum, b_resnum, model_id, Mol_ID = 0; char buffer[80], a_atomtyp[5], b_atomtyp[5]; CifString a_chnid, a_resnam, a_inscode, cifstring, b_chnid, b_resnam, b_inscode; float bond_length; ISTable *Table = NULL; One_Card_Info_Format *newCard = NULL; if (!_CifObj) return; Table = _CifObj->GetTablePtr(_StructureId, "ebi_validate_bond"); if (is_empty_table(Table)) return; ndb_to_pdb_get_general_remark(Num_Remark_500_BOND, Remark_500_BOND, 0, 0, 0, 0); rowNo = Table->GetNumRows(); model_id = Table->GetColumnIndex("model_id"); auth_atom_id_1 = Table->GetColumnIndex("auth_atom_id_1"); auth_asym_id_1 = Table->GetColumnIndex("auth_asym_id_1"); auth_comp_id_1 = Table->GetColumnIndex("auth_comp_id_1"); auth_seq_id_1 = Table->GetColumnIndex("auth_seq_id_1"); insert_id_1 = Table->GetColumnIndex("insert_id_1"); auth_atom_id_2 = Table->GetColumnIndex("auth_atom_id_2"); auth_asym_id_2 = Table->GetColumnIndex("auth_asym_id_2"); auth_comp_id_2 = Table->GetColumnIndex("auth_comp_id_2"); auth_seq_id_2 = Table->GetColumnIndex("auth_seq_id_2"); insert_id_2 = Table->GetColumnIndex("insert_id_2"); bond_deviation = Table->GetColumnIndex("bond_deviation"); for (i = 0; i < rowNo; i++) { get_value(a_chnid, Table, auth_asym_id_1, i); get_value(a_resnam, Table, auth_comp_id_1, i); get_value(cifstring, Table, auth_seq_id_1, i); a_resnum = atoi(cifstring.Text()); get_value(a_inscode, Table, insert_id_1, i); get_value(cifstring, Table, auth_atom_id_1, i); print_atom_atomName_field("", 0, a_atomtyp, cifstring.Text(), a_resnam.Text(), 0); if (a_chnid == "") a_chnid.Copy(" "); if (a_inscode == "") a_inscode.Copy(" "); get_value(b_chnid, Table, auth_asym_id_2, i); get_value(b_resnam, Table, auth_comp_id_2, i); get_value(cifstring, Table, auth_seq_id_2, i); b_resnum = atoi(cifstring.Text()); get_value(b_inscode, Table, insert_id_2, i); get_value(cifstring, Table, auth_atom_id_2, i); print_atom_atomName_field("", 0, b_atomtyp, cifstring.Text(), b_resnam.Text(), 0); if (b_chnid == "") b_chnid.Copy(" "); if (b_inscode == "") b_inscode.Copy(" "); get_value(cifstring, Table, bond_deviation, i); bond_length = atof(cifstring.Text()); get_value(cifstring, Table, model_id, i); Mol_ID = atoi(cifstring.Text()); if (_num_mol > 1) sprintf(buffer, "%2d %3s %c%4d%c %4s %3s %c%4d%c %4s", Mol_ID, a_resnam.Text(), a_chnid.Text()[0], a_resnum, a_inscode.Text()[0], a_atomtyp, b_resnam.Text(), b_chnid.Text()[0], b_resnum, b_inscode.Text()[0], b_atomtyp); else sprintf(buffer, " %3s %c%4d%c %4s %3s %c%4d%c %4s", a_resnam.Text(), a_chnid.Text()[0], a_resnum, a_inscode.Text()[0], a_atomtyp, b_resnam.Text(), b_chnid.Text()[0], b_resnum, b_inscode.Text()[0], b_atomtyp); len = strlen(buffer); sprintf(&buffer[len], " %6.3f", bond_length); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(500, 1); newCard->AddElementToField(buffer, 2); } } void _MAXIT::rms_deviation_of_angles() { int i, len, rowNo, auth_atom_id_1, auth_asym_id_2, auth_comp_id_2, auth_seq_id_2; int insert_id_2, auth_atom_id_2, auth_atom_id_3, resnum_2, model_id, Mol_ID = 0; int angle_deviation; char atomtyp_1[5], atomtyp_2[5], atomtyp_3[5], buffer[80]; CifString cifstring, chnid_2, resnam_2, inscode_2; float angle_value; ISTable *Table = NULL; One_Card_Info_Format *newCard = NULL; if (!_CifObj) return; Table = _CifObj->GetTablePtr(_StructureId, "ebi_validate_angle"); if (is_empty_table(Table)) return; ndb_to_pdb_get_general_remark(Num_Remark_500_ANGLE, Remark_500_ANGLE, 0, 0, 0, 0); rowNo = Table->GetNumRows(); model_id = Table->GetColumnIndex("model_id"); auth_atom_id_1 = Table->GetColumnIndex("auth_atom_id_1"); auth_asym_id_2 = Table->GetColumnIndex("auth_asym_id_2"); auth_comp_id_2 = Table->GetColumnIndex("auth_comp_id_2"); auth_seq_id_2 = Table->GetColumnIndex("auth_seq_id_2"); insert_id_2 = Table->GetColumnIndex("insert_id_2"); auth_atom_id_2 = Table->GetColumnIndex("auth_atom_id_2"); auth_atom_id_3 = Table->GetColumnIndex("auth_atom_id_3"); angle_deviation = Table->GetColumnIndex("angle_deviation"); for (i = 0; i < rowNo; i++) { get_value(chnid_2, Table, auth_asym_id_2, i); get_value(resnam_2, Table, auth_comp_id_2, i); get_value(cifstring, Table, auth_seq_id_2, i); resnum_2 = atoi(cifstring.Text()); get_value(inscode_2, Table, insert_id_2, i); get_value(cifstring, Table, auth_atom_id_1, i); print_atom_atomName_field("", 0, atomtyp_1, cifstring.Text(), resnam_2.Text(), 0); get_value(cifstring, Table, auth_atom_id_2, i); print_atom_atomName_field("", 0, atomtyp_2, cifstring.Text(), resnam_2.Text(), 0); get_value(cifstring, Table, auth_atom_id_3, i); print_atom_atomName_field("", 0, atomtyp_3, cifstring.Text(), resnam_2.Text(), 0); get_value(cifstring, Table, angle_deviation, i); angle_value = atof(cifstring.Text()); get_value(cifstring, Table, model_id, i); Mol_ID = atoi(cifstring.Text()); if (chnid_2 == "") chnid_2.Copy(" "); if (inscode_2 == "") inscode_2.Copy(" "); if (_num_mol > 1) sprintf(buffer, "%2d %3s %c%4d%c", Mol_ID, resnam_2.Text(), chnid_2.Text()[0], resnum_2, inscode_2.Text()[0]); else sprintf(buffer, " %3s %c%4d%c", resnam_2.Text(), chnid_2.Text()[0], resnum_2, inscode_2.Text()[0]); len = strlen(buffer); sprintf(&buffer[len], " %4s - %4s - %4s ANGL. DEV. =%5.1f DEGREES", atomtyp_1, atomtyp_2, atomtyp_3, angle_value); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(500, 1); newCard->AddElementToField(buffer, 2); } } void _MAXIT::outside_torsions() { int i, rowNo, model_id, auth_comp_id, auth_asym_id, auth_seq_id, insert_id; int phi_index, psi_index, Mol_ID, resnum; char buffer[80]; CifString cifstring, resnam, chnid, inscode; float phi, psi; ISTable *Table = NULL; One_Card_Info_Format *newCard = NULL; if (!_CifObj) return; Table = _CifObj->GetTablePtr(_StructureId, "ebi_validate_torsion"); if (is_empty_table(Table)) return; ndb_to_pdb_get_general_remark(Num_Remark_500_TORSION, Remark_500_TORSION, 0, 0, 0, 0); rowNo = Table->GetNumRows(); model_id = Table->GetColumnIndex("model_id"); auth_comp_id = Table->GetColumnIndex("auth_comp_id"); auth_asym_id = Table->GetColumnIndex("auth_asym_id"); auth_seq_id = Table->GetColumnIndex("auth_seq_id"); insert_id = Table->GetColumnIndex("insert_id"); phi_index = Table->GetColumnIndex("phi"); psi_index = Table->GetColumnIndex("psi"); for (i = 0; i < rowNo; i++) { get_value(cifstring, Table, model_id, i); Mol_ID = atoi(cifstring.Text()); get_value(resnam, Table, auth_comp_id, i); get_value(chnid, Table, auth_asym_id, i); get_value(cifstring, Table, auth_seq_id, i); resnum = atoi(cifstring.Text()); get_value(inscode, Table, insert_id, i); get_value(cifstring, Table, phi_index, i); phi = atof(cifstring.Text()); get_value(cifstring, Table, psi_index, i); psi = atof(cifstring.Text()); if (chnid == "") chnid.Copy(" "); if (inscode == "") inscode.Copy(" "); if (_num_mol > 1) sprintf(buffer, "%2d %3s %c%4d%c %7.2f %7.2f", Mol_ID, resnam.Text(), chnid.Text()[0], resnum, inscode.Text()[0], psi, phi); else sprintf(buffer, " %3s %c%4d%c %7.2f %7.2f", resnam.Text(), chnid.Text()[0], resnum, inscode.Text()[0], psi, phi); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(500, 1); newCard->AddElementToField(buffer, 2); } } void _MAXIT::non_cis_trans_torsions() { int i, rowNo, model_id, auth_asym_id_1, auth_comp_id_1, auth_seq_id_1; int insert_id_1, auth_asym_id_2, auth_comp_id_2, auth_seq_id_2, insert_id_2; int omega_index, a_resnum, b_resnum, Mol_ID; char buffer[80]; CifString a_chnid, a_resnam, a_inscode, b_chnid, b_resnam, b_inscode, cifstring; float omega; ISTable *Table = NULL; One_Card_Info_Format *newCard = NULL; if (!_CifObj) return; Table = _CifObj->GetTablePtr(_StructureId, "ebi_validate_peptide_omega"); if (is_empty_table(Table)) return; ndb_to_pdb_get_general_remark(Num_Remark_500_NON_CIS, Remark_500_NON_CIS, 0, 0, 0, 0); rowNo = Table->GetNumRows(); model_id = Table->GetColumnIndex("model_id"); auth_asym_id_1 = Table->GetColumnIndex("auth_asym_id_1"); auth_comp_id_1 = Table->GetColumnIndex("auth_comp_id_1"); auth_seq_id_1 = Table->GetColumnIndex("auth_seq_id_1"); insert_id_1 = Table->GetColumnIndex("insert_id_1"); auth_asym_id_2 = Table->GetColumnIndex("auth_asym_id_2"); auth_comp_id_2 = Table->GetColumnIndex("auth_comp_id_2"); auth_seq_id_2 = Table->GetColumnIndex("auth_seq_id_2"); insert_id_2 = Table->GetColumnIndex("insert_id_2"); omega_index = Table->GetColumnIndex("omega"); for (i = 0; i < rowNo; i++) { get_value(a_chnid, Table, auth_asym_id_1, i); get_value(a_resnam, Table, auth_comp_id_1, i); get_value(cifstring, Table, auth_seq_id_1, i); a_resnum = atoi(cifstring.Text()); get_value(a_inscode, Table, insert_id_1, i); if (a_chnid == "") a_chnid.Copy(" "); if (a_inscode == "") a_inscode.Copy(" "); get_value(b_chnid, Table, auth_asym_id_2, i); get_value(b_resnam, Table, auth_comp_id_2, i); get_value(cifstring, Table, auth_seq_id_2, i); b_resnum = atoi(cifstring.Text()); get_value(b_inscode, Table, insert_id_2, i); if (b_chnid == "") b_chnid.Copy(" "); if (b_inscode == "") b_inscode.Copy(" "); get_value(cifstring, Table, omega_index, i); omega = atof(cifstring.Text()); get_value(cifstring, Table, model_id, i); Mol_ID = atoi(cifstring.Text()); if (_num_mol > 1) sprintf(buffer, "%3s %c %4d%c %3s %c %4d%c %3d %7.2f", a_resnam.Text(), a_chnid.Text()[0], a_resnum, a_inscode.Text()[0], b_resnam.Text(), b_chnid.Text()[0], b_resnum, b_inscode.Text()[0], Mol_ID, omega); else sprintf(buffer, "%3s %c %4d%c %3s %c %4d%c %7.2f", a_resnam.Text(), a_chnid.Text()[0], a_resnum, a_inscode.Text()[0], b_resnam.Text(), b_chnid.Text()[0], b_resnum, b_inscode.Text()[0], omega); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(500, 1); newCard->AddElementToField(buffer, 2); } } void _MAXIT::output_close_contact(ISTable *Table, BTreeObj<_DIndex>& _Index, const int sym) { int i = 0, j, ret = 1, auth_atom_id_1, auth_asym_id_1, auth_comp_id_1, auth_seq_id_1; int insert_id_1, auth_atom_id_2, auth_asym_id_2, auth_comp_id_2, auth_seq_id_2; int insert_id_2, symmetry_op_2, dist_index, a_resnum, b_resnum, num = 0, len = 0; char buffer[80], atomName[10]; CifString a_atomtyp, a_chnid, a_resnam, a_inscode, cifstring; CifString b_atomtyp, b_chnid, b_resnam, b_inscode, symmetry; float dist; _ATOM **atom_a = NULL, **atom_b = NULL; _DIndex _idx; One_Card_Info_Format *newCard = NULL; auth_atom_id_1 = Table->GetColumnIndex("auth_atom_id_1"); auth_asym_id_1 = Table->GetColumnIndex("auth_asym_id_1"); auth_comp_id_1 = Table->GetColumnIndex("auth_comp_id_1"); auth_seq_id_1 = Table->GetColumnIndex("auth_seq_id_1"); insert_id_1 = Table->GetColumnIndex("insert_id_1"); auth_atom_id_2 = Table->GetColumnIndex("auth_atom_id_2"); auth_asym_id_2 = Table->GetColumnIndex("auth_asym_id_2"); auth_comp_id_2 = Table->GetColumnIndex("auth_comp_id_2"); auth_seq_id_2 = Table->GetColumnIndex("auth_seq_id_2"); insert_id_2 = Table->GetColumnIndex("insert_id_2"); symmetry_op_2 = Table->GetColumnIndex("symmetry_op_2"); dist_index = Table->GetColumnIndex("dist"); _Index.GoFirst(); while (ret >= 0) { _idx = _Index.GetCurrData(); i = _idx.pos(); get_value(a_atomtyp, Table, auth_atom_id_1, i); get_value(a_chnid, Table, auth_asym_id_1, i); get_value(a_resnam, Table, auth_comp_id_1, i); get_value(cifstring, Table, auth_seq_id_1, i); a_resnum = atoi(cifstring.Text()); get_value(a_inscode, Table, insert_id_1, i); get_value(b_atomtyp, Table, auth_atom_id_2, i); get_value(b_chnid, Table, auth_asym_id_2, i); get_value(b_resnam, Table, auth_comp_id_2, i); get_value(cifstring, Table, auth_seq_id_2, i); b_resnum = atoi(cifstring.Text()); get_value(b_inscode, Table, insert_id_2, i); get_value(symmetry, Table, symmetry_op_2, i); get_value(cifstring, Table, dist_index, i); dist = atof(cifstring.Text()); if (sym && symmetry == "1_555" || !sym && symmetry != "1_555") { ret = _Index.GoToNext(); continue; } strcpy(buffer, symmetry.Text()); symmetry.Clear(); len = strlen(buffer); for (j = 0; j < len; j++) { if (buffer[j] == '_') continue; symmetry += buffer[j]; } atom_a = _molecules[0]->find_pdb_atom(a_atomtyp.Text(), a_chnid.Text(), a_resnam.Text(), a_resnum, a_inscode.Text(), num); atom_b = _molecules[0]->find_pdb_atom(b_atomtyp.Text(), b_chnid.Text(), b_resnam.Text(), b_resnum, b_inscode.Text(), num); if (!atom_a || !atom_b) { if (atom_a) delete [] atom_a; if (atom_b) delete [] atom_b; ret = _Index.GoToNext(); continue; } print_atom_atomName_field(atom_a[0]->atom_type(), 0, atomName, atom_a[0]->pdb_atmnam(), atom_a[0]->pdb_resnam(), atom_a[0]->align()); sprintf(buffer, " %-4s %-3s", atomName, atom_a[0]->pdb_resnam()); len = strlen(buffer); strcpy(atomName, " "); if (strcmp(atom_a[0]->pdb_chnid(), "")) strcpy(atomName, atom_a[0]->pdb_chnid()); sprintf(&buffer[len], " %c %4d", atomName[0], atom_a[0]->pdb_resnum()); len = strlen(buffer); strcpy(atomName, " "); if (strcmp(atom_a[0]->ins_code(), "")) strcpy(atomName, atom_a[0]->ins_code()); sprintf(&buffer[len], "%c ", atomName[0]); print_atom_atomName_field(atom_b[0]->atom_type(), 0, atomName, atom_b[0]->pdb_atmnam(), atom_b[0]->pdb_resnam(), atom_b[0]->align()); len = strlen(buffer); sprintf(&buffer[len], " %-4s %-3s", atomName, atom_b[0]->pdb_resnam()); len = strlen(buffer); strcpy(atomName, " "); if (strcmp(atom_b[0]->pdb_chnid(), "")) strcpy(atomName, atom_b[0]->pdb_chnid()); sprintf(&buffer[len], " %c %4d", atomName[0], atom_b[0]->pdb_resnum()); len = strlen(buffer); strcpy(atomName, " "); if (strcmp(atom_b[0]->ins_code(), "")) strcpy(atomName, atom_b[0]->ins_code()); sprintf(&buffer[len], "%c", atomName[0]); if (atom_a) delete [] atom_a; if (atom_b) delete [] atom_b; len = strlen(buffer); if (!sym) sprintf(&buffer[len], " %5.2f", dist); else sprintf(&buffer[len], " %5s %5.2f", symmetry.Text(), dist); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(500, 1); newCard->AddElementToField(buffer, 2); ret = _Index.GoToNext(); } } void _MAXIT::get_cispep_cards() { if (_n_torsion == 0 || _torsion == NULL) return; if (_torsionIndex.Root() < 0) return; int CISPEP_TOKEN = find_card_id("CISPEP"); if (CISPEP_TOKEN == -1) return; _CardInfo[CISPEP_TOKEN].clear_Cards(); _RESIDUE *residue = NULL; One_Card_Info_Format *pCard = NULL; _ATOM *atom = NULL; CifString index("OMEGA"); int serial_no = 0; int ret = _torsionIndex.Seek(index); while (ret >= 0) { if (index != _torsionIndex.GetCurrData()) break; if (fabs(_torsion[ret]->val) > 30.0) { ret = _torsionIndex.GoToNext(); continue; } residue = _molecules[0]->find_prev_residue(_torsion[ret]->ChainID, _torsion[ret]->ResName, _torsion[ret]->ResNum, _torsion[ret]->ins_code); if (!residue) { ret = _torsionIndex.GoToNext(); continue; } serial_no++; pCard = _CardInfo[CISPEP_TOKEN]. add_a_new_card(NdbToken[CISPEP_TOKEN], 0); atom = residue->GetFirstAtom(); pCard->AddElementToField(serial_no, 1); pCard->AddElementToField(residue->ResName(), 2); pCard->AddElementToField(_torsion[ret]->ChainID, 3); pCard->AddElementToField(atom->pdb_resnum(), 4); pCard->AddElementToField(atom->ins_code(), 5); pCard->AddElementToField(_torsion[ret]->ResName, 6); pCard->AddElementToField(_torsion[ret]->ChainID, 7); pCard->AddElementToField(_torsion[ret]->ResNum, 8); pCard->AddElementToField(_torsion[ret]->ins_code, 9); if (_num_mol > 1) pCard->AddElementToField(_torsion[ret]->Mol_ID, 10); else pCard->AddElementToField(0, 10); pCard->AddElementToField(_torsion[ret]->val, 11); ret = _torsionIndex.GoToNext(); } } void _MAXIT::construct_remark_900() { int max_length = 60; char buffer[62], *p; One_Card_Info_Format *pCard = _CardInfo[RENTRY_TOKEN-1].Head(); One_Card_Info_Format *newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(900, 1); newCard = _CardInfo[REMARK_TOKEN-1].add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(900, 1); newCard->AddElementToField("RELATED ENTRIES", 2); while (pCard) { newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(900, 1); sprintf(buffer, "RELATED ID: %s RELATED DB: %s", pCard->Field(3), pCard->Field(2)); newCard->AddElementToField(buffer, 2); if (strcmp(pCard->Field(4), "")) { pCard->CleanStringField(4); p = get_max_length_word(pCard->Field(4), buffer, max_length); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(900, 1); newCard->AddElementToField(buffer, 2); while (p) { p = get_max_length_word(p, buffer, max_length); newCard = _CardInfo[REMARK_TOKEN-1]. add_a_new_card(NdbToken[REMARK_TOKEN-1], 0); newCard->AddElementToField(900, 1); newCard->AddElementToField(buffer, 2); } } pCard = pCard->Next(); } } void _MAXIT::check_atom_number_count() { if (_num_mol == 0) return; int card_id = find_card_id("ATNUMS"); One_Card_Info_Format *pCard = _CardInfo[card_id].Head(); if (pCard == NULL) { pCard = _CardInfo[card_id].add_a_new_card(NdbToken[card_id], 0); int atom_no = _molecules[0]->count_atom_no(ATOMP_TOKEN); pCard->AddElementToField(atom_no, 2); atom_no = _molecules[0]->count_atom_no(ATOMN_TOKEN); pCard->AddElementToField(atom_no, 3); atom_no = 0; atom_no += _molecules[0]->count_atom_no(HETAD_TOKEN); atom_no += _molecules[0]->count_atom_no(ATOMMN_TOKEN); atom_no += _molecules[0]->count_atom_no(ATOMMP_TOKEN); atom_no += _molecules[0]->count_atom_no(HETAC_TOKEN); atom_no += _molecules[0]->count_atom_no(HETAI_TOKEN); atom_no += _molecules[0]->count_atom_no(HETIC_TOKEN); atom_no += _molecules[0]->count_atom_no(HETAIN_TOKEN); atom_no += _molecules[0]->count_atom_no(ATOMS_TOKEN); pCard->AddElementToField(atom_no, 4); atom_no = _molecules[0]->count_atom_no(HETAS_TOKEN); pCard->AddElementToField(atom_no, 5); } if (!strcmp(pCard->Field(1), "")) pCard->AddElementToField("LAST", 1); if (!strcmp(pCard->Field(6), "")) { int atom_no = atoi(pCard->Field(2)) + atoi(pCard->Field(3)) + atoi(pCard->Field(4)) + atoi(pCard->Field(5)); pCard->AddElementToField(atom_no, 6); } } void separation_string_base_word(char *old_string, char *str1, char *str2, const char *word) { str1[0] = '\0'; str2[0] = '\0'; if (old_string == NULL) return; char *p = strstr(old_string, word); if (!p) strcpy(str1, old_string); if (!strcmp(old_string, "") || p == NULL) return; char *q = old_string; while (q < p) { *str1 = *q; str1++; q++; } *str1 = '\0'; p += strlen(word); strcpy(str2, p); ndb_clean_string(str1); ndb_clean_string(str2); } static void print_null_remark_value(One_Card_Info_Format *newCard, const int fieldLength, const int fieldJustification) { char fieldFormat[82], buffer[82]; if (fieldJustification == PDB_REMARK_LEFT_JUSTIFIED) sprintf(fieldFormat, "%%-%ds", fieldLength); else sprintf(fieldFormat, "%%%ds", fieldLength); sprintf(buffer, fieldFormat, "NULL"); newCard->AttachToField(buffer, 2); } static void print_space_between_remark_field(One_Card_Info_Format *newCard, REMARKS *Remark, const int field_no) { char FieldFormat[82], buffer[82]; if (field_no == 0) sprintf(FieldFormat, "%%-%ds", Remark->FieldList[field_no].FieldStCol - 1); else sprintf(FieldFormat, "%%-%ds", Remark->FieldList[field_no].FieldStCol - (Remark->FieldList[field_no-1].FieldStCol + Remark->FieldList[field_no-1].FieldWidth)); sprintf(buffer, FieldFormat, ""); newCard->AttachToField(buffer, 2); } static void get_remark_field_format(char *FieldFormat, REMARKS *Remark, const int field_no) { if (Remark->FieldList[field_no].FieldType >=3) { if (Remark->FieldList[field_no].FieldJustification == PDB_REMARK_LEFT_JUSTIFIED) sprintf(FieldFormat, "%%-%ds", Remark->FieldList[field_no].FieldWidth); else sprintf(FieldFormat, "%%%ds", Remark->FieldList[field_no].FieldWidth); } else { if (Remark->FieldList[field_no].FieldJustification == PDB_REMARK_LEFT_JUSTIFIED) sprintf(FieldFormat, "%%-%d.%dlf", Remark->FieldList[field_no].FieldWidth, Remark->FieldList[field_no].FieldPrec); else sprintf(FieldFormat, "%%%d.%dlf", Remark->FieldList[field_no].FieldWidth, Remark->FieldList[field_no].FieldPrec); } } static void clean_descriptor(char *string, char *ec) { ec[0] = '\0'; char *q = ec; char *p = strstr(string, "PROTEIN ("); if (p) strcpy(string, &string[9]); for (int i = strlen(string) - 1; i >= 0; i--) { if (string[i] == ')') { string[i] = '\0'; break; } else if (string[i] != ' ' && string[i] != '\0') break; } if ((p = strstr(string, "E.C."))) { if (*(p-1) == '(' && isdigit(*(p+4))) { *(p-1) = ' '; while (p) { if (*p == ')') { *p = ' '; break; } if (*p == '\0') break; *q = *p; *p = ' '; q++; p++; } } *q = '\0'; strcpy(ec, &ec[4]); } ndb_clean_string(string); } static void delete_space_between_string(char *string) { int str_len = strlen(string); for (int i = str_len - 1; i > 0; i--) { if (string[i] == ' ' && string[i-1] == ',') strcpy(&string[i], &string[i+1]); } } static float cal_min_distance(_MOLECULE *mol, _ATOM *atom) { float min_distance = 100.0; double dist = 0; _RESIDUE *Residue = NULL; _ATOM *atom1 = NULL; _CHAIN *chain = mol->GetFirstChain(); while (chain) { if (chain->chain_type() == HETAS_TOKEN || chain->op() != 1) { chain = mol->GetNextChain(); continue; } Residue = chain->GetFirstResidue(); while (Residue) { atom1 = Residue->GetFirstAtom(); while (atom1) { dist = cal_dist(atom, atom1); if (dist < min_distance) min_distance = dist; atom1 = Residue->GetNextAtom(); } Residue = chain->GetNextResidue(); } chain = mol->GetNextChain(); } return (min_distance); } static float cal_dist(_ATOM *atom_a, _ATOM *atom_b) { float min_distance = 100.0; if (!atom_a || !atom_b || strcmp(atom_a->alt_loc(), "") && strcmp(atom_b->alt_loc(), "") && strcmp(atom_a->alt_loc(), atom_b->alt_loc())) return min_distance; if (!strcmp(atom_b->atom_type(), "N") || !strcmp(atom_b->atom_type(), "O")) { float dist = (atom_a->orig().x - atom_b->orig().x) * (atom_a->orig().x - atom_b->orig().x) + (atom_a->orig().y - atom_b->orig().y) * (atom_a->orig().y - atom_b->orig().y) + (atom_a->orig().z - atom_b->orig().z) * (atom_a->orig().z - atom_b->orig().z); dist = sqrt(dist); if (dist > 5.0) { if (dist < min_distance) min_distance = dist; } } return min_distance; } static int check_align(const int Remark_No, REMARK_FIELD *FieldList) { int align = 1; if (!strcmp(FieldList->TokenName, "XFILE1") && FieldList->FieldId == 3 && Remark_No != 210 || !strcmp(FieldList->TokenName, "DTMEA1") && FieldList->FieldId == 2 || !strcmp(FieldList->TokenName, "XFILE2") && FieldList->FieldId == 2 || !strcmp(FieldList->TokenName, "CRMET1") && FieldList->FieldId == 3 || !strcmp(FieldList->TokenName, "REFREM") && FieldList->FieldId == 3 || !strcmp(FieldList->TokenName, "CRDTLS") && FieldList->FieldId == 3 || !strcmp(FieldList->TokenName, "CEMFIT") && FieldList->FieldId == 7 || !strcmp(FieldList->TokenName, "CMRNST") && FieldList->FieldId == 7 || !strcmp(FieldList->TokenName, "CMRNST") && FieldList->FieldId == 8 || !strcmp(FieldList->TokenName, "EMSAMP") && FieldList->FieldId == 9 || !strcmp(FieldList->TokenName, "EMDATA") && FieldList->FieldId == 19 || !strcmp(FieldList->TokenName, "ASSEMB") && FieldList->FieldId == 7 || !strcmp(FieldList->TokenName, "SOLMDL") && (FieldList->FieldId == 6 || FieldList->FieldId == 9)) align = 0; return align; } static int biol_id_compare(const void *biol1, const void *biol2) { return (atoi(((_BIOL_ID *) biol1)->biol_id) - atoi(((_BIOL_ID *) biol2)->biol_id)); }