/* FILE: addcard_util.C */ /* VERSION: 1.600 */ /* DATE: 2/3/2005 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. The user of this software shall indemnify, hold harmless and defend Rutgers, its governors, trustees, officers, employees, students, agents and the authors against any and all claims, suits, losses, liabilities, damages, costs, fees, and expenses including reasonable attorneys' fees resulting from or arising out of the use of this software. This indemnification shall include, but is not limited to, any and all claims alleging products liability. */ /* PDB SOFTWARE LICENSE AGREEMENT BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS BECOMING A PARTY TO THIS AGREEMENT. IF LICENSEE DOES NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE. 1. LICENSE AGREEMENT This is a license between you ("Licensee") and the Protein Data Bank (PDB) at Rutgers, The State University of New Jersey (hereafter referred to as "RUTGERS"). The software is owned by RUTGERS and protected by copyright laws, and some elements are protected by laws governing trademarks, trade dress and trade secrets, and may be protected by patent laws. 2. LICENSE GRANT RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, and distribute in binary and source code format, or any derivative work thereof, together with any associated media, printed materials, and on-line or electronic documentation (if any) provided by RUTGERS (collectively, the "SOFTWARE"), subject to the following terms and conditions: (i) any distribution of the SOFTWARE shall bind the receiver to the terms and conditions of this Agreement; (ii) any distribution of the SOFTWARE in modified form shall clearly state that the SOFTWARE has been modified from the version originally obtained from RUTGERS. 2. COPYRIGHT; RETENTION OF RIGHTS. The above license grant is conditioned on the following: (i) you must reproduce all copyright notices and other proprietary notices on any copies of the SOFTWARE and you must not remove such notices; (ii) in the event you compile the SOFTWARE, you will include the copyright notice with the binary in such a manner as to allow it to be easily viewable; (iii) if you incorporate the SOFTWARE into other code, you must provide notice that the code contains the SOFTWARE and include a copy of the copyright notices and other proprietary notices. All copies of the SOFTWARE shall be subject to the terms of this Agreement. 3. NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS RUTGERS is under no obligation whatsoever to: (i) provide maintenance or support for the SOFTWARE; or (ii) to notify you of bug fixes, patches, or upgrades to the features, functionality or performance of the SOFTWARE ("Enhancements") (if any), whether developed by RUTGERS or third parties. If, in its sole discretion, RUTGERS makes an Enhancement available to you and RUTGERS does not separately enter into a written license agreement with you relating to such bug fix, patch or upgrade, then it shall be deemed incorporated into the SOFTWARE and subject to this Agreement. You are under no obligation whatsoever to provide any Enhancements to RUTGERS or the public that you may develop over time; however, if you choose to provide your Enhancements to RUTGERS, or if you choose to otherwise publish or distribute your Enhancements, in source code form without contemporaneously requiring end users or RUTGERS to enter into a separate written license agreement for such Enhancements, then you hereby grant RUTGERS a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into the SOFTWARE or other computer software, distribute, and sublicense your Enhancements or derivative works thereof, in binary and source code form. 4. FEES. There is no license fee for the SOFTWARE. If Licensee wishes to receive the SOFTWARE on media, there may be a small charge for the media and for shipping and handling. Licensee is responsible for any and all taxes. 5. TERMINATION. Without prejudice to any other rights, Licensor may terminate this Agreement if Licensee breaches any of its terms and conditions. Upon termination, Licensee shall destroy all copies of the SOFTWARE. 6. PROPRIETARY RIGHTS. Title, ownership rights, and intellectual property rights in the Product shall remain with RUTGERS. Licensee acknowledges such ownership and intellectual property rights and will not take any action to jeopardize, limit or interfere in any manner with RUTGERS' ownership of or rights with respect to the SOFTWARE. The SOFTWARE is protected by copyright and other intellectual property laws and by international treaties. Title and related rights in the content accessed through the SOFTWARE is the property of the applicable content owner and is protected by applicable law. The license granted under this Agreement gives Licensee no rights to such content. 7. DISCLAIMER OF WARRANTY. THE SOFTWARE IS PROVIDED FREE OF CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE. SHOULD THE SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS AGREEMENT. NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER. 8. LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. */ #include #include #include #include "_maxit.h" #include "ndb_misclib.h" #include "erf_category.h" #include "erf_util.h" #include "util.h" #define NUM_NAT_TOKEN 11 #define NUM_GEN_TOKEN 17 #define NUM_REM_TOKEN 6 static const char *nat_token_name[NUM_NAT_TOKEN] = { "SRCNCC", "SRCNDS", "SRCNFR", "SRCNN1", "SRCNNM", "SRCNOR", "SRCNPL", "SRCNSC", "SRCNSE", "SRCNSP", "SRCNTS" }; static const char *gen_token_name[NUM_GEN_TOKEN] = { "SRCGCC", "SRCGDS", "SRCGE1", "SRCGE2", "SRCGE3", "SRCGFR", "SRCGH1", "SRCGHC", "SRCGHN", "SRCGHS", "SRCGHT", "SRCGHV", "SRCGNM", "SRCGPL", "SRCGSP", "SRCGTS", "SRCGVE" }; static const char *remove_token[NUM_REM_TOKEN] = { "CAVEAT", "REVDAT", "SPRSDE", "DBREF", "SEQADV", "MODRES" }; static _ENTITY *realloc_entity(_ENTITY *entity, const int n_size); static char *get_entity_description(_CHAIN *chain); static char *get_line_from_string(char *line, char *string); void _MAXIT::Output_Stbiol() { int i, j, k, op, t[3], len; char sym_name[40]; if (_n_stbiol == 0 || _stbiol == NULL) return; One_Card_Info_Format *pCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[STBIOL_TOKEN-1].delete_a_card(pCard); for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; pCard = _CardInfo[STBIOL_TOKEN-1].add_a_new_card(NdbToken[STBIOL_TOKEN-1], 0); pCard->AddElementToField(i+1, 1); pCard->AddElementToField(_stbiol[i]->Biol_ID, 2); pCard->AddElementToField(_stbiol[i]->Asym_ID.Text(), 3); pCard->AddElementToField(_stbiol[i]->Symmetry, 4); if (_stbiol[i]->bbrn != -99999) pCard->AddElementToField(_stbiol[i]->bbrn, 5); if (_stbiol[i]->bern != -99999) pCard->AddElementToField(_stbiol[i]->bern, 6); if (_stbiol[i]->abrn != -99999) pCard->AddElementToField(_stbiol[i]->abrn, 7); if (_stbiol[i]->aern != -99999) pCard->AddElementToField(_stbiol[i]->aern, 8); pCard->AddElementToField(_stbiol[i]->NDB_Strand_ID.Text(), 12); pCard->AddElementToField(_stbiol[i]->PDB_Strand_ID, 13); pCard->AddElementToField(_stbiol[i]->order, 15); pCard->AddElementToField(_stbiol[i]->PDB_Strand_ID_Flag, 16); op = atoi(_stbiol[i]->Symmetry) - 1; t[0] = t[1] = t[2] = 0; len = strlen(_stbiol[i]->Symmetry); for (j = 0; j < len; j++) if (_stbiol[i]->Symmetry[j] == '_') break; if (j + 3 < len) { for (k = 0; k < 3; k++) t[k] = _stbiol[i]->Symmetry[j+k+1] - '5'; } sym_name[0] ='\0'; ndb_get_symmetry_operation_name(_cell, op, t[0], t[1], t[2], sym_name); pCard->AddElementToField(sym_name, 14); } } void _MAXIT::Input_Entity() { int count = 0, i, len; One_Card_Info_Format *pCard = NULL, *qCard = NULL; pCard = _CardInfo[ENTITY_TOKEN-1].Head(); while (pCard) { count++; pCard = pCard->Next(); } if (!count) return; if (_entity) { for (i = 0; i < _n_entity; i++) { if (_entity[i].Type) delete _entity[i].Type; if (_entity[i].Source) delete _entity[i].Source; if (_entity[i].Description) delete _entity[i].Description; } delete _entity; } _n_entity = count; _entity = new _ENTITY[_n_entity]; count = 0; pCard = _CardInfo[ENTITY_TOKEN-1].Head(); while (pCard) { _entity[count].Entity_ID = atoi(pCard->Field(1)); _entity[count].Old_Entity_ID = _entity[count].Entity_ID; len = strlen(pCard->Field(2)); if (len) { _entity[count].Type = new char[len+1]; strcpy(_entity[count].Type, pCard->Field(2)); } else _entity[count].Type = NULL; len = strlen(pCard->Field(3)); if (len) { _entity[count].Source = new char[len+1]; strcpy(_entity[count].Source, pCard->Field(3)); } else _entity[count].Source = NULL; _entity[count].Number = atoi(pCard->Field(4)); qCard = _CardInfo[ENTDES_TOKEN-1].Head(); while (qCard) { if (!strcmp(pCard->Field(1), qCard->Field(1))) break; qCard = qCard->Next(); } if (qCard) { len = strlen(qCard->Field(3)); if (len) { _entity[count].Description = new char[len+1]; strcpy(_entity[count].Description, qCard->Field(3)); } else _entity[count].Description = NULL; } else _entity[count].Description = NULL; count++; pCard = pCard->Next(); } pCard = _CardInfo[ENTITY_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[ENTITY_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[ENTDES_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[ENTDES_TOKEN-1].delete_a_card(pCard); } void _MAXIT::Output_Entity() { if (_n_entity == 0 || _entity == NULL) return; One_Card_Info_Format *pCard = _CardInfo[ENTITY_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[ENTITY_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[ENTDES_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[ENTDES_TOKEN-1].delete_a_card(pCard); for (int i = 0; i < _n_entity; i++) { pCard = _CardInfo[ENTITY_TOKEN-1].add_a_new_card(NdbToken[ENTITY_TOKEN-1], 0); pCard->AddElementToField(_entity[i].Entity_ID, 1); if (_entity[i].Type) pCard->AddElementToField(_entity[i].Type, 2); if (_entity[i].Source) pCard->AddElementToField(_entity[i].Source, 3); pCard->AddElementToField(_entity[i].Number, 4); if (_entity[i].Description && strcmp(_entity[i].Description, "")) { pCard = _CardInfo[ENTDES_TOKEN-1]. add_a_new_card(NdbToken[ENTDES_TOKEN-1], 0); pCard->AddElementToField(_entity[i].Entity_ID, 1); pCard->AddElementToField(_entity[i].Description, 3); } } } void _MAXIT::match_entity_with_molecules() { if (_n_entity == 0 || _entity == NULL || _num_mol == 0 || _molecules == NULL) return; for (int i = 0; i < _n_entity; i++) { _entity[i].Old_Entity_ID = _entity[i].Entity_ID; int Entity_ID = find_entity_index(_entity[i].Entity_ID); if (Entity_ID >= 0) _entity[i].Entity_ID = Entity_ID; } } int _MAXIT::find_entity_index(const int Old_Entity_ID) { int found = 0, Entity_ID = -1, id, entity_id, rowNo, i, j, len; CifString ChainID, chain_id, entity; ISTable *Table = NULL; One_Card_Info_Format *pCard = _CardInfo[STASYM_TOKEN-1].Head(); while (pCard) { if (atoi(pCard->Field(4)) == Old_Entity_ID) { ChainID.Copy(pCard->Field(3)); found = 1; break; } pCard = pCard->Next(); } if (!found && _CifObj) { Table = _CifObj->GetTablePtr(_StructureId, "struct_asym"); if (!is_empty_table(Table)) { id = Table->GetColumnIndex("id"); entity_id = Table->GetColumnIndex("entity_id"); if (id >= 0 && entity_id >= 0) { rowNo = Table->GetNumRows(); for (i = 0; i < rowNo; i++) { get_value(chain_id, Table, id, i); get_value(entity, Table, entity_id, i); if (atoi(entity.Text()) == Old_Entity_ID) { ChainID.Copy(chain_id); found = 1; break; } } } } } if (found) { for (i = 0; i < _n_chain_corr; i++) { if (ChainID == _chain_corr[i].old_chn) { ChainID.Copy(_chain_corr[i].new_chn); break; } } } if (!found && _CifObj) { Table = _CifObj->GetTablePtr(_StructureId, "entity_poly"); if (!is_empty_table(Table)) { entity_id = Table->GetColumnIndex("entity_id"); id = Table->GetColumnIndex("ndb_chain_id"); if (id >= 0 && entity_id >= 0) { rowNo = Table->GetNumRows(); for (i = 0; i < rowNo; i++) { get_value(chain_id, Table, id, i); len = strlen(chain_id.Text()); for (j = 0; j < len; j++) { if (chain_id.Text()[j] == ' ' || chain_id.Text()[j] == ',') { chain_id.Text()[j] = '\0'; break; } } get_value(entity, Table, entity_id, i); if (atoi(entity.Text()) == Old_Entity_ID) { ChainID.Copy(chain_id); found = 1; break; } } } } } if (!found) return Entity_ID; _CHAIN *chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { if (ChainID == chain->ChainID()) { Entity_ID = chain->entity_id(); break; } chain = _molecules[_rep_mol]->GetNextChain(); } return Entity_ID; } void _MAXIT::get_entity_card() { int asym_no = 0, SerialNo = 0, entity_id = 0, NCHAIN_TOKEN; int i = 0, j = 0, k = 0, len = 0, n_tmp, found, syn_token; int nat_token[NUM_NAT_TOKEN], gen_token[NUM_GEN_TOKEN]; char polymer[80], method[20]; _CHAIN *chain = NULL; _ENTITY *tmp = NULL; One_Card_Info_Format *pCard = NULL; if (_num_mol == 0 || _molecules == NULL) return; for (i = 0; i < NUM_NAT_TOKEN; i++) nat_token[i] = find_card_id(nat_token_name[i]); for (i = 0; i < NUM_GEN_TOKEN; i++) gen_token[i] = find_card_id(gen_token_name[i]); syn_token = find_card_id("SRCSYN"); chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { if (chain->chain_type() == ATOMN_TOKEN) { asym_no++; if (chain->biol_id() == 1) SerialNo++; } chain = _molecules[_rep_mol]->GetNextChain(); } if (asym_no || SerialNo) { NCHAIN_TOKEN = find_card_id("NCHAIN"); pCard = _CardInfo[NCHAIN_TOKEN].Head(); if (pCard == NULL) pCard = _CardInfo[NCHAIN_TOKEN]. add_a_new_card(NdbToken[NCHAIN_TOKEN], 0); if (asym_no && !strcmp(pCard->Field(2), "")) pCard->AddElementToField(asym_no, 2); if (SerialNo && !strcmp(pCard->Field(3), "")) pCard->AddElementToField(SerialNo, 3); } pCard = _CardInfo[STASYM_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[STASYM_TOKEN-1].delete_a_card(pCard); n_tmp = _n_entity; tmp = _entity; _n_entity = 0; _entity = NULL; chain = _molecules[_rep_mol]->GetFirstChain(); i = 0; while (chain) { i++; entity_id = chain->entity_id(); pCard = _CardInfo[STASYM_TOKEN-1].add_a_new_card(NdbToken[STASYM_TOKEN-1], 0); pCard->AddElementToField(i, 1); pCard->AddElementToField(chain->ChainID(), 3); pCard->AddElementToField(entity_id, 4); for (j = 0; j < _n_entity; j++) { if (_entity[j].Entity_ID == entity_id) break; } if (j < _n_entity) { if (!strcmp(chain->SeqRes(0)->Field[0], "HOH") || !strcmp(chain->SeqRes(0)->Field[0], "DOD")) _entity[j].Number += chain->ResidueNumbers(); else _entity[j].Number++; } else { _entity = realloc_entity(_entity, _n_entity); _n_entity++; _entity[j].Entity_ID = entity_id; if (!strcmp(chain->SeqRes(0)->Field[0], "HOH") || !strcmp(chain->SeqRes(0)->Field[0], "DOD")) _entity[j].Number = chain->ResidueNumbers(); else _entity[j].Number = 1; } polymer[0] = '\0'; method[0] = '\0'; if (chain->chain_type() == ATOMP_TOKEN || chain->chain_type() == ATOMS_TOKEN || chain->chain_type() == ATOMN_TOKEN) { strcpy(polymer, NDB_POLYMER_TEXT); found = 0; for (k = 0; k < NUM_NAT_TOKEN; k++) { if (nat_token[k] < 0) continue; pCard = _CardInfo[nat_token[k]].Head(); while (pCard) { if (entity_id == atoi(pCard->Field(1))) { found = 1; break; } pCard = pCard->Next(); } if (found) break; } if (found) strcpy(method, "nat"); else { for (k = 0; k < NUM_GEN_TOKEN; k++) { if (gen_token[k] < 0) continue; pCard = _CardInfo[gen_token[k]].Head(); while (pCard) { if (entity_id == atoi(pCard->Field(1))) { found = 1; break; } pCard = pCard->Next(); } if (found) break; } if (found) strcpy(method, "man"); else { if (syn_token >= 0) { pCard = _CardInfo[syn_token].Head(); while (pCard) { if (entity_id == atoi(pCard->Field(1))) { found = 1; break; } pCard = pCard->Next(); } } if (found) strcpy(method, "syn"); else { strcpy(method, "man"); if (chain->chain_type() == ATOMN_TOKEN) strcpy(method, "syn"); } } } if (chain->chain_type() == ATOMS_TOKEN && chain->ResidueNumbers() == 1) strcpy(polymer, NDB_NON_POLYMER_TEXT); for (k = 0; k < n_tmp; k++) { if (tmp[k].Entity_ID == _entity[j].Entity_ID) { if (tmp[k].Source && strcmp(tmp[k].Source, "")) { _entity[j].Source = tmp[k].Source; tmp[k].Source = NULL; } if (tmp[k].Description && strcmp(tmp[k].Description, "")) { _entity[j].Description = tmp[k].Description; tmp[k].Description = NULL; } break; } } } else if (chain->chain_type() == HETAS_TOKEN && (!strcmp(chain->SeqRes(0)->Field[0], "HOH") || !strcmp(chain->SeqRes(0)->Field[0], "DOD"))) { strcpy(polymer, NDB_WATER_TEXT); strcpy(method, "nat"); } else { strcpy(polymer, NDB_NON_POLYMER_TEXT); strcpy(method, "syn"); } len = strlen(polymer); if (len) { if (_entity[j].Type) delete [] _entity[j].Type; _entity[j].Type = new char[len+1]; strcpy(_entity[j].Type, polymer); } len = strlen(method); if (len && !_entity[j].Source) { _entity[j].Source = new char[len+1]; strcpy(_entity[j].Source, method); } else ndb_set_string_to_lower(_entity[j].Source); if (!_entity[j].Description) { if (chain->chain_type() == ATOMP_TOKEN) _entity[j].Description = get_protein_descriptor(chain); else _entity[j].Description = get_entity_description(chain); } chain = _molecules[_rep_mol]->GetNextChain(); } if (tmp) { for (i = 0; i < n_tmp; i++) { if (tmp[i].Type) delete [] tmp[i].Type; if (tmp[i].Source) delete [] tmp[i].Source; if (tmp[i].Description) delete [] tmp[i].Description; } delete [] tmp; } } char* _MAXIT::get_protein_descriptor(_CHAIN *chain) { char *buff = NULL; int len; One_Card_Info_Format *pCard = _CardInfo[PROTEI_TOKEN-1].Head(); while (pCard) { if (atoi(pCard->Field(1)) == chain->entity_id()) break; pCard = pCard->Next(); } if (pCard && strcmp(pCard->Field(3), "")) { len = strlen(pCard->Field(3)) + 12; buff = new char[len]; sprintf(buff, "%s (%s)", NDB_PR_TEXT, pCard->Field(3)); } else { /* buff = new char[22]; sprintf(buff, "%s (%d-MER)", NDB_PR_TEXT, chain->ResidueNumbers()); */ buff = new char[2]; strcpy(buff, ""); } return buff; } void _MAXIT::get_compnd_card() { One_Card_Info_Format *pCard = _CardInfo[COMPND_TOKEN-1].Head(); if (pCard) return; if (_num_mol == 0 || _molecules == NULL) return; _CHAIN *chain = _molecules[0]->GetFirstChain(); if (!chain) return; int i, len; char CompndString[10000], proteinName[10000]; CompndString[0] = '\0'; memset(CompndString, 0, MxLen); if (chain->chain_type() == ATOMN_TOKEN) { ndb_get_protein_name(proteinName, 0); if (strcmp(proteinName, "")) { if (chain->na_type() == ATOMN_TYPE_DNA_ONLY) sprintf(CompndString, "%s/DNA Complex", proteinName); else if (chain->na_type() == ATOMN_TYPE_RNA_ONLY || chain->na_type() == ATOMN_TYPE_TRNA) sprintf(CompndString, "%s/RNA Complex", proteinName); else if (chain->na_type() < 0) { for (i = 0; i < _n_entity; i++) { if (_entity[i].Entity_ID == chain->entity_id()) break; } if (i < _n_entity && _entity[i].Description && (strstr(_entity[i].Description, "RIBOSOM") || strstr(_entity[i].Description, "ribiosom") || strstr(_entity[i].Description, "RNA") || strstr(_entity[i].Description, "rna"))) sprintf(CompndString, "%s/RNA Complex", proteinName); else sprintf(CompndString, "%s/DNA Complex", proteinName); } } else { chain->get_descriptor(CompndString); _CHAIN *chain1 = _molecules[0]->GetNextChain(); if (chain1 && chain1->chain_type() == ATOMN_TOKEN && chain1->entity_id() != chain->entity_id()) { strcat(CompndString, ", "); len = strlen(CompndString); chain1->get_descriptor(&CompndString[len]); } } get_descriptor_ligand(CompndString); } else { if (_CardInfo[PROTEI_TOKEN-1].Head()) ndb_get_protein_name(CompndString, 1); else if (_CardInfo[HEADER_TOKEN-1].Head()) strcpy(CompndString, _CardInfo[HEADER_TOKEN-1].Head()->Field(1)); } pCard = _CardInfo[COMPND_TOKEN-1].add_a_new_card(NdbToken[COMPND_TOKEN-1], 0); pCard->AddElementToField(CompndString, 2); } void _MAXIT::ndb_get_protein_name(char *name, const int add_ec) { int len, i, str_len; One_Card_Info_Format *pCard = NULL, *qCard = NULL; name[0] = '\0'; pCard = _CardInfo[PROTEI_TOKEN-1].Head(); while (pCard) { if (strcmp(pCard->Field(3), "") && !strstr(name, pCard->Field(3))) { qCard = _CardInfo[ECNUM_TOKEN-1].Head(); while (qCard) { if (!strcmp(qCard->Field(1), pCard->Field(1))) break; qCard = qCard->Next(); } len = strlen(name); if (add_ec && qCard && qCard->Field(2) && strcmp(qCard->Field(2), "")) { str_len = strlen(qCard->Field(2)); for (i = 0; i < str_len; i++) { if (isdigit(qCard->Field(2)[i])) break; } if (i < str_len) sprintf(&name[len], "%s (E.C.%s), ", pCard->Field(3), &(qCard->Field(2)[i])); else sprintf(&name[len], "%s, ", pCard->Field(3)); } else sprintf(&name[len], "%s, ", pCard->Field(3)); } pCard = pCard->Next(); } str_len = strlen(name); for (len = str_len - 1; len >= 0; len--) { if (name[len] == ',') { name[len] = '\0'; break; } } if (name[0] == '\0') { _CHAIN *chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() == ATOMP_TOKEN) { strcpy(name, "PROTEIN"); break; } chain = _molecules[0]->GetNextChain(); } } } void _MAXIT::get_descriptor_ligand(char *CompndString) { char ligand_name[800]; int tokenid[2], i, len; One_Card_Info_Format *pCard = NULL; ligand_name[0] = '\0'; tokenid[0] = DCHEM_TOKEN-1; tokenid[1] = INHIBT_TOKEN-1; for (i = 0; i < 2; i++) { pCard = _CardInfo[tokenid[i]].Head(); while (pCard) { if (strcmp(pCard->Field(3), "") && !strstr(ligand_name, pCard->Field(3))) { len = strlen(ligand_name); sprintf(&ligand_name[len], ", %s", pCard->Field(3)); } pCard = pCard->Next(); } } strcat(CompndString, ligand_name); } void _MAXIT::get_origx_card() { One_Card_Info_Format *pCard = _CardInfo[ORIGX_TOKEN-1].Head(); if (pCard) return; pCard = _CardInfo[ORIGX_TOKEN-1].add_a_new_card(NdbToken[ORIGX_TOKEN-1], 0); pCard->AddElementToField("1.000000", 1); pCard->AddElementToField("0.000000", 2); pCard->AddElementToField("0.000000", 3); pCard->AddElementToField("0.00000", 4); pCard = _CardInfo[ORIGX_TOKEN-1].add_a_new_card(NdbToken[ORIGX_TOKEN-1], 0); pCard->AddElementToField("0.000000", 1); pCard->AddElementToField("1.000000", 2); pCard->AddElementToField("0.000000", 3); pCard->AddElementToField("0.00000", 4); pCard = _CardInfo[ORIGX_TOKEN-1].add_a_new_card(NdbToken[ORIGX_TOKEN-1], 0); pCard->AddElementToField("0.000000", 1); pCard->AddElementToField("0.000000", 2); pCard->AddElementToField("1.000000", 3); pCard->AddElementToField("0.00000", 4); } void _MAXIT::get_scale_card() { int i, j; char buffer[10]; One_Card_Info_Format *pCard = NULL; if (_cell == NULL) return; i = 0; pCard = _CardInfo[SCALE_TOKEN-1].Head(); while (pCard) { for (j = 1; j < 5; j++) { if (!strcmp(pCard->Field(j), "")) break; } if (j < 5) break; i++; pCard = pCard->Next(); } if (i == 3) return; pCard = _CardInfo[SCALE_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[SCALE_TOKEN-1].delete_a_card(pCard); if (_cell->is_artifical) { pCard = _CardInfo[SCALE_TOKEN-1].add_a_new_card(NdbToken[SCALE_TOKEN-1], 0); pCard->AddElementToField("1.000000", 1); pCard->AddElementToField("0.000000", 2); pCard->AddElementToField("0.000000", 3); pCard->AddElementToField("0.00000", 4); pCard = _CardInfo[SCALE_TOKEN-1].add_a_new_card(NdbToken[SCALE_TOKEN-1], 0); pCard->AddElementToField("0.000000", 1); pCard->AddElementToField("1.000000", 2); pCard->AddElementToField("0.000000", 3); pCard->AddElementToField("0.00000", 4); pCard = _CardInfo[SCALE_TOKEN-1].add_a_new_card(NdbToken[SCALE_TOKEN-1], 0); pCard->AddElementToField("0.000000", 1); pCard->AddElementToField("0.000000", 2); pCard->AddElementToField("1.000000", 3); pCard->AddElementToField("0.00000", 4); } else { for (i = 0; i < 3; i++) { pCard = _CardInfo[SCALE_TOKEN-1]. add_a_new_card(NdbToken[SCALE_TOKEN-1], 0); for (j = 0; j < 3; j++) { if (fabs(_cell->o_to_f[i][j]) < 0.000001) strcpy(buffer, "0.000000"); else sprintf(buffer, "%.6f", _cell->o_to_f[i][j]); pCard->AddElementToField(buffer, j + 1); } pCard->AddElementToField("0.00000", 4); } } } void _MAXIT::get_cryst_card() { One_Card_Info_Format *pCard = _CardInfo[CRYST1_TOKEN-1].Head(); if (pCard) { if (_cell->is_artifical) { if (!strcmp(pCard->Field(1), "")) pCard->AddElementToField("1.000", 1); if (!strcmp(pCard->Field(2), "")) pCard->AddElementToField("1.000", 2); if (!strcmp(pCard->Field(3), "")) pCard->AddElementToField("1.000", 3); if (!strcmp(pCard->Field(4), "")) pCard->AddElementToField("90.00", 4); if (!strcmp(pCard->Field(5), "")) pCard->AddElementToField("90.00", 5); if (!strcmp(pCard->Field(6), "")) pCard->AddElementToField("90.00", 6); if (!strcmp(pCard->Field(7), "")) pCard->AddElementToField("P 1", 7); if (!strcmp(pCard->Field(8), "")) pCard->AddElementToField(1, 8); } return; } if (_cell == NULL) return; pCard = _CardInfo[CRYST1_TOKEN-1].add_a_new_card(NdbToken[CRYST1_TOKEN-1], 0); if (_cell->is_artifical) { pCard->AddElementToField("1.000", 1); pCard->AddElementToField("1.000", 2); pCard->AddElementToField("1.000", 3); pCard->AddElementToField("90.00", 4); pCard->AddElementToField("90.00", 5); pCard->AddElementToField("90.00", 6); pCard->AddElementToField("P 1", 7); pCard->AddElementToField(1, 8); } else { char buffer[15]; sprintf(buffer, "%-9.3f", _cell->a); ndb_clean_string(buffer); pCard->AddElementToField(buffer, 1); sprintf(buffer, "%-9.3f", _cell->b); ndb_clean_string(buffer); pCard->AddElementToField(buffer, 2); sprintf(buffer, "%-9.3f", _cell->c); ndb_clean_string(buffer); pCard->AddElementToField(buffer, 3); sprintf(buffer, "%-7.2f", _cell->alpha); ndb_clean_string(buffer); pCard->AddElementToField(buffer, 4); ndb_clean_string(buffer); sprintf(buffer, "%-7.2f", _cell->beta); ndb_clean_string(buffer); pCard->AddElementToField(buffer, 5); sprintf(buffer, "%-7.2f", _cell->gamma); ndb_clean_string(buffer); pCard->AddElementToField(buffer, 6); pCard->AddElementToField(_cell->space_group, 7); if (_cell->z) pCard->AddElementToField(_cell->z, 8); pCard->AddElementToField(_cell->full_space_group, 10); } } /* void _MAXIT::get_expdta_card() { One_Card_Info_Format *pCard = _CardInfo[EXPDTA_TOKEN-1].Head(); if (pCard) return; pCard = _CardInfo[EXPDTA_TOKEN-1]. add_a_new_card(NdbToken[EXPDTA_TOKEN-1], 0); pCard->AddElementToField("X-RAY DIFFRACTION", 2); } */ void _MAXIT::get_title_card() { int caid_id = find_card_id("TITLE"); One_Card_Info_Format *pCard = _CardInfo[caid_id].Head(); if (pCard) return; int jrnl_id = find_jrnl_id("TITL"); One_Card_Info_Format *qCard = _JrnlCardInfo[jrnl_id].Head(); if (qCard == NULL) return; pCard = _CardInfo[caid_id].add_a_new_card(NdbToken[caid_id], 0); pCard->AddElementToField(qCard->Field(4), 2); } void _MAXIT::get_dchem_and_inhibt_cards() { if (_num_mol == 0 || _molecules == NULL) return; int DNOMOL_TOKEN = find_card_id("DNOMOL"); int i, j = 0, num = 0, serial_no = 0, card_id = -1, chain_type = -1; int NSOLVT_TOKEN, NION_TOKEN, water_no; One_Card_Info_Format *pCard = NULL, *qCard = NULL; _CHAIN *chain = NULL; _RESIDUE *residue = NULL; ConnectFormat *drug = NULL; for (i = 0; i < 2; i++) { card_id = INHIBT_TOKEN; chain_type = HETAIN_TOKEN; if (i) { card_id = DCHEM_TOKEN; chain_type = HETAD_TOKEN; } pCard = _CardInfo[card_id-1].Head(); if (pCard) continue; chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() != chain_type) { chain = _molecules[0]->GetNextChain(); continue; } residue = chain->GetFirstResidue(); while (residue) { drug = find_drug(residue->ResName()); if (!drug) { residue = chain->GetNextResidue(); continue; } pCard = _CardInfo[card_id-1].Head(); serial_no = 0; while (pCard) { pCard->AddElementToField(++serial_no, 1); if (drug->chemical_name() && !strcmp(pCard->Field(3), drug->chemical_name())) break; pCard = pCard->Next(); } if (pCard) { if (card_id == INHIBT_TOKEN) { num = atoi(pCard->Field(4)); pCard->AddElementToField(num + 1, 4); } else if (card_id == DCHEM_TOKEN) { qCard = _CardInfo[DNOMOL_TOKEN].Head(); while (qCard) { if (!strcmp(qCard->Field(1), pCard->Field(1))) break; qCard = qCard->Next(); } if (qCard) { num = atoi(qCard->Field(2)); qCard->AddElementToField(num + 1, 2); } else { qCard = _CardInfo[DNOMOL_TOKEN]. add_a_new_card(NdbToken[DNOMOL_TOKEN], 0); qCard->AddElementToField(serial_no, 1); qCard->AddElementToField(1, 2); } } } else { pCard = _CardInfo[card_id-1].add_a_new_card(NdbToken[card_id-1], 0); pCard->AddElementToField(++serial_no, 1); if (drug->chemical_name()) pCard->AddElementToField(drug->chemical_name(), 3); if (card_id == INHIBT_TOKEN) { pCard->AddElementToField(1, 4); sprintf(pCard->Field(4), "%d", 1); } else if (card_id == DCHEM_TOKEN) { qCard = _CardInfo[DNOMOL_TOKEN]. add_a_new_card(NdbToken[DNOMOL_TOKEN], 0); qCard->AddElementToField(serial_no, 1); qCard->AddElementToField(1, 2); } } residue = chain->GetNextResidue(); } chain = _molecules[0]->GetNextChain(); } } NSOLVT_TOKEN = find_card_id("NSOLVT"); water_no = 0; pCard = _CardInfo[NSOLVT_TOKEN].Head(); if (!pCard || !strcmp(pCard->Field(3), "")) { water_no = 0; chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() == HETAS_TOKEN && (!strcmp(chain->SeqRes(0)->Field[0], "HOH") || !strcmp(chain->SeqRes(0)->Field[0], "DOD"))) { water_no += chain->ResidueNumbers(); } chain = _molecules[0]->GetNextChain(); } if (water_no > 0) { if (!pCard) pCard = _CardInfo[NSOLVT_TOKEN]. add_a_new_card(NdbToken[NSOLVT_TOKEN], FALSE); pCard->AddElementToField("water", 2); pCard->AddElementToField(water_no, 3); } } pCard = _CardInfo[PROTEI_TOKEN-1].Head(); if (!pCard) { chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() == ATOMP_TOKEN) { pCard = _CardInfo[PROTEI_TOKEN-1].Head(); while (pCard) { if (atoi(pCard->Field(1)) == chain->entity_id()) break; pCard = pCard->Next(); } if (!pCard) pCard = _CardInfo[PROTEI_TOKEN-1]. add_a_new_card(NdbToken[PROTEI_TOKEN-1], FALSE); if (!strcmp(pCard->Field(1), "")) pCard->AddElementToField(chain->entity_id(), 1); if (!strcmp(pCard->Field(3), "")) { for (j = 0; j < _n_entity; j++) { if (_entity[j].Entity_ID == chain->entity_id()) { if (_entity[j].Description && strcmp(_entity[j].Description, "")) { pCard->AddElementToField(_entity[j].Description, 3); } break; } } } num = atoi(pCard->Field(4)) + 1; pCard->AddElementToField(num, 4); } chain = _molecules[0]->GetNextChain(); } } NION_TOKEN = find_card_id("NION"); pCard = _CardInfo[NION_TOKEN].Head(); if (!pCard) { chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() == HETAI_TOKEN || chain->chain_type() == HETIC_TOKEN) { pCard = _CardInfo[NION_TOKEN].Head(); while (pCard) { if (atoi(pCard->Field(1)) == chain->entity_id()) break; pCard = pCard->Next(); } if (!pCard) pCard = _CardInfo[NION_TOKEN]. add_a_new_card(NdbToken[NION_TOKEN], FALSE); if (!strcmp(pCard->Field(1), "")) pCard->AddElementToField(chain->entity_id(), 1); if (!strcmp(pCard->Field(2), "")) { for (j = 0; j < _n_entity; j++) { if (_entity[j].Entity_ID == chain->entity_id()) { if (_entity[j].Description && strcmp(_entity[j].Description, "")) { pCard->AddElementToField(_entity[j].Description, 2); } break; } } } num = atoi(pCard->Field(3)) + 1; pCard->AddElementToField(num, 3); } chain = _molecules[0]->GetNextChain(); } } } void _MAXIT::get_het_card() { int i = 0, j = 0, serialNo = 0, num = 0, len; char PDB_ID[15], buff[100], buffer[20], *p = NULL; _ATOM *atom = NULL; _RESIDUE *residue = NULL; _CHAIN *chain = NULL; ConnectFormat *drug = NULL; One_Card_Info_Format *pCard = NULL, *pHetNam = NULL, *pHetSyn = NULL; if (_num_mol == 0 || _molecules == NULL) return; if (_het) delete [] _het; _het = NULL; _n_het = 0; pCard = _CardInfo[HET_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[HET_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[FORMUL_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[FORMUL_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[HETNAM_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[HETNAM_TOKEN-1].delete_a_card(pCard); pCard = _CardInfo[HETSYN_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[HETSYN_TOKEN-1].delete_a_card(pCard); PDB_ID[0] = '\0'; pCard = _CardInfo[PDBFIL_TOKEN-1].Head(); if (pCard) strcpy(PDB_ID, pCard->Field(1)); chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { serialNo++; if (chain->chain_type() == HETAS_TOKEN && (!strcmp(chain->SeqRes(0)->Field[0], "HOH") || !strcmp(chain->SeqRes(0)->Field[0], "DOD"))) { if (!strcmp(chain->SeqRes(0)->Field[0], "HOH")) insert_formul_card("HOH", serialNo, chain->ResidueNumbers()); else insert_formul_card("DOD", serialNo, chain->ResidueNumbers()); chain = _molecules[_rep_mol]->GetNextChain(); continue; } for (i = 0; i < chain->SeqLen(); i++) { if (chain->SeqRes(i)->Deleted) continue; residue = chain->SeqRes(i)->Residue; if (!residue) continue; atom = residue->GetFirstAtom(); if (!is_a_standard_residue(residue->ResName())) { insert_formul_card(residue->ResName(), serialNo, 1); insert_het_card(chain, residue->ResName(), atom->pdb_resnum(), atom->ins_code(), residue->AtomNumbers()); if ((chain->chain_type() == ATOMP_TOKEN || chain->chain_type() == ATOMN_TOKEN) && strcmp(residue->ResName(), "ACE") && strcmp(residue->ResName(), "NH2") && strcmp(residue->ResName(), "NH3") && strcmp(residue->ResName(), "CH2")) { drug = find_drug(residue->ResName()); if (drug && drug->parent_residue() && strcmp(drug->parent_residue(), "")) { memset(buff, 0, 100); strcpy(buff, drug->parent_residue()); len = strlen(buff); for (j = 0; j < len; j++) { if (buff[j] == ',' || buff[j] == ';') buff[j] = ' '; } ndb_clean_string(buff); p = buff; while (p) { p = get_word(p, buffer); if (!strcmp(buffer, "")) continue; if (strlen(drug->chemical_name()) < 40) Insert_a_Modres(PDB_ID, chain->index(), chain->SeqRes(i)->ResIndex, buffer, // drug->parent_residue(), drug->chemical_name()); else Insert_a_Modres(PDB_ID, chain->index(), chain->SeqRes(i)->ResIndex, buffer, ""); // drug->parent_residue(), ""); } } } } else if (is_a_standard_residue(residue->ResName()) && chain->chain_type() != ATOMP_TOKEN && chain->chain_type() != ATOMN_TOKEN) { insert_formul_card(residue->ResName(), serialNo, 1); insert_het_card(chain, residue->ResName(), atom->pdb_resnum(), atom->ins_code(), residue->AtomNumbers()); } } chain = _molecules[_rep_mol]->GetNextChain(); } serialNo = 0; pCard = _CardInfo[FORMUL_TOKEN-1].Head(); while (pCard) { num = atoi(pCard->Field(5)); if (!strcmp(pCard->Field(2), "UNL")) { pHetNam = _CardInfo[HETNAM_TOKEN-1]. add_a_new_card(NdbToken[HETNAM_TOKEN-1], 0); pHetNam->AddElementToField(pCard->Field(2), 2); pHetNam->AddElementToField("UNKNOWN LIGAND", 3); pHetNam->AddElementToField(++serialNo, 4); pCard = _CardInfo[FORMUL_TOKEN-1].delete_a_card(pCard); } else if (!strcmp(pCard->Field(2), "HOH")) { pCard->AddElementToField("*", 4); if (num > 1) { sprintf(buffer, "%d(H2 O1)", num); pCard->AddElementToField(buffer, 5); } else pCard->AddElementToField("(H2 O1)", 5); pCard = pCard->Next(); } else { drug = find_drug(pCard->Field(2)); if (drug) { buff[0] = '\0'; if (num > 1) { if (drug->formal_charge() && strcmp(drug->formal_charge(), "") && strcmp(drug->formal_charge(), "0")) sprintf(buff, "%d(%s %s)", num, drug->formula(), drug->formal_charge()); else sprintf(buff, "%d(%s)", num, drug->formula()); } else { if (drug->formal_charge() && strcmp(drug->formal_charge(), "") && strcmp(drug->formal_charge(), "0")) sprintf(buff, "%s %s", drug->formula(), drug->formal_charge()); else strcpy(buff, drug->formula()); } pCard->AddElementToField(buff, 5); if (drug->chemical_name() && strcmp(drug->chemical_name(), "")) { pHetNam = _CardInfo[HETNAM_TOKEN-1]. add_a_new_card(NdbToken[HETNAM_TOKEN-1], 0); pHetNam->AddElementToField(pCard->Field(2), 2); pHetNam->AddElementToField(drug->chemical_name(), 3); pHetNam->AddElementToField(++serialNo, 4); } if (drug->synonym() && strcmp(drug->synonym(), "")) { pHetSyn = _CardInfo[HETSYN_TOKEN-1]. add_a_new_card(NdbToken[HETSYN_TOKEN-1], 0); pHetSyn->AddElementToField(pCard->Field(2), 2); pHetSyn->AddElementToField(drug->synonym(), 3); } } else pCard->AddElementToField("", 5); pCard = pCard->Next(); } } } void _MAXIT::insert_formul_card(const char *hetID, const int serialNo, const int num) { One_Card_Info_Format *pCard = NULL; if (!strcmp(hetID, "DUM") || !strcmp(hetID, "UNK") || !strcmp(hetID, "N") /* || !strcmp(hetID, "UNX") || !strcmp(hetID, "UNL") */ ) return; pCard = _CardInfo[FORMUL_TOKEN-1].Head(); while (pCard) { if (!strcmp(pCard->Field(2), hetID)) break; pCard = pCard->Next(); } if (pCard) { int n = atoi(pCard->Field(5)) + num; pCard->AddElementToField(n, 5); } else { pCard = _CardInfo[FORMUL_TOKEN-1]. add_a_new_card(NdbToken[FORMUL_TOKEN-1], 0); pCard->AddElementToField(serialNo, 1); pCard->AddElementToField(hetID, 2); pCard->AddElementToField(num, 5); } } void _MAXIT::insert_het_card(_CHAIN *chain, const char *resname, const int resnum, const char *ins_code, const int atmnum) { if (!strcmp(resname, "DUM") || !strcmp(resname, "UNK") || !strcmp(resname, "N") /* || !strcmp(resname, "UNX") || !strcmp(resname, "UNL") */ ) return; _FIELD* initRes = chain->find_pdb_Residue(resname, resnum, ins_code); if (initRes) { int FstIndex = chain->index(); int FstRes = initRes->ResIndex; Insert_a_Het(FstIndex, FstRes, atmnum); } } void _MAXIT::ndb_add_missing_information(const char *TokenName, const int TokenField, const char *TokenValue) { int TokenId = find_card_id(TokenName); int FieldId = TokenField - 1; if (TokenId < 0 || FieldId < 1) return; One_Card_Info_Format *pCard = _CardInfo[TokenId].Head(); if (pCard) { while (pCard) { pCard->AddElementToField(TokenValue, FieldId); pCard = pCard->Next(); } } else { pCard = _CardInfo[TokenId].add_a_new_card(NdbToken[TokenId], 0); pCard->AddElementToField(TokenValue, FieldId); } } void _MAXIT::write_restraints_correspondences(FILE *outfile) { int i, serial_no = 1, token_ids[8], numRemark = 0; char atom_name[5]; _ATOM *atom = NULL; _RESIDUE *residue = NULL; _CHAIN *chain = NULL; One_Card_Info_Format *pCard = NULL, *qCard = NULL; token_ids[0] = HEADER_TOKEN-1; token_ids[1] = find_card_id("TITLE"); token_ids[2] = COMPND_TOKEN-1; token_ids[3] = SOURCE_TOKEN-1; token_ids[4] = find_card_id("KEYWDS"); token_ids[5] = EXPDTA_TOKEN-1; token_ids[6] = AUTHOR_TOKEN-1; token_ids[7] = REVDAT_TOKEN-1; pCard = _CardInfo[HEADER_TOKEN-1].Head(); qCard = _CardInfo[PDBFIL_TOKEN-1].Head(); if (pCard && qCard) strcpy(pCard->Field(3), qCard->Field(1)); replace_pdb_compnd_source_card(); update_tokens(NDB_FILE_FORMAT_PDB); for (i = 0; i < 8; i++) { print_general_cards(outfile, token_ids[i], NDB_FILE_FORMAT_PDB, numRemark, 1); } fprintf(outfile, "\n"); fprintf(outfile, " Entry H atom name Submitted Coord H atom name\n"); for (i = 0; i < _num_mol; i++) { if (_num_mol > 1) fprintf(outfile, " Start of MODEL %4d\n", i + 1); serial_no = 1; chain = _molecules[i]->GetFirstChain(); while (chain) { residue = chain->GetFirstResidue(); while (residue) { atom = residue->GetFirstAtom(); while (atom) { if (!atom->is_hydrogen()) { atom = residue->GetNextAtom(); continue; } atom_name[0] = '\0'; print_atom_atomName_field(atom->atom_type(), 0, atom_name, atom->pdb_atmnam(), atom->pdb_resnam(), atom->align()); fprintf(outfile, "%5d %4s ", serial_no++, atom_name); fprintf(outfile, "%3s%4d ", atom->pdb_resnam(), atom->pdb_resnum()); print_atom_atomName_field(atom->atom_type(), 0, atom_name, atom->pub_atmnam(), atom->pub_resnam(), atom->align()); fprintf(outfile, "%4s %3s%4d%8.3f%8.3f%8.3f\n", atom_name, atom->pub_resnam(), atom->pub_resnum(), atom->orig().x, atom->orig().y, atom->orig().z); atom = residue->GetNextAtom(); } residue = chain->GetNextResidue(); } chain = _molecules[i]->GetNextChain(); } } } void _MAXIT::switch_hydrogen_labeling() { int l; _CHAIN *chain = NULL; _RESIDUE *residue = NULL; for (l = 0; l < _num_mol; l++) { chain = _molecules[l]->GetFirstChain(); while (chain) { if (chain->chain_type() != ATOMP_TOKEN) { chain = _molecules[l]->GetNextChain(); continue; } chain->labeling_iupac_hydrogen(); residue = chain->GetFirstResidue(); while (residue) { residue->labeling_iupac_hydrogen(); residue = chain->GetNextResidue(); } chain = _molecules[l]->GetNextChain(); } } } void _MAXIT::ndb_write_hydrogen_index() { char filename[100]; _ATOM *atom = NULL; _RESIDUE *residue = NULL; _CHAIN *chain = NULL; sprintf(filename, "%s.index", _input_filename); FILE *outfile = fopen(filename, "w"); if (_num_mol) { chain = _molecules[0]->GetFirstChain(); while (chain) { residue = chain->GetFirstResidue(); while (residue) { atom = residue->GetFirstAtom(); while (atom) { if (!atom->is_hydrogen()) { atom = residue->GetNextAtom(); continue; } if (strcmp(atom->pdb_atmnam(), atom->pub_atmnam())) { fprintf(outfile, "%s %s %d %s\n", atom->pub_atmnam(), atom->pdb_resnam(), atom->pdb_resnum(), atom->pdb_atmnam()); } atom = residue->GetNextAtom(); } } chain = _molecules[0]->GetNextChain(); } } fclose (outfile); } void _MAXIT::add_modification_information() { int i, is_sugar = 0, exist_unknown = 0; char PDB_ID[15], comments[40]; _FIELD *Fst = NULL, *Snd = NULL; _CHAIN *ch1 = NULL, *ch2 = NULL; if (_num_mol == 0) return; PDB_ID[0] = '\0'; One_Card_Info_Format *pCard = _CardInfo[PDBFIL_TOKEN-1].Head(); if (pCard) strcpy(PDB_ID, pCard->Field(1)); _MOLECULE *mol = _molecules[0]; for (i = 0; i < _n_link; i++) { if (strcmp(_link[i]->SymOP_1, "") || strcmp(_link[i]->SymOP_2, "")) continue; ch1 = mol->GetIndexChain(_link[i]->FstIndex); ch2 = mol->GetIndexChain(_link[i]->SndIndex); if (!ch1 || !ch2 || ch1 == ch2) continue; Fst = ch1->SeqResIndex(_link[i]->FstRes); Snd = ch2->SeqResIndex(_link[i]->SndRes); if (!Fst || !Snd) continue; comments[0] = '\0'; if (_link[i]->details && strlen(_link[i]->details) < 40) strcpy(comments, _link[i]->details); if (ch1->chain_type() == ATOMN_TOKEN && ch2->chain_type() != ATOMP_TOKEN && ch2->chain_type() != ATOMN_TOKEN) { if (strcmp(comments, "")) Insert_a_Modres(PDB_ID, _link[i]->FstIndex, _link[i]->FstRes, Fst->Field[0], comments); /* if (!strcmp(_link[i]->FstAtom, "P") || !strcmp(_link[i]->FstAtom, "O1P") || !strcmp(_link[i]->FstAtom, "O2P")) Insert_a_Modifp(Snd->Field[0], _link[i]->SndAtom, _link[i]->SndIndex, _link[i]->SndRes, _link[i]->FstAtom, _link[i]->FstIndex, _link[i]->FstRes, ""); else if (_link[i]->FstAtom[2] == '*') Insert_a_Modifs(Snd->Field[0], _link[i]->SndAtom, _link[i]->SndIndex, _link[i]->SndRes, _link[i]->FstAtom, _link[i]->FstIndex, _link[i]->FstRes, "", ""); else Insert_a_Modifb(Snd->Field[0], _link[i]->SndAtom, _link[i]->SndIndex, _link[i]->SndRes, _link[i]->FstAtom, _link[i]->FstIndex, _link[i]->FstRes, ""); */ } else if (ch2->chain_type() == ATOMN_TOKEN && ch1->chain_type() != ATOMP_TOKEN && ch1->chain_type() != ATOMN_TOKEN) { if (strcmp(comments, "")) Insert_a_Modres(PDB_ID, _link[i]->SndIndex, _link[i]->SndRes, Snd->Field[0], comments); /* if (!strcmp(_link[i]->SndAtom, "P") || !strcmp(_link[i]->SndAtom, "O1P") || !strcmp(_link[i]->SndAtom, "O2P")) Insert_a_Modifp(Fst->Field[0], _link[i]->FstAtom, _link[i]->FstIndex, _link[i]->FstRes, _link[i]->SndAtom, _link[i]->SndIndex, _link[i]->SndRes, ""); else if (_link[i]->SndAtom[2] == '*') Insert_a_Modifs(Fst->Field[0], _link[i]->FstAtom, _link[i]->FstIndex, _link[i]->FstRes, _link[i]->SndAtom, _link[i]->SndIndex, _link[i]->SndRes, "", ""); else Insert_a_Modifb(Fst->Field[0], _link[i]->FstAtom, _link[i]->FstIndex, _link[i]->FstRes, _link[i]->SndAtom, _link[i]->SndIndex, _link[i]->SndRes, ""); */ } else if (ch1->chain_type() == ATOMP_TOKEN && ch2->chain_type() != ATOMP_TOKEN && ch2->chain_type() != ATOMN_TOKEN) { if (is_a_standard_residue(Fst->Field[0])) { if (!strcmp(comments, "")) { is_sugar = 0; if (find_residue_type(Snd->Field[0], exist_unknown) == ATOMS_TOKEN) is_sugar = 1; if ((!strcmp(Fst->Field[0], "ASN") || !strcmp(Fst->Field[0], "SER") || !strcmp(Fst->Field[0], "THR")) && is_sugar) strcpy(comments, "GLYCOSYLATION SITE"); } if (strcmp(comments, "")) Insert_a_Modres(PDB_ID, _link[i]->FstIndex, _link[i]->FstRes, Fst->Field[0], comments); } } else if (ch2->chain_type() == ATOMP_TOKEN && ch1->chain_type() != ATOMP_TOKEN && ch1->chain_type() != ATOMN_TOKEN) { if (is_a_standard_residue(Snd->Field[0])) { if (!strcmp(comments, "")) { is_sugar = 0; if (find_residue_type(Fst->Field[0], exist_unknown) == ATOMS_TOKEN) is_sugar = 1; if ((!strcmp(Snd->Field[0], "ASN") || !strcmp(Snd->Field[0], "SER") || !strcmp(Snd->Field[0], "THR")) && is_sugar) strcpy(comments, "GLYCOSYLATION SITE"); } if (strcmp(comments, "")) Insert_a_Modres(PDB_ID, _link[i]->SndIndex, _link[i]->SndRes, Snd->Field[0], comments); } } } } void _MAXIT::get_virus_matrix_from_remark_350(const int add_identical) { int id, id_index, text_idex, rowNo, row_no, irow, num; char buffer[50], text[100], m1[10], m2[10], m3[10], v[15], *p, *q; CifString string; ISTable *Table = NULL, *Table1 = NULL; Table = _CifObj->GetTablePtr(_StructureId, "struct_ncs_oper"); if (!is_empty_table(Table)) return; Table1 = _CifObj->GetTablePtr(_StructureId, "database_PDB_remark"); if (is_empty_table(Table1)) return; id_index = Table1->GetColumnIndex("id"); text_idex = Table1->GetColumnIndex("text"); if (id_index < 0 || text_idex < 0) return; if (_CifObj->IsTablePresent(_StructureId, "struct_ncs_oper")) _CifObj->DeleteTable(_StructureId, "struct_ncs_oper"); Table = new ISTable("struct_ncs_oper"); Table->AddColumn("id"); Table->AddColumn("code"); Table->AddColumn("details"); Table->AddColumn("matrix[1][1]"); Table->AddColumn("matrix[1][2]"); Table->AddColumn("matrix[1][3]"); Table->AddColumn("matrix[2][1]"); Table->AddColumn("matrix[2][2]"); Table->AddColumn("matrix[2][3]"); Table->AddColumn("matrix[3][1]"); Table->AddColumn("matrix[3][2]"); Table->AddColumn("matrix[3][3]"); Table->AddColumn("vector[1]"); Table->AddColumn("vector[2]"); Table->AddColumn("vector[3]"); rowNo = Table1->GetNumRows(); row_no = -1; if (add_identical) { row_no++; Table->AddRow(); string.Copy("1"); Table->UpdateCell(string, 0, row_no); string.Copy("given"); Table->UpdateCell(string, 1, row_no); string.Copy("1.000000"); Table->UpdateCell(string, 3, row_no); Table->UpdateCell(string, 7, row_no); Table->UpdateCell(string, 11, row_no); string.Copy("0.000000"); Table->UpdateCell(string, 4, row_no); Table->UpdateCell(string, 5, row_no); Table->UpdateCell(string, 6, row_no); Table->UpdateCell(string, 8, row_no); Table->UpdateCell(string, 9, row_no); Table->UpdateCell(string, 10, row_no); string.Copy("0.00000"); Table->UpdateCell(string, 12, row_no); Table->UpdateCell(string, 13, row_no); Table->UpdateCell(string, 14, row_no); } for (irow = 0; irow < rowNo; irow++) { Table1->GetCell(string, id_index, irow); if (string != "350") continue; Table1->GetCell(string, text_idex, irow); q = string.Text(); while (q) { q = get_line_from_string(text, q); if (!strcmp(text, "")) continue; p = get_word(text, buffer); if (strncmp(buffer, "BIOMT", 5) || strlen(buffer) < 6) continue; num = atoi(&buffer[5]); if (!p) continue; p = get_word(p, buffer); id = atoi(buffer); strcpy(v, "0.00000"); if (!p) continue; p = get_word(p, m1); if (!p) continue; p = get_word(p, m2); if (!p) continue; p = get_word(p, m3); if (p) p = get_word(p, v); if (num == 1) { row_no++; Table->AddRow(); } if (row_no < 0) continue; if (num == 1) { if (add_identical) sprintf(buffer, "%d", id + 1); else sprintf(buffer, "%d", id); string.Copy(buffer); Table->UpdateCell(string, 0, row_no); if (!add_identical && id == 1) string.Copy("given"); else string.Copy("generate"); Table->UpdateCell(string, 1, row_no); string.Copy(m1); Table->UpdateCell(string, 3, row_no); string.Copy(m2); Table->UpdateCell(string, 4, row_no); string.Copy(m3); Table->UpdateCell(string, 5, row_no); string.Copy(v); Table->UpdateCell(string, 12, row_no); } else if (num == 2) { string.Copy(m1); Table->UpdateCell(string, 6, row_no); string.Copy(m2); Table->UpdateCell(string, 7, row_no); string.Copy(m3); Table->UpdateCell(string, 8, row_no); string.Copy(v); Table->UpdateCell(string, 13, row_no); } else if (num == 3) { string.Copy(m1); Table->UpdateCell(string, 9, row_no); string.Copy(m2); Table->UpdateCell(string, 10, row_no); string.Copy(m3); Table->UpdateCell(string, 11, row_no); string.Copy(v); Table->UpdateCell(string, 14, row_no); } } break; } _CifObj->WriteTable(Table, _StructureId, "struct_ncs_oper"); } void _MAXIT::classification(FILE *summary, FILE *summary1, char *het) { int is_p = 0, is_d = 0, is_r = 0, is_h = 0, is_e = 0, is_c = 0; int is_g = 0, is_enzyme = 0; _CHAIN *chain = NULL; One_Card_Info_Format *pCard = NULL; if (_num_mol == 0) return; het[0] = '\0'; pCard = _CardInfo[HET_TOKEN-1].Head(); while (pCard) { if (strcmp(pCard->Field(1), "HOH") && strcmp(pCard->Field(1), "DOD") && strcmp(pCard->Field(1), "HN2") && strcmp(pCard->Field(1), "CH2") && strcmp(pCard->Field(1), "ACE")) { if (!strcmp(het, "")) strcpy(het, pCard->Field(1)); else { strcat(het, " "); strcat(het, pCard->Field(1)); } } pCard = pCard->Next(); } chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() != ATOMN_TOKEN && chain->chain_type() != ATOMP_TOKEN && chain->chain_type() != ATOMS_TOKEN) { chain = _molecules[0]->GetNextChain(); continue; } if (chain->chain_type() == ATOMS_TOKEN && (chain->is_linked() || chain->ResidueNumbers() < 3)) { chain = _molecules[0]->GetNextChain(); continue; } fprintf(summary, "%s\t", _CardInfo[PDBFIL_TOKEN-1].Head()->Field(1)); if (strcmp(chain->PDB_ChainID(), "")) fprintf(summary, "%s\t", chain->PDB_ChainID()); else fprintf(summary, "\t"); fprintf(summary, "%s\t%d\t", chain->ChainID(), chain->entity_id()); pCard = _CardInfo[ECNUM_TOKEN-1].Head(); while (pCard) { if (atoi(pCard->Field(1)) == chain->entity_id()) break; pCard = pCard->Next(); } is_enzyme = 0; if (pCard && strcmp(pCard->Field(2), "")) { fprintf(summary, "%s", pCard->Field(2)); is_enzyme = 1; } fprintf(summary, "\t"); if (chain->chain_type() == ATOMN_TOKEN) { if (chain->na_type() == ATOMN_TYPE_DNA_ONLY) { fprintf(summary, "DNA"); is_d = 1; } else if (chain->na_type() == ATOMN_TYPE_DNA_RNA) { fprintf(summary, "HYBRID"); is_h = 1; } else if (chain->na_type() & ATOMN_TYPE_RNA_ONLY) { fprintf(summary, "RNA"); is_r = 1; } else if (chain->na_type() < 0) { pCard = _CardInfo[ENTDES_TOKEN-1].Head(); while (pCard) { if (atoi(pCard->Field(1)) == chain->entity_id()) break; pCard = pCard->Next(); } if (pCard && (strstr(pCard->Field(3), "RIBOSOM") || strstr(pCard->Field(3), "ribiosom") || strstr(pCard->Field(3), "RNA") || strstr(pCard->Field(3), "rna"))) fprintf(summary, "RNA"); else fprintf(summary, "DNA"); } } else if (chain->chain_type() == ATOMP_TOKEN) fprintf(summary, "PROTEIN"); fprintf(summary, "\t"); pCard = NULL; if (chain->chain_type() == ATOMP_TOKEN || chain->chain_type() == ATOMN_TOKEN) { pCard = _CardInfo[DBREF_TOKEN-1].Head(); while (pCard) { if (!strcmp(chain->PDB_ChainID(), pCard->Field(2))) break; pCard = pCard->Next(); } } if (pCard && strcmp(pCard->Field(8), "")) fprintf(summary, "%s", pCard->Field(8)); fprintf(summary, "\t"); if (pCard && strcmp(pCard->Field(7), "")) fprintf(summary, "%s", pCard->Field(7)); fprintf(summary, "\t"); if (chain->chain_type() == ATOMP_TOKEN) { fprintf(summary, "Y\t"); is_p = 1; } else fprintf(summary, "N\t"); if (chain->chain_type() == ATOMN_TOKEN) fprintf(summary, "Y\t"); else fprintf(summary, "N\t"); if (chain->chain_type() == ATOMP_TOKEN && is_enzyme) { fprintf(summary, "Y\t"); is_e = 1; } else fprintf(summary, "N\t"); if (chain->chain_type() == ATOMS_TOKEN) { fprintf(summary, "Y\t"); is_c = 1; } else fprintf(summary, "N\t"); if (chain->chain_type() == ATOMP_TOKEN && chain->is_linked()) { fprintf(summary, "Y\n"); is_g = 1; } else fprintf(summary, "N\n"); chain = _molecules[0]->GetNextChain(); } fprintf(summary1, "%s\t", _CardInfo[PDBFIL_TOKEN-1].Head()->Field(1)); if (is_p) fprintf(summary1, "Y\t"); else fprintf(summary1, "N\t"); if (is_d || is_h) fprintf(summary1, "Y\t"); else fprintf(summary1, "N\t"); if (is_r || is_h) fprintf(summary1, "Y\t"); else fprintf(summary1, "N\t"); if (is_h) fprintf(summary1, "Y\t"); else fprintf(summary1, "N\t"); if (is_e) fprintf(summary1, "Y\t"); else fprintf(summary1, "N\t"); if (is_c) fprintf(summary1, "Y\t"); else fprintf(summary1, "N\t"); if (is_g) fprintf(summary1, "Y\n"); else fprintf(summary1, "N\n"); } void _MAXIT::delete_na_structural_features() { if (!_CifObj) return; if (_CifObj->IsTablePresent(_StructureId, "ndb_struct_conf_na")) _CifObj->DeleteTable(_StructureId, "ndb_struct_conf_na"); if (_CifObj->IsTablePresent(_StructureId, "ndb_struct_na_base_pair")) _CifObj->DeleteTable(_StructureId, "ndb_struct_na_base_pair"); if (_CifObj->IsTablePresent(_StructureId, "ndb_struct_na_base_pair_step")) _CifObj->DeleteTable(_StructureId, "ndb_struct_na_base_pair_step"); if (_CifObj->IsTablePresent(_StructureId, "ndb_entity_poly_na_type")) _CifObj->DeleteTable(_StructureId, "ndb_entity_poly_na_type"); if (_CifObj->IsTablePresent(_StructureId, "ndb_entity_poly_na_nonstandard")) _CifObj->DeleteTable(_StructureId, "ndb_entity_poly_na_nonstandard"); } void _MAXIT::update_na_structural_features() { int i, entity_id[100], n_entity_id = 0, irow = 0, j = 0, e_idx, f_idx; char buff[50], num1[10], num2[10], num3[10], num4[10]; CifString string, string1, string2; _CHAIN *ch1 = NULL, *ch2 = NULL, *chain = NULL; ConnectFormat *drug = NULL; _RESIDUE *residue = NULL; ISTable *Table = NULL, *Table1 = NULL; if (_num_mol == 0 || _molecules == NULL) return; if (!_CifObj) return; na_classification(); Table = _CifObj->GetTablePtr(_StructureId, "ndb_struct_na_base_pair"); if (is_empty_table(Table) && _n_bb_params) { if (_CifObj->IsTablePresent(_StructureId, "ndb_struct_na_base_pair")) _CifObj->DeleteTable(_StructureId, "ndb_struct_na_base_pair"); Table = new ISTable("ndb_struct_na_base_pair"); Table->AddColumn("model_number"); Table->AddColumn("i_label_asym_id"); Table->AddColumn("i_label_comp_id"); Table->AddColumn("i_label_seq_id"); Table->AddColumn("i_symmetry"); Table->AddColumn("j_label_asym_id"); Table->AddColumn("j_label_comp_id"); Table->AddColumn("j_label_seq_id"); Table->AddColumn("j_symmetry"); Table->AddColumn("shear"); Table->AddColumn("stretch"); Table->AddColumn("stagger"); Table->AddColumn("buckle"); Table->AddColumn("propel"); Table->AddColumn("opening"); Table->AddColumn("pair_number"); Table->AddColumn("pair_name"); Table->AddColumn("i_auth_asym_id"); Table->AddColumn("i_auth_seq_id"); Table->AddColumn("i_PDB_ins_code"); Table->AddColumn("j_auth_asym_id"); Table->AddColumn("j_auth_seq_id"); Table->AddColumn("j_PDB_ins_code"); Table->AddColumn("hbond_type_28"); Table->AddColumn("hbond_type_12"); _CifObj->WriteTable(Table, _StructureId, "ndb_struct_na_base_pair"); for (i = 0; i < _n_bb_params; i++) { Table->AddRow(); string.Copy("1"); Table->UpdateCell(string, 0, i); string.Copy(_bb_params[i]->ChnID_I); Table->UpdateCell(string, 1, i); string.Copy(_bb_params[i]->Base_I); Table->UpdateCell(string, 2, i); sprintf(buff, "%d", _bb_params[i]->ResNum_I); string.Copy(buff); Table->UpdateCell(string, 3, i); string.Copy(_bb_params[i]->Sym_I); Table->UpdateCell(string, 4, i); string.Copy(_bb_params[i]->ChnID_J); Table->UpdateCell(string, 5, i); string.Copy(_bb_params[i]->Base_J); Table->UpdateCell(string, 6, i); sprintf(buff, "%d", _bb_params[i]->ResNum_J); string.Copy(buff); Table->UpdateCell(string, 7, i); string.Copy(_bb_params[i]->Sym_J); Table->UpdateCell(string, 8, i); sprintf(buff, "%.3f", _bb_params[i]->Shear); string.Copy(buff); Table->UpdateCell(string, 9, i); sprintf(buff, "%.3f", _bb_params[i]->Stretch); string.Copy(buff); Table->UpdateCell(string, 10, i); sprintf(buff, "%.3f", _bb_params[i]->Stagger); string.Copy(buff); Table->UpdateCell(string, 11, i); sprintf(buff, "%.3f", _bb_params[i]->Buckle); string.Copy(buff); Table->UpdateCell(string, 12, i); sprintf(buff, "%.3f", _bb_params[i]->Propel); string.Copy(buff); Table->UpdateCell(string, 13, i); sprintf(buff, "%.3f", _bb_params[i]->Opening); string.Copy(buff); Table->UpdateCell(string, 14, i); sprintf(buff, "%d", i+1); string.Copy(buff); Table->UpdateCell(string, 15, i); if (strcmp(_bb_params[i]->InsCode_I, "")) sprintf(num1, "%d%s", _bb_params[i]->ResNum_I_PDB, _bb_params[i]->InsCode_I); else sprintf(num1, "%d", _bb_params[i]->ResNum_I_PDB); if (strcmp(_bb_params[i]->InsCode_J, "")) sprintf(num2, "%d%s", _bb_params[i]->ResNum_J_PDB, _bb_params[i]->InsCode_J); else sprintf(num2, "%d", _bb_params[i]->ResNum_J_PDB); sprintf(buff, "%s_%s%s:%s%s_%s", _bb_params[i]->ChnID_I_PDB, _bb_params[i]->Base_I, num1, _bb_params[i]->Base_J, num2, _bb_params[i]->ChnID_J_PDB); string.Copy(buff); Table->UpdateCell(string, 16, i); string.Copy(_bb_params[i]->ChnID_I_PDB); Table->UpdateCell(string, 17, i); sprintf(buff, "%d", _bb_params[i]->ResNum_I_PDB); string.Copy(buff); Table->UpdateCell(string, 18, i); string.Copy(_bb_params[i]->InsCode_I); Table->UpdateCell(string, 19, i); string.Copy(_bb_params[i]->ChnID_J_PDB); Table->UpdateCell(string, 20, i); sprintf(buff, "%d", _bb_params[i]->ResNum_J_PDB); string.Copy(buff); Table->UpdateCell(string, 21, i); string.Copy(_bb_params[i]->InsCode_J); Table->UpdateCell(string, 22, i); string.Copy(_bb_params[i]->_saenger_classification); Table->UpdateCell(string, 23, i); string.Copy(_bb_params[i]->_leontis_westhof_classification); Table->UpdateCell(string, 24, i); } } Table = _CifObj->GetTablePtr(_StructureId, "ndb_struct_na_base_pair_step"); if (is_empty_table(Table) && _n_ib_params) { if (_CifObj->IsTablePresent(_StructureId, "ndb_struct_na_base_pair_step")) _CifObj->DeleteTable(_StructureId, "ndb_struct_na_base_pair_step"); Table = new ISTable("ndb_struct_na_base_pair_step"); Table->AddColumn("model_number"); Table->AddColumn("i_label_asym_id_1"); Table->AddColumn("i_label_comp_id_1"); Table->AddColumn("i_label_seq_id_1"); Table->AddColumn("i_symmetry_1"); Table->AddColumn("j_label_asym_id_1"); Table->AddColumn("j_label_comp_id_1"); Table->AddColumn("j_label_seq_id_1"); Table->AddColumn("j_symmetry_1"); Table->AddColumn("i_label_asym_id_2"); Table->AddColumn("i_label_comp_id_2"); Table->AddColumn("i_label_seq_id_2"); Table->AddColumn("i_symmetry_2"); Table->AddColumn("j_label_asym_id_2"); Table->AddColumn("j_label_comp_id_2"); Table->AddColumn("j_label_seq_id_2"); Table->AddColumn("j_symmetry_2"); Table->AddColumn("shift"); Table->AddColumn("slide"); Table->AddColumn("rise"); Table->AddColumn("tilt"); Table->AddColumn("roll"); Table->AddColumn("twist"); Table->AddColumn("x_displacement"); Table->AddColumn("y_displacement"); Table->AddColumn("helical_rise"); Table->AddColumn("inclination"); Table->AddColumn("tip"); Table->AddColumn("helical_twist"); Table->AddColumn("step_number"); Table->AddColumn("step_name"); Table->AddColumn("i_auth_asym_id_1"); Table->AddColumn("i_auth_seq_id_1"); Table->AddColumn("i_PDB_ins_code_1"); Table->AddColumn("j_auth_asym_id_1"); Table->AddColumn("j_auth_seq_id_1"); Table->AddColumn("j_PDB_ins_code_1"); Table->AddColumn("i_auth_asym_id_2"); Table->AddColumn("i_auth_seq_id_2"); Table->AddColumn("i_PDB_ins_code_2"); Table->AddColumn("j_auth_asym_id_2"); Table->AddColumn("j_auth_seq_id_2"); Table->AddColumn("j_PDB_ins_code_2"); _CifObj->WriteTable(Table, _StructureId, "ndb_struct_na_base_pair_step"); for (i = 0; i < _n_ib_params; i++) { Table->AddRow(); string.Copy("1"); Table->UpdateCell(string, 0, i); string.Copy(_ib_params[i]->ChnID_I1); Table->UpdateCell(string, 1, i); string.Copy(_ib_params[i]->Base_I1); Table->UpdateCell(string, 2, i); sprintf(buff, "%d", _ib_params[i]->ResNum_I1); string.Copy(buff); Table->UpdateCell(string, 3, i); string.Copy(_ib_params[i]->Sym_I1); Table->UpdateCell(string, 4, i); string.Copy(_ib_params[i]->ChnID_J1); Table->UpdateCell(string, 5, i); string.Copy(_ib_params[i]->Base_J1); Table->UpdateCell(string, 6, i); sprintf(buff, "%d", _ib_params[i]->ResNum_J1); string.Copy(buff); Table->UpdateCell(string, 7, i); string.Copy(_ib_params[i]->Sym_J1); Table->UpdateCell(string, 8, i); string.Copy(_ib_params[i]->ChnID_I2); Table->UpdateCell(string, 9, i); string.Copy(_ib_params[i]->Base_I2); Table->UpdateCell(string, 10, i); sprintf(buff, "%d", _ib_params[i]->ResNum_I2); string.Copy(buff); Table->UpdateCell(string, 11, i); string.Copy(_ib_params[i]->Sym_I2); Table->UpdateCell(string, 12, i); string.Copy(_ib_params[i]->ChnID_J2); Table->UpdateCell(string, 13, i); string.Copy(_ib_params[i]->Base_J2); Table->UpdateCell(string, 14, i); sprintf(buff, "%d", _ib_params[i]->ResNum_J2); string.Copy(buff); Table->UpdateCell(string, 15, i); string.Copy(_ib_params[i]->Sym_J2); Table->UpdateCell(string, 16, i); sprintf(buff, "%.3f", _ib_params[i]->Shift); string.Copy(buff); Table->UpdateCell(string, 17, i); sprintf(buff, "%.3f", _ib_params[i]->Slide); string.Copy(buff); Table->UpdateCell(string, 18, i); sprintf(buff, "%.3f", _ib_params[i]->Rise); string.Copy(buff); Table->UpdateCell(string, 19, i); sprintf(buff, "%.3f", _ib_params[i]->Tilt); string.Copy(buff); Table->UpdateCell(string, 20, i); sprintf(buff, "%.3f", _ib_params[i]->Roll); string.Copy(buff); Table->UpdateCell(string, 21, i); sprintf(buff, "%.3f", _ib_params[i]->Twist); string.Copy(buff); Table->UpdateCell(string, 22, i); sprintf(buff, "%.3f", _ib_params[i]->X_disp); string.Copy(buff); Table->UpdateCell(string, 23, i); sprintf(buff, "%.3f", _ib_params[i]->Y_disp); string.Copy(buff); Table->UpdateCell(string, 24, i); sprintf(buff, "%.3f", _ib_params[i]->H_rise); string.Copy(buff); Table->UpdateCell(string, 25, i); sprintf(buff, "%.3f", _ib_params[i]->Incl); string.Copy(buff); Table->UpdateCell(string, 26, i); sprintf(buff, "%.3f", _ib_params[i]->Tip); string.Copy(buff); Table->UpdateCell(string, 27, i); sprintf(buff, "%.3f", _ib_params[i]->H_twist); string.Copy(buff); Table->UpdateCell(string, 28, i); sprintf(buff, "%d", i+1); string.Copy(buff); Table->UpdateCell(string, 29, i); if (strcmp(_ib_params[i]->InsCode_I1, "")) sprintf(num1, "%d%s", _ib_params[i]->ResNum_I1_PDB, _ib_params[i]->InsCode_I1); else sprintf(num1, "%d", _ib_params[i]->ResNum_I1_PDB); if (strcmp(_ib_params[i]->InsCode_J1, "")) sprintf(num2, "%d%s", _ib_params[i]->ResNum_J1_PDB, _ib_params[i]->InsCode_J1); else sprintf(num2, "%d", _ib_params[i]->ResNum_J1_PDB); if (strcmp(_ib_params[i]->InsCode_I2, "")) sprintf(num3, "%d%s", _ib_params[i]->ResNum_I2_PDB, _ib_params[i]->InsCode_I2); else sprintf(num3, "%d", _ib_params[i]->ResNum_I2_PDB); if (strcmp(_ib_params[i]->InsCode_J2, "")) sprintf(num4, "%d%s", _ib_params[i]->ResNum_J2_PDB, _ib_params[i]->InsCode_J2); else sprintf(num4, "%d", _ib_params[i]->ResNum_J2_PDB); sprintf(buff, "%s%s_%s%s%s%s:%s%s%s%s_%s%s", _ib_params[i]->ChnID_I1_PDB, _ib_params[i]->ChnID_I2_PDB, _ib_params[i]->Base_I1, num1, _ib_params[i]->Base_I2, num3, _ib_params[i]->Base_J2, num4, _ib_params[i]->Base_J1, num2, _ib_params[i]->ChnID_J2_PDB, _ib_params[i]->ChnID_J1_PDB); string.Copy(buff); Table->UpdateCell(string, 30, i); string.Copy(_ib_params[i]->ChnID_I1_PDB); Table->UpdateCell(string, 31, i); sprintf(buff, "%d", _ib_params[i]->ResNum_I1_PDB); string.Copy(buff); Table->UpdateCell(string, 32, i); string.Copy(_ib_params[i]->InsCode_I1); Table->UpdateCell(string, 33, i); string.Copy(_ib_params[i]->ChnID_J1_PDB); Table->UpdateCell(string, 34, i); sprintf(buff, "%d", _ib_params[i]->ResNum_J1_PDB); string.Copy(buff); Table->UpdateCell(string, 35, i); string.Copy(_ib_params[i]->InsCode_J1); Table->UpdateCell(string, 36, i); string.Copy(_ib_params[i]->ChnID_I2_PDB); Table->UpdateCell(string, 37, i); sprintf(buff, "%d", _ib_params[i]->ResNum_I2_PDB); string.Copy(buff); Table->UpdateCell(string, 38, i); string.Copy(_ib_params[i]->InsCode_I2); Table->UpdateCell(string, 39, i); string.Copy(_ib_params[i]->ChnID_J2_PDB); Table->UpdateCell(string, 40, i); sprintf(buff, "%d", _ib_params[i]->ResNum_J2_PDB); string.Copy(buff); Table->UpdateCell(string, 41, i); string.Copy(_ib_params[i]->InsCode_J2); Table->UpdateCell(string, 42, i); } } Table = _CifObj->GetTablePtr(_StructureId, "ndb_entity_poly_na_type"); if (is_empty_table(Table)) { if (_CifObj->IsTablePresent(_StructureId, "ndb_entity_poly_na_type")) _CifObj->DeleteTable(_StructureId, "ndb_entity_poly_na_type"); Table = new ISTable("ndb_entity_poly_na_type"); Table->AddColumn("entity_id"); Table->AddColumn("type"); _CifObj->WriteTable(Table, _StructureId, "ndb_entity_poly_na_type"); } else Table = NULL; Table1 = _CifObj->GetTablePtr(_StructureId, "ndb_entity_poly_na_nonstandard"); if (is_empty_table(Table1)) { if (_CifObj->IsTablePresent(_StructureId, "ndb_entity_poly_na_nonstandard")) _CifObj->DeleteTable(_StructureId, "ndb_entity_poly_na_nonstandard"); Table1 = new ISTable("ndb_entity_poly_na_nonstandard"); Table1->AddColumn("entity_id"); Table1->AddColumn("feature"); _CifObj->WriteTable(Table1, _StructureId, "ndb_entity_poly_na_nonstandard"); } else Table1 = NULL; for (i = 0; i < 100; i++) entity_id[i] = -1; chain = _molecules[0]->GetFirstChain(); while (chain) { if (chain->chain_type() != ATOMN_TOKEN) { chain = _molecules[0]->GetNextChain(); continue; } for (j = 0; j < n_entity_id; j++) { if (entity_id[j] == chain->entity_id()) break; } if (j < n_entity_id) { chain = _molecules[0]->GetNextChain(); continue; } entity_id[j] = chain->entity_id(); n_entity_id++; if (Table) { Table->AddRow(); sprintf(buff, "%d", entity_id[j]); string.Copy(buff); Table->UpdateCell(string, 0, j); if (chain->na_type() == ATOMN_TYPE_DNA_ONLY) string.Copy("DNA"); else if (chain->na_type() == ATOMN_TYPE_RNA_ONLY || chain->na_type() == ATOMN_TYPE_DNA_RNA) string.Copy("RNA"); else if (chain->na_type() == ATOMN_TYPE_TRNA) string.Copy("t-RNA"); else string.Copy("RNA"); Table->UpdateCell(string, 1, j); } if (Table1) { e_idx = Table1->GetColumnIndex("entity_id"); f_idx = Table1->GetColumnIndex("feature"); for (j = 0; j < _n_modifb; j++) { ch1 = _molecules[0]->GetIndexChain(_modifb[j]->FstIndex); ch2 = _molecules[0]->GetIndexChain(_modifb[j]->SndIndex); if (ch1 == chain || ch2 == chain) { sprintf(buff, "%d", chain->entity_id()); for (i = 0; i < irow; i++) { Table1->GetCell(string, e_idx, i); Table1->GetCell(string1, f_idx, i); if (string == buff && string1 == "base modification") break; } if (i < irow) continue; Table1->AddRow(); string.Copy(buff); Table1->UpdateCell(string, e_idx, irow); string.Copy("base modification"); Table1->UpdateCell(string, f_idx, irow); irow++; } } for (j = 0; j < _n_modifp; j++) { ch1 = _molecules[0]->GetIndexChain(_modifp[j]->FstIndex); ch2 = _molecules[0]->GetIndexChain(_modifp[j]->SndIndex); if (ch1 == chain || ch2 == chain) { sprintf(buff, "%d", chain->entity_id()); for (i = 0; i < irow; i++) { Table1->GetCell(string, e_idx, i); Table1->GetCell(string1, f_idx, i); if (string == buff && string1 == "phosphate modification") break; } if (i < irow) continue; Table1->AddRow(); string.Copy(buff); Table1->UpdateCell(string, e_idx, irow); string.Copy("phosphate modification"); Table1->UpdateCell(string, f_idx, irow); irow++; } } for (j = 0; j < _n_modifs; j++) { ch1 = _molecules[0]->GetIndexChain(_modifs[j]->FstIndex); ch2 = _molecules[0]->GetIndexChain(_modifs[j]->SndIndex); if (ch1 == chain || ch2 == chain) { sprintf(buff, "%d", chain->entity_id()); for (i = 0; i < irow; i++) { Table1->GetCell(string, e_idx, i); Table1->GetCell(string1, f_idx, i); if (string == buff && string1 == "sugar modification") break; } if (i < irow) continue; Table1->AddRow(); string.Copy(buff); Table1->UpdateCell(string, e_idx, irow); string.Copy("sugar modification"); Table1->UpdateCell(string, f_idx, irow); irow++; } } residue = chain->GetFirstResidue(); while (residue) { drug = find_drug(residue->ResName()); if (drug && drug->numModification()) { for (j = 0; j < drug->numModification(); j++) { string2.Copy(drug->Modification(j)); string2.ToLower(); sprintf(buff, "%d", chain->entity_id()); for (i = 0; i < irow; i++) { Table1->GetCell(string, e_idx, i); Table1->GetCell(string1, f_idx, i); if (string == buff && string1 == string2) break; } if (i < irow) continue; Table1->AddRow(); string.Copy(buff); Table1->UpdateCell(string, e_idx, irow); Table1->UpdateCell(string2, f_idx, irow); irow++; } } residue = chain->GetNextResidue(); } } chain = _molecules[0]->GetNextChain(); } } void _MAXIT::delete_terminal_atoms() { static int num_aa = 5 /* , num_na = 3 */ ; static const char *aa[] = { "OXT", "HXT", "1H", "2H", "3H" }; // static char *na[] = { "O3P", "3HOP", "H3T" }; int l = 0, j = 0, k = 0; _CHAIN *chain = NULL; _RESIDUE *residue = NULL; for (l = 0; l < _num_mol; l++) { chain = _molecules[l]->GetFirstChain(); while (chain) { if (chain->chain_type() != ATOMP_TOKEN /* && chain->chain_type() != ATOMN_TOKEN*/ ) { chain = _molecules[l]->GetNextChain(); continue; } for (j = 1; j < chain->SeqLen() - 1; j++) { if (chain->SeqRes(j)->Deleted) continue; residue = chain->SeqRes(j)->Residue; if (!residue) continue; // if (chain->SeqRes(j+1)->Residue) continue; /* if (chain->chain_type() == ATOMP_TOKEN) { */ for (k = 0; k < num_aa; k++) { residue->delete_a_atom(aa[k]); } /* } else if (chain->chain_type() == ATOMN_TOKEN) { for (k = 0; k < num_na; k++) { residue->delete_a_atom(na[k]); } } */ } chain = _molecules[l]->GetNextChain(); } } } void _MAXIT::correct_atom_name() { int l, first_residue, need_hydrogen = 0; char *p = NULL; _CHAIN *chain = NULL; _RESIDUE *residue = NULL; if (_experiment_type & EXPERIMENT_TYPE_NMR) need_hydrogen = 1; for (l = 0; l < _num_mol; l++) { chain = _molecules[l]->GetFirstChain(); while (chain) { first_residue = 0; residue = chain->GetFirstResidue(); while (residue) { residue->find_missing_or_extra_atoms(chain->chain_type(), !first_residue, need_hydrogen); p = residue->extras().Text(); if (p && strcmp(p, "")) residue->correction_atom_name(_error_message_s); first_residue = 1; residue = chain->GetNextResidue(); } chain = _molecules[l]->GetNextChain(); } } } void _MAXIT::renumber_pdb_numbers() { int i = 0, found_redundancy = 0, serial_no = 0, start_number = 0; char buffer[10]; _CHAIN *chain = NULL; CifString string; TblIndexObj index; if (!_num_mol || !_molecules) return; index.Clear(); chain = _molecules[0]->GetFirstChain(); while (chain) { if (!strcmp(chain->PDB_ChainID(), "")) { for (i = 0; i < chain->SeqLen(); i++) { if (chain->SeqRes(i)->Deleted) continue; if (!chain->SeqRes(i)->Residue) continue; sprintf(buffer, "%s%s", chain->SeqRes(i)->Field[4], chain->SeqRes(i)->InsCode); string.Copy(buffer); if (index.Seek(string) >= 0) found_redundancy = 1; index.Add(string); if ((chain->chain_type() == ATOMP_TOKEN || chain->chain_type() == ATOMN_TOKEN) && atoi(chain->SeqRes(i)->Field[4]) > serial_no) { serial_no = atoi(chain->SeqRes(i)->Field[4]); } } } chain = _molecules[0]->GetNextChain(); } if (!found_redundancy) return; for (i = 0; i < _num_mol; i++) { start_number = serial_no; chain = _molecules[i]->GetFirstChain(); while (chain) { if (!strcmp(chain->PDB_ChainID(), "") && chain->chain_type() != ATOMP_TOKEN && chain->chain_type() != ATOMN_TOKEN) chain->update_residues_pdb_numbers(start_number); chain = _molecules[i]->GetNextChain(); } } } void _MAXIT::search_complexity() { ISTable *Table = _CifObj->GetTablePtr(_StructureId, "entity"); if (is_empty_table(Table)) return; int rowNo = Table->GetNumRows(); if (rowNo < 3) return; int type_index = Table->GetColumnIndex("type"); int weight_index = Table->GetColumnIndex("formula_weight"); if (type_index < 0 || weight_index < 0) return; CifString type, weight; int count = 0; for (int i = 0; i < rowNo; i++) { get_value(type, Table, type_index, i); get_value(weight, Table, weight_index, i); if (!strcasecmp(type.Text(), "POLYMER") && atof(weight.Text()) > 8000.0) count++; } if (count > 2) printf("-%s-\n", _StructureId); } void _MAXIT::generate_symmetry_and_ncs_related_strands(const char *outfilename, const int pdbid_flag) { int i = 0, j = 0, k = 0, add_mol, ret, op = 0, trans[3], len, num_mol_org; _CHAIN *chain = NULL, *new_chain = NULL; CifString string; TblIndexObj index; if (_num_mol == 0 || _molecules == NULL) return; for (j = 0; j < _num_mol; j++) { chain = _molecules[j]->GetFirstChain(); while (chain) { for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; if (_stbiol[i]->Asym_ID == chain->ChainID() && !strcmp(_stbiol[i]->Symmetry, NDB_BASE_SYMMETRY)) { chain->set_biol_id(_stbiol[i]->Biol_ID); break; } } chain = _molecules[j]->GetNextChain(); } } index.Clear(); for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; if (strcmp(_stbiol[i]->Symmetry, NDB_BASE_SYMMETRY)) { string.Copy(_stbiol[i]->Symmetry); ret = index.Seek(string); if (ret < 0) index.Add(string); } } if (index.Root() < 0) { generate_ncs_related_strands(outfilename, pdbid_flag); return; } for (i = 0; i < _num_mol; i++) { _molecules[i]->convert_between_orthogonal_and_fractional(_cell, NDB_TRANS_ORTHO_TO_FRAC); } num_mol_org = _num_mol; for (k = 0; k < num_mol_org; k++) { ret = index.GoFirst(); while (ret >= 0) { string = index.GetCurrData(); op = atoi(string.Text()) - 1; trans[0] = trans[1] = trans[2] = 0; len = strlen(string.Text()); for (i = 0; i < len; i++) if (string.Text()[i] == '_') break; if (i+3 < len) { for (j = 0; j < 3; j++) trans[j] = string.Text()[i+j+1] - '5'; } add_mol = 0; for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; if (string == _stbiol[i]->Symmetry) { chain = _molecules[k]->GetFirstChain(); while (chain) { if (_stbiol[i]->Asym_ID == chain->ChainID() && chain->op() == 1) break; chain = _molecules[k]->GetNextChain(); } if (!chain) continue; new_chain = new _CHAIN; new_chain->symmetry_related_chain(*chain, trans[0], trans[1], trans[2], &(_cell->symops[op]), 0); new_chain->set_biol_id(_stbiol[i]->Biol_ID); if (!add_mol) { _ManageSpace(); _molecules[_num_mol-1]->set_Mol_ID(_num_mol); add_mol = 1; } _molecules[_num_mol-1]->insert_a_chain(new_chain); } } ret = index.GoToNext(); } } for (i = 0; i < _num_mol; i++) _molecules[i]->convert_between_orthogonal_and_fractional(_cell, NDB_TRANS_FRAC_TO_ORTHO); } void _MAXIT::generate_ncs_related_strands(const char *outfilename, const int pdbid_flag) { int i, rowNo, code, m11, m12, m13, m21, m22, m23, m31, m32, m33, v1, v2, v3; int numRemark = 0, displayOrder = 0, card_id = 0, irow = 0, Mol_ID = 1; int token_id, CONECT_TOKEN; double matrix[3][4]; char buffer[100], pdbid[10]; _CHAIN *chain = NULL, *new_chain = NULL; CifString string; FILE *fp = NULL; ISTable *Table = NULL; _MOLECULE *mol = NULL; One_Card_Info_Format *pCard = NULL; if (_num_mol == 0 || _molecules == NULL) return; Table = _CifObj->GetTablePtr(_StructureId, "struct_ncs_oper"); if (is_empty_table(Table)) return; rowNo = Table->GetNumRows(); code = Table->GetColumnIndex("code"); for (i = 0; i < rowNo; i++) { Table->GetCell(string, code, i); if (string == "generate") break; } if (i == rowNo) return; _create_final_file = 1; for (i = 0; i < NUM_REM_TOKEN; i++) { token_id = find_card_id(remove_token[i]); if (token_id < 0) continue; pCard = _CardInfo[token_id].Head(); while (pCard) pCard = _CardInfo[token_id].delete_a_card(pCard); } pCard = _CardInfo[HEADER_TOKEN-1].Head(); if (pCard) pCard->AddElementToField("XXXX", 3); strcpy(pdbid, ""); if (pdbid_flag) { pCard = _CardInfo[PDBFIL_TOKEN-1].Head(); if (pCard) strcpy(pdbid, pCard->Field(1)); ndb_set_string_to_lower(pdbid); } if (strcmp(pdbid, "")) sprintf(buffer, "%s.pdb1", pdbid); else sprintf(buffer, "%s_1", outfilename); fp = fopen(buffer, "w"); _molecules[0]->reorder_chain_order(); _output_format = NDB_FILE_FORMAT_PDB; get_seqres_from_mapping(_output_format); for (displayOrder = 0; displayOrder < MxTokens; displayOrder++) { for (card_id = 0; card_id < MxTokens; card_id++) if (displayOrder == NdbToken[card_id].DisplayOrder) break; if (card_id == MxTokens || card_id + 1 != JRNL_TOKEN && _CardInfo[card_id].Head() == NULL || card_id == NDBSQN_TOKEN-1 || card_id == SYMTRA_TOKEN-1 || (NdbToken[card_id].NdbOnly || card_id + 1 == REMARK_TOKEN || card_id == MASTER_TOKEN-1)) continue; if (card_id +1 != JRNL_TOKEN) print_general_cards(fp, card_id, NDB_FILE_FORMAT_PDB, numRemark, 0); else { print_jrnl_cards(fp, NDB_FILE_FORMAT_PDB, numRemark); print_general_cards(fp, REMARK_TOKEN - 1, NDB_FILE_FORMAT_PDB, numRemark, 0); } } Mol_ID = 1; fprintf(fp, "MODEL %4d ", Mol_ID); fprintf(fp, " \n"); print_molecule(_molecules[0], NULL, irow, fp, NDB_FILE_FORMAT_PDB, 0, 1, 0); fprintf(fp, "ENDMDL "); fprintf(fp, " \n"); Mol_ID++; get_connect_cards(); m11 = Table->GetColumnIndex("matrix[1][1]"); m12 = Table->GetColumnIndex("matrix[1][2]"); m13 = Table->GetColumnIndex("matrix[1][3]"); m21 = Table->GetColumnIndex("matrix[2][1]"); m22 = Table->GetColumnIndex("matrix[2][2]"); m23 = Table->GetColumnIndex("matrix[2][3]"); m31 = Table->GetColumnIndex("matrix[3][1]"); m32 = Table->GetColumnIndex("matrix[3][2]"); m33 = Table->GetColumnIndex("matrix[3][3]"); v1 = Table->GetColumnIndex("vector[1]"); v2 = Table->GetColumnIndex("vector[2]"); v3 = Table->GetColumnIndex("vector[3]"); for (i = 0; i < rowNo; i++) { Table->GetCell(string, code, i); if (string != "generate") continue; Table->GetCell(string, m11, i); matrix[0][0] = atof(string.Text()); Table->GetCell(string, m12, i); matrix[0][1] = atof(string.Text()); Table->GetCell(string, m13, i); matrix[0][2] = atof(string.Text()); Table->GetCell(string, v1, i); matrix[0][3] = atof(string.Text()); Table->GetCell(string, m21, i); matrix[1][0] = atof(string.Text()); Table->GetCell(string, m22, i); matrix[1][1] = atof(string.Text()); Table->GetCell(string, m23, i); matrix[1][2] = atof(string.Text()); Table->GetCell(string, v2, i); matrix[1][3] = atof(string.Text()); Table->GetCell(string, m31, i); matrix[2][0] = atof(string.Text()); Table->GetCell(string, m32, i); matrix[2][1] = atof(string.Text()); Table->GetCell(string, m33, i); matrix[2][2] = atof(string.Text()); Table->GetCell(string, v3, i); matrix[2][3] = atof(string.Text()); printf("i=%2d\n", i + 1); for (int j = 0; j < 3; j++) { for (int k = 0; k < 3; k++) printf("%7.4f ", matrix[j][k]); printf("\n"); } printf("\n"); mol = new _MOLECULE; chain = _molecules[0]->GetFirstChain(); while (chain) { new_chain = new _CHAIN; new_chain->set_biol_id(1); new_chain->symmetry_related_chain(*chain, matrix); mol->insert_a_chain(new_chain); chain = _molecules[0]->GetNextChain(); } fprintf(fp, "MODEL %4d ", Mol_ID); fprintf(fp, " \n"); print_molecule(mol, NULL, irow, fp, NDB_FILE_FORMAT_PDB, 0, 0, 0); fprintf(fp, "ENDMDL "); fprintf(fp, " \n"); Mol_ID++; delete mol; } CONECT_TOKEN = find_card_id("CONECT"); print_general_cards(fp, CONECT_TOKEN, NDB_FILE_FORMAT_PDB, numRemark, 0); print_master_card(fp, numRemark); fprintf(fp, "END"); for (i = 0; i < 77; i++) fprintf(fp, " "); fprintf(fp, "\n"); fclose (fp); } void _MAXIT::generate_packing() { if (_num_mol == 0 || _molecules == NULL) return; if (strcmp(_cell->space_group, "P 1")) _molecules[0]->crystal_packing(_cell); } void _MAXIT::write_pdb_files(const char *outfilename, const int pdbid_flag) { int i, j, *biol_id = NULL, n_biol_id = 0, found = 0, token_id; char buffer[100], pdbid[10]; _CHAIN *chain = NULL; One_Card_Info_Format *pCard = NULL; if (_create_final_file) return; for (i = 0; i < NUM_REM_TOKEN; i++) { token_id = find_card_id(remove_token[i]); if (token_id < 0) continue; pCard = _CardInfo[token_id].Head(); while (pCard) pCard = _CardInfo[token_id].delete_a_card(pCard); } pCard = _CardInfo[HEADER_TOKEN-1].Head(); if (pCard) pCard->AddElementToField("XXXX", 3); strcpy(pdbid, ""); if (pdbid_flag) { pCard = _CardInfo[PDBFIL_TOKEN-1].Head(); if (pCard) strcpy(pdbid, pCard->Field(1)); ndb_set_string_to_lower(pdbid); } biol_id = new int[_n_stbiol]; for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; for (j = 0; j < n_biol_id; j++) { if (biol_id[j] == _stbiol[i]->Biol_ID) break; } if (j == n_biol_id) { n_biol_id++; biol_id[j] = _stbiol[i]->Biol_ID; } } for (i = 0; i < n_biol_id; i++) { for (j = 0; j < _num_mol; j++) { found = 0; chain = _molecules[j]->GetFirstChain(); while (chain) { if (chain->biol_id() == biol_id[i]) { chain->set_display(1); found = 1; } else chain->set_display(0); chain = _molecules[j]->GetNextChain(); } if (found) _molecules[j]->set_display(1); else _molecules[j]->set_display(0); } if (strcmp(pdbid, "")) sprintf(buffer, "%s.pdb%d", pdbid, i + 1); else sprintf(buffer, "%s_%d", outfilename, i + 1); set_output_filename(buffer); write_ndb_file(NDB_FILE_FORMAT_PDB, 0, 1, 0, 0); } delete [] biol_id; } static _ENTITY *realloc_entity(_ENTITY *entity, const int n_size) { int i; _ENTITY *new_entity = new _ENTITY[n_size+1]; for (i = 0; i <= n_size; i++) { new_entity[i].Entity_ID = 0; new_entity[i].Old_Entity_ID = 0; new_entity[i].Number = 0; new_entity[i].Type = NULL; new_entity[i].Source = NULL; new_entity[i].Description = NULL; } if (entity) { for (i = 0; i < n_size; i++) { new_entity[i].Entity_ID = entity[i].Entity_ID; new_entity[i].Old_Entity_ID = entity[i].Old_Entity_ID; new_entity[i].Number = entity[i].Number; new_entity[i].Type = entity[i].Type; new_entity[i].Source = entity[i].Source; new_entity[i].Description = entity[i].Description; entity[i].Type = NULL; entity[i].Source = NULL; entity[i].Description = NULL; } delete [] entity; } return new_entity; } static char *get_entity_description(_CHAIN *chain) { int len; char *buff = NULL, descriptor[800]; if (chain->chain_type() == HETAS_TOKEN && (!strcmp(chain->SeqRes(0)->Field[0], "HOH") || !strcmp(chain->SeqRes(0)->Field[0], "DOD"))) { len = strlen(NDB_WATER_TEXT)+1; buff = new char[len]; strcpy(buff, NDB_WATER_TEXT); } else { descriptor[0] = '\0'; chain->get_descriptor(descriptor); if (chain->chain_type() == ATOMS_TOKEN) { len = strlen(descriptor) + 10; buff = new char[len]; sprintf(buff, "SUGAR (%s)", descriptor); } else if (chain->chain_type() == ATOMN_TOKEN) { if (chain->na_type() == ATOMN_TYPE_RNA_ONLY) { len = strlen(descriptor) + 8; buff = new char[len]; sprintf(buff, "%s (%s)", NDB_RNA_TEXT, descriptor); } else if (chain->na_type() == ATOMN_TYPE_TRNA) { len = strlen(descriptor) + 10; buff = new char[len]; sprintf(buff, "%s (%s)", NDB_T_RNA_TEXT, descriptor); } else if (chain->na_type() == ATOMN_TYPE_DNA_RNA) { len = strlen(descriptor) + 12; buff = new char[len]; sprintf(buff, "%s (%s)", NDB_HYBRID_TEXT, descriptor); } else { len = strlen(descriptor) + 8; buff = new char[len]; sprintf(buff, "%s (%s)", NDB_DNA_TEXT, descriptor); } } else { len = strlen(descriptor); if (len) { buff = new char[len+1]; strcpy(buff, descriptor); } } } return buff; } static char *get_line_from_string(char *line, char *string) { unsigned int i; if (!string || *string == '\0') return NULL; *line = '\0'; for (i = 0; i < strlen(string); i++) { if (string[i] == '\n') break; *line = string[i]; line++; } *line = '\0'; i++; if (string[i] == '\0') return NULL; return &(string[i]); }