/* FILE: _validation.C */ /* VERSION: 1.600 */ /* DATE: 2/3/2005 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. The user of this software shall indemnify, hold harmless and defend Rutgers, its governors, trustees, officers, employees, students, agents and the authors against any and all claims, suits, losses, liabilities, damages, costs, fees, and expenses including reasonable attorneys' fees resulting from or arising out of the use of this software. 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Title and related rights in the content accessed through the SOFTWARE is the property of the applicable content owner and is protected by applicable law. The license granted under this Agreement gives Licensee no rights to such content. 7. DISCLAIMER OF WARRANTY. THE SOFTWARE IS PROVIDED FREE OF CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE. SHOULD THE SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS AGREEMENT. NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER. 8. LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. */ #include #include "_validation.h" #include "erf_util.h" #include "util.h" static int find_symmetry_related_chain(const int n_stbiol, _STBIOL **stbiol, const int i, const int index); static int find_symmetry_related_chains(const int n_stbiol, _STBIOL **stbiol, const int index, char *ndb_chnid); static int find_asymmetric_chains(const int n_stbiol, _STBIOL **stbiol, const int start); _VALIDATION::_VALIDATION(const int mxtokens, const int mxjrnltokens): _FileObj(mxtokens, mxjrnltokens) { _alloc_link = 0; _n_link = 0; _link = NULL; _alloc_mismat = 0; _n_mismat = 0; _mismat = NULL; _alloc_bspair = 0; _n_bspair = 0; _bspair = NULL; _alloc_a_contact = 0; _n_a_contact = 0; _a_contact = NULL; _alloc_s_contact = 0; _n_s_contact = 0; _s_contact = NULL; _alloc_waters = 0; _n_waters = 0; _waters = NULL; _alloc_moving_waters = 0; _n_moving_waters = 0; _moving_waters = NULL; _alloc_speical = 0; _n_speical = 0; _speical = NULL; _alloc_bond = 0; _n_bond = 0; _bond = NULL; _alloc_angle = 0; _n_angle = 0; _angle = NULL; _alloc_torsion = 0; _n_torsion = 0; _torsion = NULL; _alloc_t_pairs = 0; _n_t_pairs = 0; _t_pairs = NULL; _alloc_z_a_1 = 0; _n_z_a_1 = 0; _z_a_1 = NULL; _alloc_z_b_1 = 0; _n_z_b_1 = 0; _z_b_1 = NULL; _alloc_z_e = 0; _n_z_e = 0; _z_e = NULL; _alloc_a_g = 0; _n_a_g = 0; _a_g = NULL; _alloc_z_x = 0; _n_z_x = 0; _z_x = NULL; _alloc_d_x = 0; _n_d_x = 0; _d_x = NULL; _calculated_bond_angle_torsion = 0; _alloc_bb_params = 0; _n_bb_params = 0; _bb_params = NULL; _alloc_ib_params = 0; _n_ib_params = 0; _ib_params = NULL; _alloc_ribbons = 0; _n_ribbons = 0; _ribbons = NULL; _alloc_link_bonds = 0; _n_link_bonds = 0; _link_bonds = NULL; _alloc_blocks = 0; _n_blocks = 0; _blocks = NULL; _bondResIndex.Clear(); _bondNamIndex.Clear(); _bondComIndex.Clear(); _angleResIndex.Clear(); _angleNamIndex.Clear(); _angleComIndex.Clear(); _torsionIndex.Clear(); _classification = 0; _spell_check.Clear(); _large_cell.Clear(); _date_error.Clear(); } _VALIDATION::~_VALIDATION() { int i; if (_link) { for (i = 0; i < _n_link; i++) { if (_link[i]) { if (_link[i]->details) delete _link[i]->details; delete _link[i]; } } delete [] _link; } if (_mismat) { for (i = 0; i < _n_mismat; i++) if (_mismat[i]) delete _mismat[i]; delete [] _mismat; } Clear_Bspair(); Clear_Contact(); if (_bond) { for (i = 0; i < _n_bond; i++) if (_bond[i]) delete _bond[i]; delete [] _bond; } if (_angle) { for (i = 0; i < _n_angle; i++) if (_angle[i]) delete _angle[i]; delete [] _angle; } if (_torsion) { for (i = 0; i < _n_torsion; i++) if (_torsion[i]) delete _torsion[i]; delete [] _torsion; } if (_t_pairs) { for (i = 0; i < _n_t_pairs; i++) if (_t_pairs[i]) delete _t_pairs[i]; delete [] _t_pairs; } if (_z_a_1) { for (i = 0; i < _n_z_a_1; i++) if (_z_a_1[i]) delete _z_a_1[i]; delete [] _z_a_1; } if (_z_b_1) { for (i = 0; i < _n_z_b_1; i++) if (_z_b_1[i]) delete _z_b_1[i]; delete [] _z_b_1; } if (_z_e) { for (i = 0; i < _n_z_e; i++) if (_z_e[i]) delete _z_e[i]; delete [] _z_e; } if (_a_g) { for (i = 0; i < _n_a_g; i++) if (_a_g[i]) delete _a_g[i]; delete [] _a_g; } if (_z_x) { for (i = 0; i < _n_z_x; i++) if (_z_x[i]) delete _z_x[i]; delete [] _z_x; } if (_d_x) { for (i = 0; i < _n_d_x; i++) if (_d_x[i]) delete _d_x[i]; delete [] _d_x; } if (_bb_params) { for (i = 0; i < _n_bb_params; i++) if (_bb_params[i]) delete _bb_params[i]; delete [] _bb_params; } if (_ib_params) { for (i = 0; i < _n_ib_params; i++) if (_ib_params[i]) delete _ib_params[i]; delete [] _ib_params; } Clear(); } void _VALIDATION::Clear_Bspair() { int i; if (_bspair) { for (i = 0; i < _n_bspair; i++) if (_bspair[i]) delete _bspair[i]; delete [] _bspair; } _bspair = NULL; _n_bspair = 0; _alloc_bspair = 0; } void _VALIDATION::Clear_Contact() { int i; if (_a_contact) { for (i = 0; i < _n_a_contact; i++) if (_a_contact[i]) delete _a_contact[i]; delete [] _a_contact; } if (_s_contact) { for (i = 0; i < _n_s_contact; i++) if (_s_contact[i]) delete _s_contact[i]; delete [] _s_contact; } if (_waters) { for (i = 0; i < _n_waters; i++) if (_waters[i]) delete _waters[i]; delete [] _waters; } if (_moving_waters) { for (i = 0; i < _n_moving_waters; i++) if (_moving_waters[i]) delete _moving_waters[i]; delete [] _moving_waters; } if (_speical) { for (i = 0; i < _n_speical; i++) if (_speical[i]) delete _speical[i]; delete [] _speical; } _alloc_a_contact = 0; _n_a_contact = 0; _a_contact = NULL; _alloc_s_contact = 0; _n_s_contact = 0; _s_contact = NULL; _alloc_waters = 0; _n_waters = 0; _waters = NULL; _alloc_moving_waters = 0; _n_moving_waters = 0; _moving_waters = NULL; _alloc_speical = 0; _n_speical = 0; _speical = NULL; } void _VALIDATION::Clear() { int i; if (_ribbons) { for (i = 0; i < _n_ribbons; i++) { if (_ribbons[i]) { if (_ribbons[i]->ribbon) delete [] _ribbons[i]->ribbon; delete _ribbons[i]; } } delete [] _ribbons; } _alloc_ribbons = 0; _n_ribbons = 0; _ribbons = NULL; if (_link_bonds) { for (i = 0; i < _n_link_bonds; i++) if (_link_bonds[i]) delete _link_bonds[i]; delete [] _link_bonds; } _alloc_link_bonds = 0; _n_link_bonds = 0; _link_bonds = NULL; if (_blocks) { for (i = 0; i < _n_blocks; i++) if (_blocks[i]) delete _blocks[i]; delete [] _blocks; } _alloc_blocks = 0; _n_blocks = 0; _blocks = NULL; } void _VALIDATION::Get_Stbiol(const int exchange) { int i, j, rowNo, colNo, id_idx, flag_idx; CifString string; ReVarCifArray *ColumnNames = NULL; ISTable *Table = NULL; One_Card_Info_Format *pCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[STBIOL_TOKEN-1].delete_a_card(pCard); Table = _CifObj->GetTablePtr(_StructureId, "struct_biol_gen"); if (is_empty_table(Table)) return; if (Table->GetColumnIndex("ndb_new_pdb_asym_id") < 0) _exist_pdb_chain_id = 0; if (exchange) _exist_pdb_chain_id = 0; rowNo = Table->GetNumRows(); colNo = Table->GetNumColumns(); ColumnNames = Table->GetColumnNames(); if (_stbiol) { for (i = 0; i < _n_stbiol; i++) if (_stbiol[i]) delete _stbiol[i]; delete [] _stbiol; } _n_stbiol = rowNo; _stbiol = new _STBIOL*[_n_stbiol]; for (i = 0; i < rowNo ; i++) { _stbiol[i] = new _STBIOL; _stbiol[i]->internal_order = i; _stbiol[i]->order = i; _stbiol[i]->Biol_ID = 1; _stbiol[i]->Asym_ID.Clear(); _stbiol[i]->NDB_Strand_ID.Clear(); _stbiol[i]->PDB_Strand_ID[0] = '\0'; _stbiol[i]->PDB_Strand_ID_Flag[0] = '\0'; strcpy(_stbiol[i]->Symmetry, "1_555"); _stbiol[i]->bbrn = -99999; _stbiol[i]->bern = -99999; _stbiol[i]->abrn = -99999; _stbiol[i]->aern = -99999; for (j = 0; j < colNo; j++) { Table->GetCell(string, j, i); if (string == "" || string == "?" || string == ".") continue; if (!strcmp((*ColumnNames)[j].Text(), "biol_id")) _stbiol[i]->Biol_ID = atoi(string.Text()); else if (!strcmp((*ColumnNames)[j].Text(), "asym_id")) _stbiol[i]->Asym_ID.Copy(string); else if (!strcmp((*ColumnNames)[j].Text(), "ndb_new_asym_id")) _stbiol[i]->NDB_Strand_ID.Copy(string); else if (!strcmp((*ColumnNames)[j].Text(), "ndb_new_pdb_asym_id")) strcpy(_stbiol[i]->PDB_Strand_ID, string.Text()); else if (!strcmp((*ColumnNames)[j].Text(), "symmetry")) strcpy(_stbiol[i]->Symmetry, string.Text()); else if (!strcmp((*ColumnNames)[j].Text(), "ndb_before_begin_residue_no")) _stbiol[i]->bbrn = atoi(string.Text()); else if (!strcmp((*ColumnNames)[j].Text(), "ndb_before_end_residue_no")) _stbiol[i]->bern = atoi(string.Text()); else if (!strcmp((*ColumnNames)[j].Text(), "ndb_after_begin_residue_no")) _stbiol[i]->abrn = atoi(string.Text()); else if (!strcmp((*ColumnNames)[j].Text(), "ndb_after_end_residue_no")) _stbiol[i]->aern = atoi(string.Text()); else if (!strcmp((*ColumnNames)[j].Text(), "rcsb_pdb_order")) _stbiol[i]->order = atoi(string.Text()); } } if (ColumnNames) delete ColumnNames; Table = _CifObj->GetTablePtr(_StructureId, "struct_asym"); if (is_empty_table(Table)) return; rowNo = Table->GetNumRows(); id_idx = Table->GetColumnIndex("id"); flag_idx = Table->GetColumnIndex("rcsb_blank_PDB_chainid_flag"); if (flag_idx < 0 || id_idx < 0) return; for (i = 0; i < _n_stbiol; i++) { if (strcmp(_stbiol[i]->Symmetry, "1_555")) continue; for (j = 0; j < rowNo; j++) { Table->GetCell(string, id_idx, j); if (string == _stbiol[i]->Asym_ID) { Table->GetCell(string, flag_idx, j); if (string == "Y" || string == "N" || string == "y" || string == "n") { strcpy(_stbiol[i]->PDB_Strand_ID_Flag, string.Text()); } break; } } } } void _VALIDATION::Input_Stbiol() { int found_order = 1, i = 0, k = 0, tokenid[9], count = 0; int exist_symmetry_related_chain = 0; _CHAIN *chain = NULL; One_Card_Info_Format *pCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (pCard) { count++; pCard = pCard->Next(); } if (!count) return; if (_stbiol) { for (i = 0; i < _n_stbiol; i++) if (_stbiol[i]) delete _stbiol[i]; delete [] _stbiol; } _n_stbiol = count; _stbiol = new _STBIOL*[_n_stbiol]; for (i = 0; i < _n_stbiol; i++) _stbiol[i] = NULL; count = 0; pCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (pCard) { _stbiol[count] = new _STBIOL; _stbiol[count]->internal_order = atoi(pCard->Field(1)); if (strcmp(pCard->Field(15), "")) _stbiol[count]->order = atoi(pCard->Field(15)); else found_order = 0; _stbiol[count]->Biol_ID = atoi(pCard->Field(2)); _stbiol[count]->Asym_ID.Copy(pCard->Field(3)); _stbiol[count]->NDB_Strand_ID.Copy(pCard->Field(12)); strcpy(_stbiol[count]->PDB_Strand_ID, pCard->Field(13)); strcpy(_stbiol[count]->PDB_Strand_ID_Flag, pCard->Field(16)); strcpy(_stbiol[count]->Symmetry, pCard->Field(4)); if (strcmp(_stbiol[count]->Symmetry, "1_555")) exist_symmetry_related_chain = 1; if (strcmp(pCard->Field(5), "")) _stbiol[count]->bbrn = atoi(pCard->Field(5)); else _stbiol[count]->bbrn = -99999; if (strcmp(pCard->Field(6), "")) _stbiol[count]->bern = atoi(pCard->Field(6)); else _stbiol[count]->bern = -99999; if (strcmp(pCard->Field(7), "")) _stbiol[count]->abrn = atoi(pCard->Field(7)); else _stbiol[count]->abrn = -99999; if (strcmp(pCard->Field(8), "")) _stbiol[count]->aern = atoi(pCard->Field(8)); else _stbiol[count]->aern = -99999; count++; pCard = pCard->Next(); } pCard = _CardInfo[STBIOL_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[STBIOL_TOKEN-1].delete_a_card(pCard); if (exist_symmetry_related_chain) Reorder_Stbiol(); if (!found_order && _num_mol) { count = 1; tokenid[0] = ATOMP_TOKEN; tokenid[1] = ATOMN_TOKEN; tokenid[2] = ATOMS_TOKEN; tokenid[3] = HETAD_TOKEN; tokenid[4] = HETAI_TOKEN; tokenid[5] = HETIC_TOKEN; tokenid[6] = HETAC_TOKEN; tokenid[7] = HETAIN_TOKEN; tokenid[8] = HETAS_TOKEN; for (k = 0; k < 9; k++) { for (i = 0; i < _n_stbiol; i++) { chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { if (_stbiol[i]->NDB_Strand_ID == chain->ChainID()) break; chain = _molecules[_rep_mol]->GetNextChain(); } if (chain && chain->chain_type() == tokenid[k]) { _stbiol[i]->order = count; count++; } } } } } void _VALIDATION::Reorder_Stbiol() { int i, j, count, asymId, asymId_2; char asym_id[5]; _STBIOL **tmp = NULL; tmp = _stbiol; _stbiol = new _STBIOL*[_n_stbiol]; for (i = 0; i < _n_stbiol; i++) _stbiol[i] = NULL; j = -1; count = 0; asymId = 'A'; asymId_2 = '@'; while (1) { j = find_asymmetric_chains(_n_stbiol, tmp, j); if (j < 0) break; _stbiol[count] = new _STBIOL; _stbiol[count]->internal_order = tmp[j]->internal_order; _stbiol[count]->order = tmp[j]->order; _stbiol[count]->Biol_ID = tmp[j]->Biol_ID; _stbiol[count]->Asym_ID.Copy(tmp[j]->Asym_ID); strcpy(_stbiol[count]->PDB_Strand_ID, tmp[j]->PDB_Strand_ID); strcpy(_stbiol[count]->PDB_Strand_ID_Flag, tmp[j]->PDB_Strand_ID_Flag); strcpy(_stbiol[count]->Symmetry, tmp[j]->Symmetry); _stbiol[count]->bbrn = tmp[j]->bbrn; _stbiol[count]->bern = tmp[j]->bern; _stbiol[count]->abrn = tmp[j]->abrn; _stbiol[count]->aern = tmp[j]->aern; if (asymId_2 != '@') sprintf(asym_id, "%c%c", asymId, asymId_2); else sprintf(asym_id, "%c", asymId); _stbiol[count]->NDB_Strand_ID.Copy(asym_id); asymId++; if (asymId > 'Z') { asymId = 'A'; asymId_2++; if (asymId_2 > 'Z') asymId_2 = 'A'; } count++; i = -1; while (1) { i = find_symmetry_related_chain(_n_stbiol, tmp, j, i); if (i < 0) break; _stbiol[count] = new _STBIOL; _stbiol[count]->internal_order = tmp[i]->internal_order; _stbiol[count]->order = tmp[i]->order; _stbiol[count]->Biol_ID = tmp[i]->Biol_ID; _stbiol[count]->Asym_ID.Copy(tmp[i]->Asym_ID); strcpy(_stbiol[count]->PDB_Strand_ID, tmp[i]->PDB_Strand_ID); strcpy(_stbiol[count]->PDB_Strand_ID_Flag, tmp[i]->PDB_Strand_ID_Flag); strcpy(_stbiol[count]->Symmetry, tmp[i]->Symmetry); _stbiol[count]->bbrn = tmp[i]->bbrn; _stbiol[count]->bern = tmp[i]->bern; _stbiol[count]->abrn = tmp[i]->abrn; _stbiol[count]->aern = tmp[i]->aern; if (asymId_2 != '@') sprintf(asym_id, "%c%c", asymId, asymId_2); else sprintf(asym_id, "%c", asymId); _stbiol[count]->NDB_Strand_ID.Copy(asym_id); asymId++; if (asymId > 'Z') { asymId = 'A'; asymId_2++; if (asymId_2 > 'Z') asymId_2 = 'A'; } count++; } } if (tmp) { for (i = 0; i < _n_stbiol; i++) if (tmp[i]) delete tmp[i]; delete [] tmp; } } void _VALIDATION::Input_Link() { int FstIndex, FstRes, SndIndex, SndRes; if (_num_mol == 0 || _molecules == NULL) return; _MOLECULE *mol = _molecules[0]; One_Card_Info_Format *pCard = _CardInfo[LINK_TOKEN-1].Head(); while (pCard) { if (mol->find_pdb_residue(pCard->Field(4), pCard->Field(3), atoi(pCard->Field(5)), pCard->Field(6), FstIndex, FstRes) && mol->find_pdb_residue(pCard->Field(10), pCard->Field(9), atoi(pCard->Field(11)), pCard->Field(12), SndIndex, SndRes)) { Insert_a_Link(pCard->Field(1), pCard->Field(2), FstIndex, FstRes, pCard->Field(7), pCard->Field(8), SndIndex, SndRes, pCard->Field(13), pCard->Field(14), pCard->Field(16)); } pCard = pCard->Next(); } _CardInfo[LINK_TOKEN-1].clear_Cards(); } void _VALIDATION::update_residues_nomenclature(const int ndb_only) { int m; _CHAIN *chain = NULL; if (_num_mol == 0 || _molecules == NULL) return; for (m = 0; m < _num_mol; m++) { chain = _molecules[m]->GetFirstChain(); while (chain) { chain->update_residues_nomenclature(ndb_only); chain = _molecules[m]->GetNextChain(); } } } void _VALIDATION::match_stbiol_with_molecules() { int i, j, m, serialNo, prOrder, naOrder, count, n_tmp; int asymId, asymId_2, index; char asym_id[5], old_asym_id[5]; _STBIOL **tmp = NULL, **tmp1 = NULL; _CHAIN *chain = NULL; One_Card_Info_Format *pCard = NULL; if (_num_mol == 0 || _molecules == NULL) return; chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { for (j = 0; j < _n_stbiol; j++) { if (_stbiol[j]->Asym_ID == chain->ChainID() && !strcmp(_stbiol[j]->Symmetry, "1_555")) break; } if (j == _n_stbiol) break; chain = _molecules[_rep_mol]->GetNextChain(); } if (!chain) { pCard = _CardInfo[SEQIFO_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[SEQIFO_TOKEN-1].delete_a_card(pCard); serialNo = 0; prOrder = 0; naOrder = 0; chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { if (!chain->has_sequence()) { chain = _molecules[_rep_mol]->GetNextChain(); continue; } pCard = _CardInfo[SEQIFO_TOKEN-1]. add_a_new_card(NdbToken[SEQIFO_TOKEN-1], 0); pCard->AddElementToField(++serialNo, 1); pCard->AddElementToField(chain->ChainID(), 2); pCard->AddElementToField(chain->PDB_ChainID(), 3); pCard->AddElementToField(chain->PUB_ChainID(), 4); if (chain->chain_type() == ATOMN_TOKEN) { pCard->AddElementToField("NA", 5); pCard->AddElementToField(++naOrder, 6); } else if (chain->chain_type() == ATOMP_TOKEN) { pCard->AddElementToField("PR", 5); pCard->AddElementToField(++prOrder, 6); } if (chain->isModified()) pCard->AddElementToField("Y", 7); else pCard->AddElementToField("N", 7); pCard->AddElementToField(chain->entity_id(), 9); chain = _molecules[_rep_mol]->GetNextChain(); } } tmp = _stbiol; n_tmp = _n_stbiol; count = 0; for (i = 0; i < n_tmp; i++) { if (strcmp(tmp[i]->Symmetry, "1_555")) count++; } _n_stbiol = _molecules[_rep_mol]->Num_Chain() + count; _stbiol = new _STBIOL*[_n_stbiol]; for (i = 0; i < _n_stbiol; i++) _stbiol[i] = NULL; asymId = 'A'; asymId_2 = '@'; index = 0; chain = _molecules[_rep_mol]->GetFirstChain(); while (chain) { if (asymId_2 != '@') sprintf(asym_id, "%c%c", asymId, asymId_2); else sprintf(asym_id, "%c", asymId); strcpy(old_asym_id, asym_id); if ((index + 1) > _n_stbiol) { tmp1 = _stbiol; _stbiol = new _STBIOL*[index + 1]; for (i = 0; i < _n_stbiol; i++) _stbiol[i] = tmp1[i]; for (i = _n_stbiol; i < index + 1; i++) _stbiol[i] = NULL; _n_stbiol = index + 1; if (tmp1) delete [] tmp1; } _stbiol[index] = new _STBIOL; _stbiol[index]->internal_order = index + 1; chain->set_internal_order(index + 1); _stbiol[index]->order = chain->order(); _stbiol[index]->Biol_ID = chain->biol_id(); _stbiol[index]->Asym_ID.Copy(asym_id); _stbiol[index]->NDB_Strand_ID.Copy(asym_id); strcpy(_stbiol[index]->PDB_Strand_ID, chain->PDB_ChainID()); strcpy(_stbiol[index]->PDB_Strand_ID_Flag, chain->PDB_ChainID_Flag()); strcpy(_stbiol[index]->Symmetry, "1_555"); _stbiol[index]->bbrn = 1; _stbiol[index]->bern = chain->TotalResidueNumbers(); _stbiol[index]->abrn = 1; _stbiol[index]->aern = chain->TotalResidueNumbers(); index++; if (count) { j = -1; do { j = find_symmetry_related_chains(n_tmp, tmp, j, chain->ChainID());; if (j >= 0) { if ((index + 1) > _n_stbiol) { tmp1 = _stbiol; _stbiol = new _STBIOL*[index + 1]; for (i = 0; i < _n_stbiol; i++) _stbiol[i] = tmp1[i]; for (i = _n_stbiol; i < index + 1; i++) _stbiol[i] = NULL; _n_stbiol = index + 1; if (tmp1) delete [] tmp1; } _stbiol[index] = new _STBIOL; _stbiol[index]->internal_order = index + 1; _stbiol[index]->order = tmp[j]->order; _stbiol[index]->Biol_ID = tmp[j]->Biol_ID; _stbiol[index]->Asym_ID.Copy(old_asym_id); asymId++; if (asymId > 'Z') { asymId = 'A'; asymId_2++; if (asymId_2 > 'Z') asymId_2 = 'A'; } if (asymId_2 != '@') sprintf(asym_id, "%c%c", asymId, asymId_2); else sprintf(asym_id, "%c", asymId); _stbiol[index]->NDB_Strand_ID.Copy(asym_id); strcpy(_stbiol[index]->PDB_Strand_ID, tmp[j]->PDB_Strand_ID); strcpy(_stbiol[index]->PDB_Strand_ID_Flag, tmp[j]->PDB_Strand_ID_Flag); strcpy(_stbiol[index]->Symmetry, tmp[j]->Symmetry); _stbiol[index]->bbrn = 1; _stbiol[index]->bern = chain->TotalResidueNumbers(); _stbiol[index]->abrn = 1; _stbiol[index]->aern = chain->TotalResidueNumbers(); index++; } } while (j >= 0); } asymId++; if (asymId > 'Z') { asymId = 'A'; asymId_2++; if (asymId_2 > 'Z') asymId_2 = 'A'; } chain = _molecules[_rep_mol]->GetNextChain(); } _n_stbiol = index; if (tmp) { for (i = 0; i < n_tmp; i++) if (tmp[i]) delete tmp[i]; delete [] tmp; } for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; if (_stbiol[i]->order <= 0) break; } if (i < _n_stbiol) { for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; _stbiol[i]->order = _stbiol[i]->internal_order; } } for (m = 0; m < _num_mol; m++) { j = -1; chain = _molecules[m]->GetFirstChain(); while (chain) { j = find_asymmetric_chains(_n_stbiol, _stbiol, j); if (j >= 0) { chain->set_ChainID(_stbiol[j]->NDB_Strand_ID.Text()); chain->set_order(_stbiol[j]->order); } chain = _molecules[m]->GetNextChain(); } if (!m) { pCard = _CardInfo[SEQIFO_TOKEN-1].Head(); while (pCard) pCard = _CardInfo[SEQIFO_TOKEN-1].delete_a_card(pCard); serialNo = 0; prOrder = 0; naOrder = 0; chain = _molecules[m]->GetFirstChain(); while (chain) { if (!chain->has_sequence()) { chain = _molecules[m]->GetNextChain(); continue; } pCard = _CardInfo[SEQIFO_TOKEN-1]. add_a_new_card(NdbToken[SEQIFO_TOKEN-1], 0); pCard->AddElementToField(++serialNo, 1); pCard->AddElementToField(chain->ChainID(), 2); pCard->AddElementToField(chain->PDB_ChainID(), 3); pCard->AddElementToField(chain->PUB_ChainID(), 4); if (chain->chain_type() == ATOMN_TOKEN) { pCard->AddElementToField("NA", 5); pCard->AddElementToField(++naOrder, 6); } else if (chain->chain_type() == ATOMP_TOKEN) { pCard->AddElementToField("PR", 5); pCard->AddElementToField(++prOrder, 6); } if (chain->isModified()) pCard->AddElementToField("Y", 7); else pCard->AddElementToField("N", 7); pCard->AddElementToField(chain->entity_id(), 9); chain = _molecules[m]->GetNextChain(); } } } } void _VALIDATION::Insert_a_Link(const char *FstAtom, const char *altLoc1, const int FstIndex, const int FstRes, const char *SndAtom, const char *altLoc2, const int SndIndex, const int SndRes, const char *SymOP_1, const char *SymOP_2, const char *details) { int i = 0; _LINK **tmp = NULL; for (i = 0; i < _n_link; i++) { if (!strcmp(_link[i]->FstAtom, FstAtom) && !strcmp(_link[i]->altLoc1, altLoc1) && _link[i]->FstIndex == FstIndex && _link[i]->FstRes == FstRes && !strcmp(_link[i]->SndAtom, SndAtom) && !strcmp(_link[i]->altLoc2, altLoc2) && _link[i]->SndIndex == SndIndex && _link[i]->SndRes == SndRes && !strcmp(_link[i]->SymOP_1, SymOP_1) && !strcmp(_link[i]->SymOP_2, SymOP_2) || !strcmp(_link[i]->FstAtom, SndAtom) && !strcmp(_link[i]->altLoc1, altLoc2) && _link[i]->FstIndex == SndIndex && _link[i]->FstRes == SndRes && !strcmp(_link[i]->SndAtom, FstAtom) && !strcmp(_link[i]->altLoc2, altLoc1) && _link[i]->SndIndex == FstIndex && _link[i]->SndRes == FstRes && !strcmp(_link[i]->SymOP_1, SymOP_2) && !strcmp(_link[i]->SymOP_2, SymOP_1)) break; } if (i < _n_link) return; if (_n_link >= _alloc_link) { _alloc_link += 10; tmp = _link; _link = new _LINK*[_alloc_link]; for (i = 0; i < _n_link; i++) _link[i] = tmp[i]; for (i = _n_link; i < _alloc_link; i++) _link[i] = NULL; delete [] tmp; } _link[_n_link] = new _LINK; strcpy(_link[_n_link]->FstAtom, FstAtom); strcpy(_link[_n_link]->altLoc1, altLoc1); _link[_n_link]->FstIndex = FstIndex; _link[_n_link]->FstRes = FstRes; strcpy(_link[_n_link]->SndAtom, SndAtom); strcpy(_link[_n_link]->altLoc2, altLoc2); _link[_n_link]->SndIndex = SndIndex; _link[_n_link]->SndRes = SndRes; strcpy(_link[_n_link]->SymOP_1, SymOP_1); strcpy(_link[_n_link]->SymOP_2, SymOP_2); int len = strlen(details) + 1; _link[_n_link]->details = new char[len]; strcpy(_link[_n_link]->details, details); _n_link++; } void _VALIDATION::Insert_a_Mismat(const int FstIndex, const int FstRes, const int SndIndex, const int SndRes) { int i = 0; _MISMAT **tmp = NULL; for (i = 0; i < _n_mismat; i++) { if (_mismat[i]->FstIndex == FstIndex && _mismat[i]->FstRes == FstRes && _mismat[i]->SndIndex == SndIndex && _mismat[i]->SndRes == SndRes) break; } if (i < _n_mismat) return; if (_n_mismat >= _alloc_mismat) { _alloc_mismat += 10; tmp = _mismat; _mismat = new _MISMAT*[_alloc_mismat]; for (i = 0; i < _n_mismat; i++) _mismat[i] = tmp[i]; for (i = _n_mismat; i < _alloc_mismat; i++) _mismat[i] = NULL; delete [] tmp; } _mismat[_n_mismat] = new _MISMAT; _mismat[_n_mismat]->FstIndex = FstIndex; _mismat[_n_mismat]->FstRes = FstRes; _mismat[_n_mismat]->SndIndex = SndIndex; _mismat[_n_mismat]->SndRes = SndRes; _n_mismat++; } void _VALIDATION::Insert_a_Bspair(const char *FstAtom, const int FstIndex, const int FstRes, const char *SndAtom, const int SndIndex, const int SndRes, const char *Asym_or_Gen, const char *Type) { int i = 0; _BSPAIR **tmp = NULL; for (i = 0; i < _n_bspair; i++) { if (!strcmp(_bspair[i]->FstAtom, FstAtom) && _bspair[i]->FstIndex == FstIndex && _bspair[i]->FstRes == FstRes && !strcmp(_bspair[i]->SndAtom, SndAtom) && _bspair[i]->SndIndex == SndIndex && _bspair[i]->SndRes == SndRes && !strcmp(_bspair[i]->Asym_or_Gen, Asym_or_Gen) && !strcmp(_bspair[i]->Type, Type)) break; } if (i < _n_bspair) return; if (_n_bspair >= _alloc_bspair) { _alloc_bspair += 10; tmp = _bspair; _bspair = new _BSPAIR*[_alloc_bspair]; for (i = 0; i < _n_bspair; i++) _bspair[i] = tmp[i]; for (i = _n_bspair; i < _alloc_bspair; i++) _bspair[i] = NULL; delete [] tmp; } _bspair[_n_bspair] = new _BSPAIR; strcpy(_bspair[_n_bspair]->FstAtom, FstAtom); _bspair[_n_bspair]->FstIndex = FstIndex; _bspair[_n_bspair]->FstRes = FstRes; strcpy(_bspair[_n_bspair]->SndAtom, SndAtom); _bspair[_n_bspair]->SndIndex = SndIndex; _bspair[_n_bspair]->SndRes = SndRes; strcpy(_bspair[_n_bspair]->Asym_or_Gen, Asym_or_Gen); strcpy(_bspair[_n_bspair]->Type, Type); _n_bspair++; } void _VALIDATION::generate_symmetry_strands(const int change_chnid) { int i = 0, j = 0, k = 0, op = 0, trans[3], sucessful = 0, len; if (_num_mol == 0 || _molecules == NULL) return; for (i = 0; i < _n_stbiol; i++) { if (strcmp(_stbiol[i]->Symmetry, NDB_BASE_SYMMETRY)) break; } if (i == _n_stbiol) return; _molecules[0]->convert_between_orthogonal_and_fractional(_cell, NDB_TRANS_ORTHO_TO_FRAC); for (i = 0; i < _n_stbiol; i++) { if (!_stbiol[i]) continue; if (strcmp(_stbiol[i]->Symmetry, NDB_BASE_SYMMETRY)) { op = atoi(_stbiol[i]->Symmetry) - 1; trans[0] = trans[1] = trans[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++) trans[k] = _stbiol[i]->Symmetry[j+k+1] - '5'; } sucessful = 0; if (change_chnid) sucessful = _molecules[0]->symmetry_related_chain(_stbiol[i]->internal_order, _stbiol[i]->order, _stbiol[i]->Biol_ID, _stbiol[i]->Asym_ID.Text(), _stbiol[i]->NDB_Strand_ID.Text(), _stbiol[i]->PDB_Strand_ID, _cell, op, trans[0], trans[1], trans[2], 1); else sucessful= _molecules[0]->symmetry_related_chain(_stbiol[i]->internal_order, _stbiol[i]->order, _stbiol[i]->Biol_ID, _stbiol[i]->Asym_ID.Text(), "", _stbiol[i]->PDB_Strand_ID, _cell, op, trans[0], trans[1], trans[2], 1); if (sucessful) strcpy(_stbiol[i]->Symmetry, NDB_BASE_SYMMETRY); } } _molecules[0]->convert_between_orthogonal_and_fractional(_cell, NDB_TRANS_FRAC_TO_ORTHO); } void _VALIDATION::insert_bond(const char *ChainID, const char *ResName, const int ResNum, const char *ins_code, const char *Rep_Name, const char *type, const double val, const double ept, const double std, const int mol_id, _ATOM *fst, _ATOM *snd) { int i = 0; _BOND **tmp = NULL; if (_n_bond >= _alloc_bond) { _alloc_bond += 10000; tmp = _bond; _bond = new _BOND*[_alloc_bond]; for (i = 0; i < _n_bond; i++) _bond[i] = tmp[i]; for (i = _n_bond; i < _alloc_bond; i++) _bond[i] = NULL; delete [] tmp; } _bond[_n_bond] = new _BOND; _bond[_n_bond]->Mol_ID = mol_id; strcpy(_bond[_n_bond]->ChainID, ChainID); strcpy(_bond[_n_bond]->ResName, ResName); _bond[_n_bond]->ResNum = ResNum; strcpy(_bond[_n_bond]->ins_code, ins_code); strcpy(_bond[_n_bond]->Rep_Name, Rep_Name); strcpy(_bond[_n_bond]->type, type); _bond[_n_bond]->val = val; _bond[_n_bond]->ept = ept; _bond[_n_bond]->std = std; _bond[_n_bond]->fst = fst; _bond[_n_bond]->snd = snd; _n_bond++; CifString index(ResName); if (_bondResIndex.Seek(index) < 0) _bondResIndex.Add(index); index += Rep_Name; _bondComIndex.Add(index); index.Copy(Rep_Name); _bondNamIndex.Add(index); } void _VALIDATION::insert_angle(const char *ChainID, const char *ResName, const int ResNum, const char *ins_code, const char *Rep_Name, const char *type, const double val, const double ept, const double std, const int mol_id, _ATOM *fst, _ATOM *snd, _ATOM *trd) { int i = 0; _ANGLE **tmp = NULL; if (_n_angle >= _alloc_angle) { _alloc_angle += 10000; tmp = _angle; _angle = new _ANGLE*[_alloc_angle]; for (i = 0; i < _n_angle; i++) _angle[i] = tmp[i]; for (i = _n_angle; i < _alloc_angle; i++) _angle[i] = NULL; delete [] tmp; } _angle[_n_angle] = new _ANGLE; _angle[_n_angle]->Mol_ID = mol_id; strcpy(_angle[_n_angle]->ChainID, ChainID); strcpy(_angle[_n_angle]->ResName, ResName); _angle[_n_angle]->ResNum = ResNum; strcpy(_angle[_n_angle]->ins_code, ins_code); strcpy(_angle[_n_angle]->Rep_Name, Rep_Name); strcpy(_angle[_n_angle]->type, type); _angle[_n_angle]->val = val; _angle[_n_angle]->ept = ept; _angle[_n_angle]->std = std; _angle[_n_angle]->fst = fst; _angle[_n_angle]->snd = snd; _angle[_n_angle]->trd = trd; _n_angle++; CifString index(ResName); if (_angleResIndex.Seek(index) < 0) _angleResIndex.Add(index); index += Rep_Name; _angleComIndex.Add(index); index.Copy(Rep_Name); _angleNamIndex.Add(index); } void _VALIDATION::insert_torsion(const char *ChainID, const char *ResName, const int ResNum, const char *ins_code, const char *Rep_Name, const char *type, const double val, const int mol_id, _ATOM *fst, _ATOM *snd, _ATOM *trd, _ATOM *fth) { int i = 0; _TORSION **tmp = NULL; if (_n_torsion >= _alloc_torsion) { _alloc_torsion += 10000; tmp = _torsion; _torsion = new _TORSION*[_alloc_torsion]; for (i = 0; i < _n_torsion; i++) _torsion[i] = tmp[i]; for (i = _n_torsion; i < _alloc_torsion; i++) _torsion[i] = NULL; delete [] tmp; } _torsion[_n_torsion] = new _TORSION; _torsion[_n_torsion]->Mol_ID = mol_id; strcpy(_torsion[_n_torsion]->ChainID, ChainID); strcpy(_torsion[_n_torsion]->ResName, ResName); _torsion[_n_torsion]->ResNum = ResNum; strcpy(_torsion[_n_torsion]->ins_code, ins_code); strcpy(_torsion[_n_torsion]->Rep_Name, Rep_Name); strcpy(_torsion[_n_torsion]->type, type); _torsion[_n_torsion]->val = val; _torsion[_n_torsion]->fst = fst; _torsion[_n_torsion]->snd = snd; _torsion[_n_torsion]->trd = trd; _torsion[_n_torsion]->fth = fth; _n_torsion++; CifString index(Rep_Name); _torsionIndex.Add(index); } void _VALIDATION::insert_torsion_pair(const char *ChainID, const char *ResName, const int ResNum, const char *ins_code, const double phi, const double psi, const int mol_id) { int i = 0; _TORSION **tmp = NULL; if (_n_t_pairs >= _alloc_t_pairs) { _alloc_t_pairs += 100; tmp = _t_pairs; _t_pairs = new _TORSION*[_alloc_t_pairs]; for (i = 0; i < _n_t_pairs; i++) _t_pairs[i] = tmp[i]; for (i = _n_t_pairs; i < _alloc_t_pairs; i++) _t_pairs[i] = NULL; delete [] tmp; } _t_pairs[_n_t_pairs] = new _TORSION; _t_pairs[_n_t_pairs]->Mol_ID = mol_id; strcpy(_t_pairs[_n_t_pairs]->ChainID, ChainID); strcpy(_t_pairs[_n_t_pairs]->ResName, ResName); _t_pairs[_n_t_pairs]->ResNum = ResNum; strcpy(_t_pairs[_n_t_pairs]->ins_code, ins_code); _t_pairs[_n_t_pairs]->val = phi; _t_pairs[_n_t_pairs]->ept = psi; _n_t_pairs++; } void _VALIDATION::insert_pair_z_a_1(const int res_num, const double x, const double y) { int i = 0; _PAIR_VALUE **tmp = NULL; if (_n_z_a_1 >= _alloc_z_a_1) { _alloc_z_a_1 += 100; tmp = _z_a_1; _z_a_1 = new _PAIR_VALUE*[_alloc_z_a_1]; for (i = 0; i < _n_z_a_1; i++) _z_a_1[i] = tmp[i]; for (i = _n_z_a_1; i < _alloc_z_a_1; i++) _z_a_1[i] = NULL; delete [] tmp; } _z_a_1[_n_z_a_1] = new _PAIR_VALUE; _z_a_1[_n_z_a_1]->res_num = res_num; _z_a_1[_n_z_a_1]->x = x; _z_a_1[_n_z_a_1]->y = y; _n_z_a_1++; } void _VALIDATION::insert_pair_z_b_1(const int res_num, const double x, const double y) { int i = 0; _PAIR_VALUE **tmp = NULL; if (_n_z_b_1 >= _alloc_z_b_1) { _alloc_z_b_1 += 100; tmp = _z_b_1; _z_b_1 = new _PAIR_VALUE*[_alloc_z_b_1]; for (i = 0; i < _n_z_b_1; i++) _z_b_1[i] = tmp[i]; for (i = _n_z_b_1; i < _alloc_z_b_1; i++) _z_b_1[i] = NULL; delete [] tmp; } _z_b_1[_n_z_b_1] = new _PAIR_VALUE; _z_b_1[_n_z_b_1]->res_num = res_num; _z_b_1[_n_z_b_1]->x = x; _z_b_1[_n_z_b_1]->y = y; _n_z_b_1++; } void _VALIDATION::insert_pair_z_e(const int res_num, const double x, const double y) { int i = 0; _PAIR_VALUE **tmp = NULL; if (_n_z_e >= _alloc_z_e) { _alloc_z_e += 100; tmp = _z_e; _z_e = new _PAIR_VALUE*[_alloc_z_e]; for (i = 0; i < _n_z_e; i++) _z_e[i] = tmp[i]; for (i = _n_z_e; i < _alloc_z_e; i++) _z_e[i] = NULL; delete [] tmp; } _z_e[_n_z_e] = new _PAIR_VALUE; _z_e[_n_z_e]->res_num = res_num; _z_e[_n_z_e]->x = x; _z_e[_n_z_e]->y = y; _n_z_e++; } void _VALIDATION::insert_pair_a_g(const int res_num, const double x, const double y) { int i = 0; _PAIR_VALUE **tmp = NULL; if (_n_a_g >= _alloc_a_g) { _alloc_a_g += 100; tmp = _a_g; _a_g = new _PAIR_VALUE*[_alloc_a_g]; for (i = 0; i < _n_a_g; i++) _a_g[i] = tmp[i]; for (i = _n_a_g; i < _alloc_a_g; i++) _a_g[i] = NULL; delete [] tmp; } _a_g[_n_a_g] = new _PAIR_VALUE; _a_g[_n_a_g]->res_num = res_num; _a_g[_n_a_g]->x = x; _a_g[_n_a_g]->y = y; _n_a_g++; } void _VALIDATION::insert_pair_z_x(const int res_num, const double x, const double y) { int i = 0; _PAIR_VALUE **tmp = NULL; if (_n_z_x >= _alloc_z_x) { _alloc_z_x += 100; tmp = _z_x; _z_x = new _PAIR_VALUE*[_alloc_z_x]; for (i = 0; i < _n_z_x; i++) _z_x[i] = tmp[i]; for (i = _n_z_x; i < _alloc_z_x; i++) _z_x[i] = NULL; delete [] tmp; } _z_x[_n_z_x] = new _PAIR_VALUE; _z_x[_n_z_x]->res_num = res_num; _z_x[_n_z_x]->x = x; _z_x[_n_z_x]->y = y; _n_z_x++; } void _VALIDATION::insert_pair_d_x(const int res_num, const double x, const double y) { int i = 0; _PAIR_VALUE **tmp = NULL; if (_n_d_x >= _alloc_d_x) { _alloc_d_x += 100; tmp = _d_x; _d_x = new _PAIR_VALUE*[_alloc_d_x]; for (i = 0; i < _n_d_x; i++) _d_x[i] = tmp[i]; for (i = _n_d_x; i < _alloc_d_x; i++) _d_x[i] = NULL; delete [] tmp; } _d_x[_n_d_x] = new _PAIR_VALUE; _d_x[_n_d_x]->res_num = res_num; _d_x[_n_d_x]->x = x; _d_x[_n_d_x]->y = y; _n_d_x++; } void _VALIDATION::get_link_record(ISTable *Table, const int is_rcsb_link) { int irow, BegIndex, BegRes, EndIndex, EndRes, beg, end; char comment[10]; CifString atom1, loc1, atom2, loc2, symm1, symm2, type; if (_num_mol == 0 || _molecules == NULL) return; _MOLECULE *mol = _molecules[0]; int rowNo = Table->GetNumRows(); int conn_type_id = Table->GetColumnIndex("conn_type_id"); int ptnr1_label_alt_id = Table->GetColumnIndex("ndb_ptnr1_label_alt_loc"); if (is_rcsb_link) ptnr1_label_alt_id = Table->GetColumnIndex("ptnr1_label_alt_id"); int ptnr1_label_asym_id = Table->GetColumnIndex("ptnr1_label_asym_id"); int ptnr1_label_atom_id = Table->GetColumnIndex("ptnr1_label_atom_id"); int ptnr1_label_comp_id = Table->GetColumnIndex("ptnr1_label_comp_id"); int ptnr1_label_seq_id = Table->GetColumnIndex("ptnr1_label_seq_id"); int ptnr1_label_ins_code = Table->GetColumnIndex("ndb_ptnr1_label_ins_code"); if (is_rcsb_link) ptnr1_label_ins_code = Table->GetColumnIndex("ptnr1_label_ins_code"); int ptnr1_symmetry = Table->GetColumnIndex("ptnr1_symmetry"); int ptnr2_label_alt_id = Table->GetColumnIndex("ndb_ptnr2_label_alt_loc"); if (is_rcsb_link) ptnr2_label_alt_id = Table->GetColumnIndex("ptnr2_label_alt_id"); int ptnr2_label_asym_id = Table->GetColumnIndex("ptnr2_label_asym_id"); int ptnr2_label_atom_id = Table->GetColumnIndex("ptnr2_label_atom_id"); int ptnr2_label_comp_id = Table->GetColumnIndex("ptnr2_label_comp_id"); int ptnr2_label_seq_id = Table->GetColumnIndex("ptnr2_label_seq_id"); int ptnr2_label_ins_code = Table->GetColumnIndex("ndb_ptnr2_label_ins_code"); if (is_rcsb_link) ptnr2_label_ins_code = Table->GetColumnIndex("ptnr2_label_ins_code"); int ptnr2_symmetry = Table->GetColumnIndex("ptnr2_symmetry"); for (irow = 0; irow < rowNo; irow++) { memset(comment, '\0', 10); atom1.Clear(); loc1.Clear(); atom2.Clear(); loc2.Clear(); symm1.Clear(); symm2.Clear(); type.Clear(); if (!is_rcsb_link) { get_value(type, Table, conn_type_id, irow); if (strcasecmp(type.Text(), "link")) continue; } get_value(loc1, Table, ptnr1_label_alt_id, irow); get_value(atom1, Table, ptnr1_label_atom_id, irow); get_value(symm1, Table, ptnr1_symmetry, irow); get_value(loc2, Table, ptnr2_label_alt_id, irow); get_value(atom2, Table, ptnr2_label_atom_id, irow); get_value(symm2, Table, ptnr2_symmetry, irow); beg = get_residue_index(mol, Table, irow, -1, -1, -1, ptnr1_label_comp_id, ptnr1_label_asym_id, ptnr1_label_seq_id, ptnr1_label_ins_code, BegIndex, BegRes); end = get_residue_index(mol, Table, irow, -1, -1, -1, ptnr2_label_comp_id, ptnr2_label_asym_id, ptnr2_label_seq_id, ptnr2_label_ins_code, EndIndex, EndRes); if (!beg || !end) continue; if (symm1 == "1_555") symm1.Clear(); if (symm2 == "1_555") symm2.Clear(); Insert_a_Link(atom1.Text(), loc1.Text(), BegIndex, BegRes, atom2.Text(), loc2.Text(), EndIndex, EndRes, symm1.Text(), symm2.Text(), comment); } } int get_residue_index(_MOLECULE *mol, ISTable *Table, const int irow, const int ndb_comp_id, const int ndb_asym_id, const int ndb_seq_id, const int pdb_comp_id, const int pdb_asym_id, const int pdb_seq_id, const int ins_code_id, int &FstIndex, int &FstRes) { FstIndex = -1; FstRes = -1; CifString res_name, chain_id, ins_code, value; int seq_num = -99999; get_value(res_name, Table, ndb_comp_id, irow); get_value(chain_id, Table, ndb_asym_id, irow); if (get_value(value, Table, ndb_seq_id, irow)) seq_num = atoi(value.Text()); get_value(ins_code, Table, ins_code_id, irow); if (chain_id != "" && res_name != "" && seq_num != -99999 && mol->find_ndb_residue(chain_id.Text(), res_name.Text(), seq_num, ins_code.Text(), FstIndex, FstRes)) return 1; get_value(res_name, Table, pdb_comp_id, irow); get_value(chain_id, Table, pdb_asym_id, irow); if (get_value(value, Table, pdb_seq_id, irow)) seq_num = atoi(value.Text()); if (pdb_comp_id >= 0 && pdb_asym_id >= 0 && pdb_seq_id >= 0 && mol->find_pdb_residue(chain_id.Text(), res_name.Text(), seq_num, ins_code.Text(), FstIndex, FstRes)) return 1; return 0; } static int find_symmetry_related_chain(const int n_stbiol, _STBIOL **stbiol, const int i, const int index) { int j; if (!stbiol[i]) return -1; for (j = 0; j < n_stbiol; j++) { if (!stbiol[j]) continue; if (stbiol[i]->Asym_ID == stbiol[j]->Asym_ID && strcmp(stbiol[j]->Symmetry, "1_555") && j > index) break; } if (j < n_stbiol) return j; else return -1; } static int find_symmetry_related_chains(const int n_stbiol, _STBIOL **stbiol, const int index, char *ndb_chnid) { int i = 0, j = 0; for (i = 0; i < n_stbiol; i++) { if (!stbiol[i]) continue; if (stbiol[i]->NDB_Strand_ID == ndb_chnid) break; } if (i == n_stbiol) return -1; for (j = 0; j < n_stbiol; j++) { if (!stbiol[j]) continue; if (stbiol[i]->Asym_ID == stbiol[j]->Asym_ID && strcmp(stbiol[j]->Symmetry, "1_555") && j > index) break; } if (j < n_stbiol) return j; else return -1; } static int find_asymmetric_chains(const int n_stbiol, _STBIOL **stbiol, const int start) { int j = 0; if ((start + 1) >= n_stbiol) return -1; for (j = start + 1; j < n_stbiol; j++) { if (!stbiol[j]) continue; if (!strcmp(stbiol[j]->Symmetry, "1_555")) break; } if (j < n_stbiol) return j; else return -1; }