/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
H A D | em_ascii.cpp | 1402 thtg = mol_info.GetTech(); in GetDescrEmblBlock() 1449 mol_info.ResetTech(); in GetDescrEmblBlock() 1557 if (mol_info.IsSetTech()) in GetDescrEmblBlock() 1743 GetFlatBiomol(mol_info->SetBiomol(), mol_info->GetTech(), bptr, pp, entry, org_ref); in GetEmblMolInfo() 1745 mol_info->ResetBiomol(); in GetEmblMolInfo() 1750 return mol_info; in GetEmblMolInfo() 2132 if (mol_info->IsSetBiomol() || mol_info->IsSetTech()) in GetEmblDescr() 2138 …if (mol_info->IsSetTech() && (mol_info->GetTech() == objects::CMolInfo::eTech_htgs_0 || mol_info->… in GetEmblDescr() 2144 mol_info.Reset(); in GetEmblDescr() 3102 thtg = mol_info.GetTech(); in XMLGetEMBLBlock() [all …]
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H A D | gb_ascii.cpp | 789 else if (mol_info.IsSetTech()) in GetGBBlock() 801 if (mol_info.IsSetTech()) in GetGBBlock() 893 mol_info->SetTechexp("cage"); in GetGenBankMolInfo() 896 GetFlatBiomol(mol_info->SetBiomol(), mol_info->GetTech(), molstr, pp, entry, org_ref); in GetGenBankMolInfo() 898 mol_info->ResetBiomol(); in GetGenBankMolInfo() 900 return mol_info; in GetGenBankMolInfo() 1395 ibp->is_contig && (!mol_info->IsSetTech() || mol_info->GetTech() == 0)) in GetGenBankDescr() 1399 mol_info->ResetTech(); in GetGenBankDescr() 1401 mol_info->SetTech(tech); in GetGenBankDescr() 1404 if (mol_info->IsSetBiomol() || mol_info->IsSetTech()) in GetGenBankDescr() [all …]
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H A D | xm_ascii.cpp | 530 thtg = mol_info.GetTech(); in XMLGetGBBlock() 566 mol_info.SetTech(tech); in XMLGetGBBlock() 568 mol_info.ResetTech(); in XMLGetGBBlock() 691 else if (mol_info.IsSetTech()) in XMLGetGBBlock() 703 if (mol_info.IsSetTech()) in XMLGetGBBlock() 771 GetFlatBiomol(mol_info->SetBiomol(), mol_info->GetTech(), molstr, pp, entry, org_ref); in XMLGetMolInfo() 772 if (mol_info->GetBiomol() == 0) // not set in XMLGetMolInfo() 773 mol_info->ResetBiomol(); in XMLGetMolInfo() 778 return mol_info; in XMLGetMolInfo() 1107 if (mol_info->IsSetBiomol() || mol_info->IsSetTech()) in XMLGetDescr() [all …]
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H A D | fcleanup.cpp | 158 static bool IsEmptyMolInfo(const objects::CMolInfo& mol_info) in IsEmptyMolInfo() argument 160 return !(mol_info.IsSetBiomol() || mol_info.IsSetCompleteness() || mol_info.IsSetGbmoltype() || in IsEmptyMolInfo() 161 mol_info.IsSetTech() || mol_info.IsSetTechexp()); in IsEmptyMolInfo() 551 objects::CSeqdesc_CI mol_info(bioseq_h, objects::CSeqdesc::E_Choice::e_Molinfo); in FinalCleanup() local 553 …if (mol_info && mol_info->GetMolinfo().IsSetBiomol() && mol_info->GetMolinfo().GetBiomol() == obje… in FinalCleanup()
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H A D | prf_ascii.cpp | 504 CRef<objects::CMolInfo> mol_info(new objects::CMolInfo); in PrfGetMolInfo() local 511 mol_info->SetBiomol(objects::CMolInfo::eBiomol_peptide); in PrfGetMolInfo() 512 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_complete); in PrfGetMolInfo() 518 mol_info->SetTech(objects::CMolInfo::eTech_seq_pept); in PrfGetMolInfo() 520 mol_info->SetTech(objects::CMolInfo::eTech_concept_trans); in PrfGetMolInfo() 529 return mol_info; in PrfGetMolInfo() 567 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_no_ends); in PrfGetMolInfo() 573 return mol_info; in PrfGetMolInfo() 585 CRef<objects::CMolInfo> mol_info = PrfGetMolInfo(entry, comm); in PrfGetDescr() local 608 if (mol_info.NotEmpty()) in PrfGetDescr() [all …]
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H A D | em_ascii.h | 45 CRef<objects::CEMBL_block> XMLGetEMBLBlock(ParserPtr pp, char* entry, objects::CMolInfo& mol_info,
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H A D | add.h | 57 bool fta_check_htg_kwds(TKeywordList& kwds, IndexblkPtr ibp, objects::CMolInfo& mol_info);
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H A D | utilfun.h | 142 bool fta_check_mga_keywords(objects::CMolInfo& mol_info, const TKeywordList& kwds);
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H A D | add.cpp | 960 bool fta_check_htg_kwds(TKeywordList& kwds, IndexblkPtr ibp, objects::CMolInfo& mol_info) in fta_check_htg_kwds() argument 979 mol_info.SetTech(objects::CMolInfo::eTech_htgs_0); in fta_check_htg_kwds() 994 mol_info.SetTech(objects::CMolInfo::eTech_htgs_1); in fta_check_htg_kwds() 1009 mol_info.SetTech(objects::CMolInfo::eTech_htgs_2); in fta_check_htg_kwds() 1024 mol_info.SetTech(objects::CMolInfo::eTech_htgs_3); in fta_check_htg_kwds() 1033 mol_info.SetTech(objects::CMolInfo::eTech_htgs_3); in fta_check_htg_kwds() 3242 objects::CMolInfo* mol_info = nullptr; in fta_set_molinfo_completeness() local 3247 mol_info = &(*descr)->SetMolinfo(); in fta_set_molinfo_completeness() 3252 if (mol_info != nullptr) in fta_set_molinfo_completeness() 3254 mol_info->SetCompleteness(1); in fta_set_molinfo_completeness()
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H A D | nucprot.cpp | 795 CRef<objects::CMolInfo> mol_info(new objects::CMolInfo); in GetProtRefDescr() local 796 mol_info->SetBiomol(objects::CMolInfo::eBiomol_peptide); /* peptide */ in GetProtRefDescr() 802 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_no_ends); in GetProtRefDescr() 804 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_no_left); in GetProtRefDescr() 806 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_no_right); in GetProtRefDescr() 808 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_partial); in GetProtRefDescr() 811 mol_info->SetTech(objects::CMolInfo::eTech_concept_trans_a); in GetProtRefDescr() 813 mol_info->SetTech(objects::CMolInfo::eTech_concept_trans); in GetProtRefDescr() 816 descr->SetMolinfo(*mol_info); in GetProtRefDescr()
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H A D | sp_ascii.cpp | 3084 objects::CMolInfo& mol_info = mol_info_descr->SetMolinfo(); in GetSprotDescr() local 3085 mol_info.SetBiomol(objects::CMolInfo::eBiomol_peptide); in GetSprotDescr() 5097 objects::CMolInfo* mol_info = nullptr; in CkNonTerSP() local 5106 mol_info = &((*descr)->SetMolinfo()); in CkNonTerSP() 5147 if (mol_info == nullptr) in CkNonTerSP() 5150 if (segm && mol_info->GetCompleteness() != 2) in CkNonTerSP() 5152 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_partial); in CkNonTerSP() 5156 … else if (spfbp->nonter && mol_info->GetCompleteness() != objects::CMolInfo::eCompleteness_partial) in CkNonTerSP() 5158 mol_info->SetCompleteness(objects::CMolInfo::eCompleteness_partial); in CkNonTerSP() 5167 else if (mol_info->GetCompleteness() != 2) in CkNonTerSP() [all …]
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H A D | utilfun.cpp | 1834 bool fta_check_mga_keywords(objects::CMolInfo& mol_info, const TKeywordList& kwds) in fta_check_mga_keywords() argument 1862 if (!mol_info.IsSetTechexp() || !kwds.empty() || in fta_check_mga_keywords() 1863 mol_info.GetTechexp() != "cage") in fta_check_mga_keywords() 1884 mol_info.SetTechexp("5'-sage"); in fta_check_mga_keywords()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
H A D | seqtitle.cpp | 115 CConstRef<CMolInfo> mol_info(NULL); in GetTitle() local 201 if ( !mol_info ) { in GetTitle() 203 tech = mol_info->GetTech(); in GetTitle() 296 && mol_info.NotEmpty()) { in GetTitle() 297 switch (mol_info->GetBiomol()) { in GetTitle() 560 CConstRef<CMolInfo> mol_info(NULL); in GetTitle() local 637 mol_info = &desc->GetMolinfo(); in GetTitle() 638 tech = mol_info->GetTech(); in GetTitle() 700 && mol_info.NotEmpty()) { in GetTitle() 701 switch (mol_info->GetBiomol()) { in GetTitle() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/ |
H A D | seqtitle.cpp | 115 CConstRef<CMolInfo> mol_info(NULL); in GetTitle() local 201 if ( !mol_info ) { in GetTitle() 203 tech = mol_info->GetTech(); in GetTitle() 296 && mol_info.NotEmpty()) { in GetTitle() 297 switch (mol_info->GetBiomol()) { in GetTitle() 560 CConstRef<CMolInfo> mol_info(NULL); in GetTitle() local 637 mol_info = &desc->GetMolinfo(); in GetTitle() 638 tech = mol_info->GetTech(); in GetTitle() 700 && mol_info.NotEmpty()) { in GetTitle() 701 switch (mol_info->GetBiomol()) { in GetTitle() [all …]
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/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/ |
H A D | topology_util.F | 882 SUBROUTINE find_molecule(atom_bond_list, mol_info, mol_name) argument 884 INTEGER, DIMENSION(:), POINTER :: mol_info, mol_name local 891 IF (mol_info(I) == -1) THEN 894 CALL spread_mol(atom_bond_list, mol_info, i, nmol, my_mol_name, & 910 RECURSIVE SUBROUTINE spread_mol(atom_bond_list, mol_info, iatom, imol, & argument 913 INTEGER, DIMENSION(:), POINTER :: mol_info local 919 mol_info(iatom) = imol 925 IF (mol_info(atom_b) == -1 .AND. my_mol_name == mol_name(atom_b)) THEN 926 CALL spread_mol(atom_bond_list, mol_info, atom_b, imol, my_mol_name, mol_name) 927 IF (mol_info(atom_b) /= imol) CPABORT("internal error")
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H A D | topology_generate_util.F | 1003 ALLOCATE (mol_info(nsize, 4)) 1004 mol_info(1:nsize, 1:2) = mol_info_tmp(1:nsize, 1:2) 1008 mol_info(i, 3) = 0 1009 mol_info(i, 4) = 0 1019 DO j = 1, SIZE(mol_info) 1020 IF (itype == mol_info(j, 1)) EXIT 1022 mol_info(j, 3) = mol_info(j, 3) + 1 1023 IF (mol_info(j, 4) == 0) mol_info(j, 4) = mol_natom 1024 IF (mol_info(j, 4) /= mol_natom) THEN 1038 CALL integer_to_string(mol_info(j, 4), ctmp3) [all …]
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/dports/science/cp2k-data/cp2k-7.1.0/src/ |
H A D | topology_util.F | 882 SUBROUTINE find_molecule(atom_bond_list, mol_info, mol_name) argument 884 INTEGER, DIMENSION(:), POINTER :: mol_info, mol_name local 891 IF (mol_info(I) == -1) THEN 894 CALL spread_mol(atom_bond_list, mol_info, i, nmol, my_mol_name, & 910 RECURSIVE SUBROUTINE spread_mol(atom_bond_list, mol_info, iatom, imol, & argument 913 INTEGER, DIMENSION(:), POINTER :: mol_info local 919 mol_info(iatom) = imol 925 IF (mol_info(atom_b) == -1 .AND. my_mol_name == mol_name(atom_b)) THEN 926 CALL spread_mol(atom_bond_list, mol_info, atom_b, imol, my_mol_name, mol_name) 927 IF (mol_info(atom_b) /= imol) CPABORT("internal error")
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H A D | topology_generate_util.F | 1003 ALLOCATE (mol_info(nsize, 4)) 1004 mol_info(1:nsize, 1:2) = mol_info_tmp(1:nsize, 1:2) 1008 mol_info(i, 3) = 0 1009 mol_info(i, 4) = 0 1019 DO j = 1, SIZE(mol_info) 1020 IF (itype == mol_info(j, 1)) EXIT 1022 mol_info(j, 3) = mol_info(j, 3) + 1 1023 IF (mol_info(j, 4) == 0) mol_info(j, 4) = mol_natom 1024 IF (mol_info(j, 4) /= mol_natom) THEN 1038 CALL integer_to_string(mol_info(j, 4), ctmp3) [all …]
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/dports/science/ergo/ergo-3.8/source/dft/ |
H A D | grid_reader.h | 54 DftGridReader* grid_open_full(const class GridGenMolInfo *mol_info,
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H A D | integrator.cc | 203 ErgoMolInfo mol_info(bis, mol); in dft_integrate() local 214 rawgrid = grid_open_full(&mol_info, gss, NULL, mat, bis); in dft_integrate()
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H A D | grid_reader.cc | 282 grid_open_full(const class GridGenMolInfo *mol_info, in grid_open_full() argument 296 grid_open_stream(*mol_info, gss, pattern, res); in grid_open_full()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
H A D | validerror_bioseqset.cpp | 444 const CMolInfo* mol_info = 0; in CheckForInconsistentBiomols() local 450 if (mol_info == 0) { in CheckForInconsistentBiomols() 451 mol_info = &(*miit); in CheckForInconsistentBiomols() 452 } else if (mol_info->GetBiomol() != miit->GetBiomol() ) { in CheckForInconsistentBiomols()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
H A D | qualifiers.cpp | 1487 const CMolInfo* mol_info = ctx.GetMolinfo(); in Format() local 1488 if( NULL != mol_info && mol_info->CanGetTech() ) { in Format() 1489 …if( mol_info->GetTech() == CMolInfo::eTech_est || mol_info->GetTech() == CMolInfo::eTech_survey ) { in Format()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
H A D | qualifiers.cpp | 1427 const CMolInfo* mol_info = ctx.GetMolinfo(); in Format() local 1428 if( NULL != mol_info && mol_info->CanGetTech() ) { in Format() 1429 …if( mol_info->GetTech() == CMolInfo::eTech_est || mol_info->GetTech() == CMolInfo::eTech_survey ) { in Format()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
H A D | discrepancy_case.cpp | 407 auto mol_info = context.GetMolinfo(); variable 408 …if (!mol_info || !FIELD_EQUALS(mol_info->GetMolinfo(), Completeness, CMolInfo::eCompleteness_compl…
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