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Searched refs:mol_info (Results 1 – 25 of 28) sorted by relevance

12

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/
H A Dem_ascii.cpp1402 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()
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H A Dgb_ascii.cpp789 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()
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H A Dxm_ascii.cpp530 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()
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H A Dfcleanup.cpp158 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()
H A Dprf_ascii.cpp504 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()
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H A Dem_ascii.h45 CRef<objects::CEMBL_block> XMLGetEMBLBlock(ParserPtr pp, char* entry, objects::CMolInfo& mol_info,
H A Dadd.h57 bool fta_check_htg_kwds(TKeywordList& kwds, IndexblkPtr ibp, objects::CMolInfo& mol_info);
H A Dutilfun.h142 bool fta_check_mga_keywords(objects::CMolInfo& mol_info, const TKeywordList& kwds);
H A Dadd.cpp960 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()
H A Dnucprot.cpp795 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()
H A Dsp_ascii.cpp3084 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()
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H A Dutilfun.cpp1834 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/
H A Dseqtitle.cpp115 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/
H A Dseqtitle.cpp115 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()
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/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/
H A Dtopology_util.F882 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")
H A Dtopology_generate_util.F1003 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)
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/dports/science/cp2k-data/cp2k-7.1.0/src/
H A Dtopology_util.F882 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")
H A Dtopology_generate_util.F1003 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)
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/dports/science/ergo/ergo-3.8/source/dft/
H A Dgrid_reader.h54 DftGridReader* grid_open_full(const class GridGenMolInfo *mol_info,
H A Dintegrator.cc203 ErgoMolInfo mol_info(bis, mol); in dft_integrate() local
214 rawgrid = grid_open_full(&mol_info, gss, NULL, mat, bis); in dft_integrate()
H A Dgrid_reader.cc282 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/
H A Dvaliderror_bioseqset.cpp444 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/
H A Dqualifiers.cpp1487 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/
H A Dqualifiers.cpp1427 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/
H A Ddiscrepancy_case.cpp407 auto mol_info = context.GetMolinfo(); variable
408 …if (!mol_info || !FIELD_EQUALS(mol_info->GetMolinfo(), Completeness, CMolInfo::eCompleteness_compl…

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