/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/ |
H A D | ace.pm | 130 my $mol_type = $bio_mol_type{lc $type} 147 -alphabet => $mol_type, 169 my $mol_type = $seq->alphabet; 176 if ($mol_type eq 'dna') { 182 elsif ($mol_type eq 'protein') { 189 $self->throw("Don't know how to produce ACeDB output for '$mol_type'");
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/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/motion/mc/ |
H A D | mc_coordinates.F | 116 nunit = nunits(mol_type(imol)) 137 nunits_i = nunits(mol_type(imol)) 140 nunits_j = nunits(mol_type(jmol)) 259 molecule_type = mol_type(imolecule) 433 mol_type) 738 NULLIFY (nunits, mol_type, nchains) 740 mol_type=mol_type) 823 molecule_type = mol_type(molecule_number) 1058 nunit = nunits(mol_type(imol)) 1090 nunits_i = nunits(mol_type(imol)) [all …]
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H A D | mc_ensembles.F | 225 mol_type=mol_type, nchain_total=nchain_total, nunits=nunits, & 328 DO iunit = 1, nunits(mol_type(imolecule + start_mol - 1)) 565 mol_type=mol_type, nchain_total=nchain_total, nunits=nunits, & 983 mol_type(start_mol:end_mol)) 1250 mol_type=mol_type, nchain_total=nchain_total, nunits=nunits, & 1288 end_atom = nunits(mol_type(1)) 1290 center_of_mass(:), mass(1:nunits(mol_type(1)), mol_type(1))) 1313 start_atom = nunits(mol_type(1)) + 1 1316 center_of_mass(:), mass(1:nunits(mol_type(2)), mol_type(2))) 1325 mass(1:nunits(mol_type(2)), mol_type(2)), & [all …]
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H A D | mc_moves.F | 156 INTEGER, DIMENSION(:), POINTER :: mol_type, nunits local 182 mol_type=mol_type, names=names) 205 atom_number = atom_number + nunits(mol_type(imolecule + start_mol - 1)) 475 nchains=nchains, nunits=nunits, mol_type=mol_type) 698 mol_type=mol_type) 1008 nunits=nunits, nunits_tot=nunits_tot, mol_type=mol_type, & 1143 nunits_mol = nunits(mol_type(imolecule + start_mol - 1)) 1997 mass=mass, nunits=nunits, nunits_tot=nunits_tot, mol_type=mol_type) 2525 nchains=nchains, nunits=nunits, mol_type=mol_type) 2609 nunit = nunits(mol_type(ipart + start_mol - 1)) [all …]
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H A D | mc_ge_moves.F | 129 INTEGER, DIMENSION(:), POINTER :: mol_type, nunits, nunits_tot local 150 … nchains=nchains, nunits_tot=nunits_tot, nunits=nunits, mol_type=mol_type) 451 INTEGER, DIMENSION(:), POINTER :: mol_type, mol_type_test, nunits, & local 482 NULLIFY (particles_old, mol_type, mol_type_test, mc_input_file, mc_bias_file) 494 atom_names=atom_names, mass=mass, mol_type=mol_type) 575 … nchains(:, remove_box), nunits, loverlap, mol_type(start_mol:end_mol)) 811 mol_type=mol_type_test) 1149 INTEGER, DIMENSION(:), POINTER :: mol_type, nunits, nunits_tot local 1181 mass=mass, nchains=nchains, nunits=nunits, mol_type=mol_type) 1288 molecule_type = mol_type(imolecule + molecule_index - 1) [all …]
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/dports/science/cp2k-data/cp2k-7.1.0/src/motion/mc/ |
H A D | mc_coordinates.F | 117 nunit = nunits(mol_type(imol)) 138 nunits_i = nunits(mol_type(imol)) 141 nunits_j = nunits(mol_type(jmol)) 260 molecule_type = mol_type(imolecule) 434 mol_type) 739 NULLIFY (nunits, mol_type, nchains) 741 mol_type=mol_type) 824 molecule_type = mol_type(molecule_number) 1059 nunit = nunits(mol_type(imol)) 1091 nunits_i = nunits(mol_type(imol)) [all …]
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H A D | mc_ensembles.F | 226 mol_type=mol_type, nchain_total=nchain_total, nunits=nunits, & 329 DO iunit = 1, nunits(mol_type(imolecule + start_mol - 1)) 566 mol_type=mol_type, nchain_total=nchain_total, nunits=nunits, & 984 mol_type(start_mol:end_mol)) 1251 mol_type=mol_type, nchain_total=nchain_total, nunits=nunits, & 1289 end_atom = nunits(mol_type(1)) 1291 center_of_mass(:), mass(1:nunits(mol_type(1)), mol_type(1))) 1314 start_atom = nunits(mol_type(1)) + 1 1317 center_of_mass(:), mass(1:nunits(mol_type(2)), mol_type(2))) 1326 mass(1:nunits(mol_type(2)), mol_type(2)), & [all …]
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H A D | mc_moves.F | 157 INTEGER, DIMENSION(:), POINTER :: mol_type, nunits local 183 mol_type=mol_type, names=names) 206 atom_number = atom_number + nunits(mol_type(imolecule + start_mol - 1)) 476 nchains=nchains, nunits=nunits, mol_type=mol_type) 699 mol_type=mol_type) 1009 nunits=nunits, nunits_tot=nunits_tot, mol_type=mol_type, & 1144 nunits_mol = nunits(mol_type(imolecule + start_mol - 1)) 1998 mass=mass, nunits=nunits, nunits_tot=nunits_tot, mol_type=mol_type) 2526 nchains=nchains, nunits=nunits, mol_type=mol_type) 2610 nunit = nunits(mol_type(ipart + start_mol - 1)) [all …]
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H A D | mc_ge_moves.F | 130 INTEGER, DIMENSION(:), POINTER :: mol_type, nunits, nunits_tot local 151 … nchains=nchains, nunits_tot=nunits_tot, nunits=nunits, mol_type=mol_type) 452 INTEGER, DIMENSION(:), POINTER :: mol_type, mol_type_test, nunits, & local 483 NULLIFY (particles_old, mol_type, mol_type_test, mc_input_file, mc_bias_file) 495 atom_names=atom_names, mass=mass, mol_type=mol_type) 576 … nchains(:, remove_box), nunits, loverlap, mol_type(start_mol:end_mol)) 812 mol_type=mol_type_test) 1150 INTEGER, DIMENSION(:), POINTER :: mol_type, nunits, nunits_tot local 1182 mass=mass, nchains=nchains, nunits=nunits, mol_type=mol_type) 1289 molecule_type = mol_type(imolecule + molecule_index - 1) [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
H A D | gather_iter.cpp | 132 CSeq_inst::TMol mol_type; in x_AddSeqEntryToStack() local 136 mol_type = CSeq_inst::eMol_not_set; in x_AddSeqEntryToStack() 138 mol_type = CSeq_inst::eMol_na; in x_AddSeqEntryToStack() 140 mol_type = CSeq_inst::eMol_aa; in x_AddSeqEntryToStack() 145 auto_ptr<CBioseq_CI> seq_iter( new CBioseq_CI(entry, mol_type, CBioseq_CI::eLevel_Mains) ); in x_AddSeqEntryToStack()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
H A D | gather_iter.cpp | 132 CSeq_inst::TMol mol_type; in x_AddSeqEntryToStack() local 136 mol_type = CSeq_inst::eMol_not_set; in x_AddSeqEntryToStack() 138 mol_type = CSeq_inst::eMol_na; in x_AddSeqEntryToStack() 140 mol_type = CSeq_inst::eMol_aa; in x_AddSeqEntryToStack() 145 auto_ptr<CBioseq_CI> seq_iter( new CBioseq_CI(entry, mol_type, CBioseq_CI::eLevel_Mains) ); in x_AddSeqEntryToStack()
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/dports/biology/py-biopython/biopython-1.79/Bio/SeqIO/ |
H A D | InsdcIO.py | 748 if mol_type is None: 750 if mol_type and len(mol_type) > 7: 752 mol_type = mol_type.replace("unassigned ", "").replace("genomic ", "") 753 if len(mol_type) > 7: 755 mol_type = "DNA" 757 mol_type = "" 759 if mol_type == "": 784 mol_type.ljust(7), 1253 if mol_type is None: 1257 mol_type_upper = mol_type.upper() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | uniform_search.cpp | 49 CSearchDatabase::CSearchDatabase(const string& dbname, EMoleculeType mol_type) in BEGIN_SCOPE() 50 : m_DbName(dbname), m_MolType(mol_type), m_GiListSet(false), in BEGIN_SCOPE() 55 CSearchDatabase::CSearchDatabase(const string& dbname, EMoleculeType mol_type, in CSearchDatabase() argument 57 : m_DbName(dbname), m_MolType(mol_type), in CSearchDatabase() 76 CSearchDatabase::SetMoleculeType(EMoleculeType mol_type) in SetMoleculeType() argument 78 m_MolType = mol_type; in SetMoleculeType()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | uniform_search.cpp | 49 CSearchDatabase::CSearchDatabase(const string& dbname, EMoleculeType mol_type) in BEGIN_SCOPE() 50 : m_DbName(dbname), m_MolType(mol_type), m_GiListSet(false), in BEGIN_SCOPE() 55 CSearchDatabase::CSearchDatabase(const string& dbname, EMoleculeType mol_type, in CSearchDatabase() argument 57 : m_DbName(dbname), m_MolType(mol_type), in CSearchDatabase() 76 CSearchDatabase::SetMoleculeType(EMoleculeType mol_type) in SetMoleculeType() argument 78 m_MolType = mol_type; in SetMoleculeType()
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/dports/biology/py-biopython/biopython-1.79/Tests/EMBL/ |
H A D | patents.embl | 14 FT /mol_type="protein" 32 FT /mol_type="protein" 56 FT /mol_type="protein" 74 FT /mol_type="protein"
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H A D | epo_prt_selection.embl | 27 FT /mol_type="protein" 59 FT /mol_type="protein" 91 FT /mol_type="protein" 124 FT /mol_type="protein" 160 FT /mol_type="protein" 192 FT /mol_type="protein" 224 FT /mol_type="protein" 254 FT /mol_type="protein" 289 FT /mol_type="protein"
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/dports/biology/py-biopython/biopython-1.79/Bio/GenBank/ |
H A D | __init__.py | 737 def molecule_type(self, mol_type): argument 739 if mol_type: 740 if "circular" in mol_type or "linear" in mol_type: 742 "Molecule type %r should not include topology" % mol_type 750 if mol_type[-3:].upper() in ("DNA", "RNA") and not mol_type[-3:].isupper(): 756 self.data.annotations["molecule_type"] = mol_type 1475 def molecule_type(self, mol_type): argument 1477 if mol_type: 1478 if "circular" in mol_type or "linear" in mol_type: 1488 if mol_type[-3:].upper() in ("DNA", "RNA") and not mol_type[-3:].isupper(): [all …]
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/dports/biology/ncbi-toolkit/ncbi/desktop/ |
H A D | salfiles.h | 64 extern SeqEntryPtr FastaRead (CharPtr path, Uint2 mol_type); 65 extern SeqEntryPtr ReadInterleaveAlign (CharPtr path, Uint1 mol_type); 66 extern SeqEntryPtr ReadContiguouseAlign (CharPtr path, Uint1 mol_type);
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tools/Analysis/ |
H A D | SimpleAnalysisBase.pm | 135 my $mol_type = $self->analysis_spec->{'type'}; 136 $self->throw("I need a [" . $mol_type . "] seq, not a [". $value->alphabet. "]") 137 unless $value->alphabet =~/$mol_type/i;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | make_cdr_prods.cpp | 105 CRef<CSeqdesc> mol_type(new CSeqdesc); in MakeCdrProds() local 106 mol_type->SetMol_type( eGIBB_mol_peptide); in MakeCdrProds() 107 bio_seq->SetDescr().Set().push_back(mol_type); in MakeCdrProds()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/ |
H A D | uniform_search.hpp | 123 CSearchDatabase(const string& dbname, EMoleculeType mol_type); 129 CSearchDatabase(const string& dbname, EMoleculeType mol_type, 140 void SetMoleculeType(EMoleculeType mol_type);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/ |
H A D | uniform_search.hpp | 123 CSearchDatabase(const string& dbname, EMoleculeType mol_type); 129 CSearchDatabase(const string& dbname, EMoleculeType mol_type, 140 void SetMoleculeType(EMoleculeType mol_type);
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/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_AlignIO_convert.py | 68 for filename, in_format, mol_type in tests: 70 self.check_convert(filename, in_format, out_format, mol_type)
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/dports/biology/py-biopython/biopython-1.79/Doc/examples/ |
H A D | ls_orchid.gbk | 25 /mol_type="genomic DNA" 75 /mol_type="genomic DNA" 125 /mol_type="genomic DNA" 175 /mol_type="genomic DNA" 225 /mol_type="genomic DNA" 275 /mol_type="genomic DNA" 324 /mol_type="genomic DNA" 374 /mol_type="genomic DNA" 423 /mol_type="genomic DNA" 473 /mol_type="genomic DNA" [all …]
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/dports/science/py-oddt/oddt-0.7/oddt/scoring/descriptors/ |
H A D | __init__.py | 172 pairs = [(mol_type, prot_type) 173 for mol_type in self.ligand_types 184 for mol_type, prot_type in pairs: 186 mol_dict[mol_type]['coords'])[..., np.newaxis]
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