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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/
H A Dace.pm130 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'");
/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/motion/mc/
H A Dmc_coordinates.F116 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 …]
H A Dmc_ensembles.F225 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 …]
H A Dmc_moves.F156 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 …]
H A Dmc_ge_moves.F129 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 …]
/dports/science/cp2k-data/cp2k-7.1.0/src/motion/mc/
H A Dmc_coordinates.F117 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 …]
H A Dmc_ensembles.F226 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 …]
H A Dmc_moves.F157 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 …]
H A Dmc_ge_moves.F130 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/
H A Dgather_iter.cpp132 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/
H A Dgather_iter.cpp132 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()
/dports/biology/py-biopython/biopython-1.79/Bio/SeqIO/
H A DInsdcIO.py748 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Duniform_search.cpp49 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Duniform_search.cpp49 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()
/dports/biology/py-biopython/biopython-1.79/Tests/EMBL/
H A Dpatents.embl14 FT /mol_type="protein"
32 FT /mol_type="protein"
56 FT /mol_type="protein"
74 FT /mol_type="protein"
H A Depo_prt_selection.embl27 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"
/dports/biology/py-biopython/biopython-1.79/Bio/GenBank/
H A D__init__.py737 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 …]
/dports/biology/ncbi-toolkit/ncbi/desktop/
H A Dsalfiles.h64 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);
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tools/Analysis/
H A DSimpleAnalysisBase.pm135 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;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dmake_cdr_prods.cpp105 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/
H A Duniform_search.hpp123 CSearchDatabase(const string& dbname, EMoleculeType mol_type);
129 CSearchDatabase(const string& dbname, EMoleculeType mol_type,
140 void SetMoleculeType(EMoleculeType mol_type);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/
H A Duniform_search.hpp123 CSearchDatabase(const string& dbname, EMoleculeType mol_type);
129 CSearchDatabase(const string& dbname, EMoleculeType mol_type,
140 void SetMoleculeType(EMoleculeType mol_type);
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_AlignIO_convert.py68 for filename, in_format, mol_type in tests:
70 self.check_convert(filename, in_format, out_format, mol_type)
/dports/biology/py-biopython/biopython-1.79/Doc/examples/
H A Dls_orchid.gbk25 /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 …]
/dports/science/py-oddt/oddt-0.7/oddt/scoring/descriptors/
H A D__init__.py172 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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