Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X A AdaptiveFancyArrow (class in biotite) add_additional_options() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) add_annotation() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) add_bond() (biotite.structure.BondList method) add_feature() (biotite.sequence.Annotation method) adjacency_matrix() (biotite.structure.BondList method) AffineTransformation (class in biotite.structure) align() (biotite.application.clustalo.ClustalOmegaApp class method) (biotite.application.mafft.MafftApp class method) (biotite.application.MSAApp class method) (biotite.application.muscle.Muscle5App class method) (biotite.application.muscle.MuscleApp class method) align_banded() (in module biotite.sequence.align) align_local_gapped() (in module biotite.sequence.align) align_local_ungapped() (in module biotite.sequence.align) align_multiple() (in module biotite.sequence.align) align_optimal() (in module biotite.sequence.align) align_ungapped() (in module biotite.sequence.align) align_vectors() (in module biotite.structure) Alignment (class in biotite.sequence.align) all_residues() (in module biotite.structure.info) Alphabet (class in biotite.sequence) AlphabetError (class in biotite.sequence) AlphabetMapper (class in biotite.sequence) ambiguous_alphabet() (biotite.sequence.NucleotideSequence static method) amino_acid_names() (in module biotite.structure.info) angle() (in module biotite.structure) annotate_sse() (biotite.application.dssp.DsspApp static method) (in module biotite.structure) AnnotatedSequence (class in biotite.sequence) Annotation (class in biotite.sequence) ANY (biotite.structure.BondType attribute) app_url() (biotite.application.blast.BlastWebApp method) (biotite.application.WebApp method) append() (biotite.sequence.io.genbank.GenBankFile method) (biotite.sequence.io.gff.GFFFile method) append_directive() (biotite.sequence.io.gff.GFFFile method) Application (class in biotite.application) apply() (biotite.structure.AffineTransformation method) apply_chain_wise() (in module biotite.structure) apply_residue_wise() (in module biotite.structure) AppState (class in biotite.application) AppStateError (class in biotite.application) AROMATIC_DOUBLE (biotite.structure.BondType attribute) AROMATIC_SINGLE (biotite.structure.BondType attribute) AROMATIC_TRIPLE (biotite.structure.BondType attribute) array() (in module biotite.structure) array_length() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) ArrayPlotter (class in biotite.sequence.graphics) as_array() (biotite.structure.BondList method) (biotite.structure.io.pdbx.BinaryCIFColumn method) (biotite.structure.io.pdbx.CIFColumn method) as_binary() (in module biotite.sequence.phylo) as_graph() (biotite.sequence.phylo.Tree method) (biotite.structure.BondList method) as_item() (biotite.structure.io.pdbx.BinaryCIFColumn method) (biotite.structure.io.pdbx.CIFColumn method) as_matrix() (biotite.structure.AffineTransformation method) as_root() (biotite.sequence.phylo.TreeNode method) as_set() (biotite.structure.BondList method) as_type() (biotite.sequence.GeneralSequence method) Atom (class in biotite.structure) AtomArray (class in biotite.structure) AtomArrayStack (class in biotite.structure) average() (in module biotite.structure) B BACK (biotite.sequence.align.CigarOp attribute) BadStructureError (class in biotite.structure) base_pairs() (in module biotite.structure) base_pairs_edge() (in module biotite.structure) base_pairs_from_dot_bracket() (in module biotite.structure) base_pairs_glycosidic_bond() (in module biotite.structure) base_stacking() (in module biotite.structure) BasicQuery (class in biotite.database.rcsb) BETWEEN (biotite.sequence.Location.Defect attribute) BEYOND_LEFT (biotite.sequence.Location.Defect attribute) BEYOND_RIGHT (biotite.sequence.Location.Defect attribute) BinaryCIFBlock (class in biotite.structure.io.pdbx) BinaryCIFCategory (class in biotite.structure.io.pdbx) BinaryCIFColumn (class in biotite.structure.io.pdbx) BinaryCIFData (class in biotite.structure.io.pdbx) BinaryCIFFile (class in biotite.structure.io.pdbx) biotite module biotite.application module biotite.application.autodock module biotite.application.blast module biotite.application.clustalo module biotite.application.dssp module biotite.application.mafft module biotite.application.muscle module biotite.application.sra module biotite.application.tantan module biotite.application.viennarna module biotite.database module biotite.database.entrez module biotite.database.pubchem module biotite.database.rcsb module biotite.database.uniprot module biotite.sequence module biotite.sequence.align module biotite.sequence.graphics module biotite.sequence.io module biotite.sequence.io.fasta module biotite.sequence.io.fastq module biotite.sequence.io.genbank module biotite.sequence.io.gff module biotite.sequence.phylo module biotite.structure module biotite.structure.graphics module biotite.structure.info module biotite.structure.io module biotite.structure.io.dcd module biotite.structure.io.gro module biotite.structure.io.mol module biotite.structure.io.netcdf module biotite.structure.io.pdb module biotite.structure.io.pdbqt module biotite.structure.io.pdbx module biotite.structure.io.trr module biotite.structure.io.xtc module BlastAlignment (class in biotite.application.blast) BlastWebApp (class in biotite.application.blast) bond_type() (in module biotite.structure.info) bond_type_matrix() (biotite.structure.BondList method) BondList (class in biotite.structure) bonds_in_residue() (in module biotite.structure.info) BondType (class in biotite.structure) box_volume() (in module biotite.structure) bucket_number() (in module biotite.sequence.align) BucketKmerTable (class in biotite.sequence.align) ByteArrayEncoding (class in biotite.structure.io.pdbx) C CachedSyncmerSelector (class in biotite.sequence.align) cancel() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) CANCELLED (biotite.application.AppState attribute) carbohydrate_names() (in module biotite.structure.info) CellList (class in biotite.structure) centroid() (in module biotite.structure) chain_iter() (in module biotite.structure) check_atom_id_continuity() (in module biotite.structure) check_backbone_continuity() (in module biotite.structure) check_duplicate_atoms() (in module biotite.structure) check_linear_continuity() (in module biotite.structure) check_res_id_continuity() (in module biotite.structure) CIFBlock (class in biotite.structure.io.pdbx) CIFCategory (class in biotite.structure.io.pdbx) CIFColumn (class in biotite.structure.io.pdbx) CIFData (class in biotite.structure.io.pdbx) CIFFile (class in biotite.structure.io.pdbx) CigarOp (class in biotite.sequence.align) CIRCULAR (biotite.application.viennarna.RNAplotApp.Layout attribute) CIS (biotite.structure.GlycosidicBond attribute) clean_up() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) ClustalOmegaApp (class in biotite.application.clustalo) CodingPlotter (class in biotite.sequence.graphics) codon_dict() (biotite.sequence.CodonTable method) CodonTable (class in biotite.sequence) common_alphabet() (in module biotite.sequence) complement() (biotite.sequence.NucleotideSequence method) CompositeQuery (class in biotite.database.entrez) (class in biotite.database.rcsb) (class in biotite.database.uniprot) compute_coordinates() (biotite.application.viennarna.RNAplotApp static method) compute_secondary_structure() (biotite.application.viennarna.RNAalifoldApp static method) (biotite.application.viennarna.RNAfoldApp static method) connect_via_distances() (in module biotite.structure) connect_via_residue_names() (in module biotite.structure) convert_letter_1to3() (biotite.sequence.ProteinSequence static method) convert_letter_3to1() (biotite.sequence.ProteinSequence static method) coord() (in module biotite.structure) coord_to_fraction() (in module biotite.structure) copy() (biotite.Copyable method) (biotite.File method) (biotite.sequence.AnnotatedSequence method) (biotite.sequence.Annotation method) (biotite.sequence.Feature method) (biotite.sequence.GeneralSequence method) (biotite.sequence.io.fasta.FastaFile method) (biotite.sequence.io.fastq.FastqFile method) (biotite.sequence.io.genbank.GenBankFile method) (biotite.sequence.io.genbank.MultiFile method) (biotite.sequence.io.gff.GFFFile method) (biotite.sequence.NucleotideSequence method) (biotite.sequence.phylo.Tree method) (biotite.sequence.phylo.TreeNode method) (biotite.sequence.ProteinSequence method) (biotite.sequence.Sequence method) (biotite.structure.Atom method) (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) (biotite.structure.BondList method) (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.gro.GROFile method) (biotite.structure.io.mol.MOLFile method) (biotite.structure.io.mol.SDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.pdb.PDBFile method) (biotite.structure.io.pdbqt.PDBQTFile method) (biotite.structure.io.pdbx.BinaryCIFFile method) (biotite.structure.io.pdbx.CIFFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) (biotite.TextFile method) Copyable (class in biotite) count() (biotite.sequence.align.BucketKmerTable method) (biotite.sequence.align.KmerTable method) (in module biotite.database.rcsb) create_adjacency_matrix() (biotite.structure.CellList method) create_atom_names() (in module biotite.structure) create_continuous_res_ids() (in module biotite.structure) create_kmers() (biotite.sequence.align.KmerAlphabet method) CREATED (biotite.application.AppState attribute) D DCDFile (class in biotite.structure.io.dcd) decode (biotite.structure.io.pdbx.IntegerPackingEncoding attribute) decode() (biotite.sequence.align.KmerAlphabet method) (biotite.sequence.Alphabet method) (biotite.sequence.LetterAlphabet method) (biotite.structure.io.pdbx.ByteArrayEncoding method) (biotite.structure.io.pdbx.DeltaEncoding method) (biotite.structure.io.pdbx.FixedPointEncoding method) (biotite.structure.io.pdbx.IntervalQuantizationEncoding method) (biotite.structure.io.pdbx.RunLengthEncoding method) (biotite.structure.io.pdbx.StringArrayEncoding method) decode_multiple() (biotite.sequence.align.KmerAlphabet method) (biotite.sequence.Alphabet method) (biotite.sequence.LetterAlphabet method) default_table() (biotite.sequence.CodonTable static method) del_annotation() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) del_feature() (biotite.sequence.Annotation method) DELETION (biotite.sequence.align.CigarOp attribute) DeltaEncoding (class in biotite.structure.io.pdbx) density() (in module biotite.structure) DepositGrouping (class in biotite.database.rcsb) DeserializationError (class in biotite) deserialize() (biotite.structure.io.mol.Header static method) (biotite.structure.io.mol.Metadata static method) (biotite.structure.io.mol.Metadata.Key static method) (biotite.structure.io.mol.SDFile static method) (biotite.structure.io.mol.SDRecord static method) (biotite.structure.io.pdbx.BinaryCIFBlock static method) (biotite.structure.io.pdbx.BinaryCIFCategory static method) (biotite.structure.io.pdbx.BinaryCIFColumn static method) (biotite.structure.io.pdbx.BinaryCIFData static method) (biotite.structure.io.pdbx.BinaryCIFFile static method) (biotite.structure.io.pdbx.ByteArrayEncoding class method) (biotite.structure.io.pdbx.CIFBlock static method) (biotite.structure.io.pdbx.CIFCategory static method) (biotite.structure.io.pdbx.CIFFile static method) (biotite.structure.io.pdbx.DeltaEncoding class method) (biotite.structure.io.pdbx.FixedPointEncoding class method) (biotite.structure.io.pdbx.IntegerPackingEncoding class method) (biotite.structure.io.pdbx.IntervalQuantizationEncoding class method) (biotite.structure.io.pdbx.RunLengthEncoding class method) (biotite.structure.io.pdbx.StringArrayEncoding static method) dict_from_db() (biotite.sequence.align.SubstitutionMatrix static method) dict_from_str() (biotite.sequence.align.SubstitutionMatrix static method) DIFFERENT (biotite.sequence.align.CigarOp attribute) dihedral() (in module biotite.structure) dihedral_backbone() (in module biotite.structure) directives() (biotite.sequence.io.gff.GFFFile method) displacement() (in module biotite.structure) distance() (in module biotite.structure) distance_to() (biotite.sequence.phylo.TreeNode method) dock() (biotite.application.autodock.VinaApp static method) dot_bracket() (in module biotite.structure) dot_bracket_from_structure() (in module biotite.structure) DOUBLE (biotite.structure.BondType attribute) draw() (biotite.AdaptiveFancyArrow method) (biotite.sequence.graphics.CodingPlotter method) (biotite.sequence.graphics.FeaturePlotter method) (biotite.sequence.graphics.MiscFeaturePlotter method) (biotite.sequence.graphics.PromoterPlotter method) (biotite.sequence.graphics.RBSPlotter method) (biotite.sequence.graphics.TerminatorPlotter method) DsspApp (class in biotite.application.dssp) dtype() (biotite.sequence.GeneralSequence static method) (biotite.sequence.NucleotideSequence static method) (biotite.sequence.ProteinSequence static method) (biotite.sequence.Sequence static method) E Edge (class in biotite.structure) encode() (biotite.sequence.align.KmerAlphabet method) (biotite.sequence.Alphabet method) (biotite.sequence.LetterAlphabet method) (biotite.structure.io.pdbx.ByteArrayEncoding method) (biotite.structure.io.pdbx.DeltaEncoding method) (biotite.structure.io.pdbx.FixedPointEncoding method) (biotite.structure.io.pdbx.IntegerPackingEncoding method) (biotite.structure.io.pdbx.IntervalQuantizationEncoding method) (biotite.structure.io.pdbx.RunLengthEncoding method) (biotite.structure.io.pdbx.StringArrayEncoding method) encode_multiple() (biotite.sequence.align.KmerAlphabet method) (biotite.sequence.Alphabet method) (biotite.sequence.LetterAlphabet method) EQUAL (biotite.sequence.align.CigarOp attribute) equal_annotation_categories() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) equal_annotations() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) evaluate() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) EValueEstimator (class in biotite.sequence.align) extends() (biotite.sequence.align.KmerAlphabet method) (biotite.sequence.Alphabet method) (biotite.sequence.LetterAlphabet method) F FastaDumpApp (class in biotite.application.sra) FastaFile (class in biotite.sequence.io.fasta) FastqDumpApp (class in biotite.application.sra) FastqFile (class in biotite.sequence.io.fastq) Feature (class in biotite.sequence) FeaturePlotter (class in biotite.sequence.graphics) fetch() (biotite.application.sra.FastaDumpApp class method) (biotite.application.sra.FastqDumpApp class method) (in module biotite.database.entrez) (in module biotite.database.pubchem) (in module biotite.database.rcsb) (in module biotite.database.uniprot) fetch_property() (in module biotite.database.pubchem) fetch_single_file() (in module biotite.database.entrez) FieldQuery (class in biotite.database.rcsb) File (class in biotite) filter_amino_acids() (in module biotite.structure) filter_canonical_amino_acids() (in module biotite.structure) filter_canonical_nucleotides() (in module biotite.structure) filter_carbohydrates() (in module biotite.structure) filter_first_altloc() (in module biotite.structure) filter_highest_occupancy_altloc() (in module biotite.structure) filter_intersection() (in module biotite.structure) filter_linear_bond_continuity() (in module biotite.structure) filter_monoatomic_ions() (in module biotite.structure) filter_nucleotides() (in module biotite.structure) filter_peptide_backbone() (in module biotite.structure) filter_phosphate_backbone() (in module biotite.structure) filter_polymer() (in module biotite.structure) filter_solvent() (in module biotite.structure) find_connected() (in module biotite.structure) find_rotatable_bonds() (in module biotite.structure) find_subsequence() (in module biotite.sequence) find_symbol() (in module biotite.sequence) find_symbol_first() (in module biotite.sequence) find_symbol_last() (in module biotite.sequence) find_terminal_gaps() (in module biotite.sequence.align) FINISHED (biotite.application.AppState attribute) FixedPointEncoding (class in biotite.structure.io.pdbx) FLOAT32 (biotite.structure.io.pdbx.TypeCode attribute) FLOAT64 (biotite.structure.io.pdbx.TypeCode attribute) FormulaQuery (class in biotite.database.pubchem) FORWARD (biotite.sequence.Location.Strand attribute) fraction_to_coord() (in module biotite.structure) FrequencyPermutation (class in biotite.sequence.align) from_alignment() (biotite.sequence.SequenceProfile static method) from_atoms() (biotite.database.pubchem.FormulaQuery static method) (biotite.database.pubchem.IdentityQuery class method) (biotite.database.pubchem.SimilarityQuery class method) (biotite.database.pubchem.SubstructureQuery class method) (biotite.database.pubchem.SuperstructureQuery class method) from_cigar_symbol() (biotite.sequence.align.CigarOp static method) from_dtype() (biotite.structure.io.pdbx.TypeCode static method) from_kmer_selection() (biotite.sequence.align.BucketKmerTable static method) (biotite.sequence.align.KmerTable static method) from_kmers() (biotite.sequence.align.BucketKmerTable static method) (biotite.sequence.align.KmerTable static method) from_newick() (biotite.sequence.phylo.Tree static method) (biotite.sequence.phylo.TreeNode static method) from_positions() (biotite.sequence.align.KmerTable static method) from_response() (biotite.database.pubchem.ThrottleStatus static method) from_samples() (biotite.sequence.align.EValueEstimator static method) from_sequences() (biotite.sequence.align.BucketKmerTable static method) (biotite.sequence.align.KmerTable static method) from_table() (biotite.sequence.align.FrequencyPermutation static method) from_tables() (biotite.sequence.align.BucketKmerTable static method) (biotite.sequence.align.KmerTable static method) from_template() (in module biotite.structure) full_matrix_calculation() (biotite.application.clustalo.ClustalOmegaApp method) full_name() (in module biotite.structure.info) fuse() (biotite.sequence.align.KmerAlphabet method) G GenBankFile (class in biotite.sequence.io.genbank) GeneralSequence (class in biotite.sequence) get_accession() (in module biotite.sequence.io.genbank) get_alignment() (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (in module biotite.sequence.io.fasta) get_alignment_order() (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) get_alignments() (biotite.application.blast.BlastWebApp method) get_all_bonds() (biotite.structure.BondList method) get_alphabet() (biotite.sequence.GeneralSequence method) (biotite.sequence.NucleotideSequence method) (biotite.sequence.ProteinSequence method) (biotite.sequence.Sequence method) get_alphabet1() (biotite.sequence.align.SubstitutionMatrix method) get_alphabet2() (biotite.sequence.align.SubstitutionMatrix method) get_annotated_sequence() (in module biotite.sequence.io.genbank) get_annotation() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) (in module biotite.sequence.io.genbank) (in module biotite.sequence.io.gff) get_annotation_categories() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) get_api_key() (in module biotite.database.entrez) get_app_state() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) get_array() (biotite.structure.AtomArrayStack method) get_assembly() (biotite.structure.io.pdb.PDBFile method) (in module biotite.structure.io.pdb) (in module biotite.structure.io.pdbx) get_atom() (biotite.structure.AtomArray method) get_atom_count() (biotite.structure.BondList method) get_atoms() (biotite.structure.CellList method) get_atoms_in_cells() (biotite.structure.CellList method) get_b_factor() (biotite.structure.io.pdb.PDBFile method) get_base_pairs() (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) get_bond_count() (biotite.structure.BondList method) get_bonds() (biotite.structure.BondList method) get_box() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) get_chain_count() (in module biotite.structure) get_chain_masks() (in module biotite.structure) get_chain_positions() (in module biotite.structure) get_chain_starts() (in module biotite.structure) get_chain_starts_for() (in module biotite.structure) get_chains() (in module biotite.structure) get_cmap() (biotite.sequence.graphics.ArrayPlotter method) get_codes() (in module biotite.sequence.align) get_color() (biotite.sequence.graphics.ArrayPlotter method) (biotite.sequence.graphics.LetterPlotter method) (biotite.sequence.graphics.LetterSimilarityPlotter method) (biotite.sequence.graphics.LetterTypePlotter method) get_color_scheme() (in module biotite.sequence.graphics) get_command() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) get_component() (in module biotite.structure.io.pdbx) get_consensus_sequence_string() (biotite.application.viennarna.RNAalifoldApp method) get_content() (biotite.database.rcsb.BasicQuery method) (biotite.database.rcsb.CompositeQuery method) (biotite.database.rcsb.DepositGrouping method) (biotite.database.rcsb.FieldQuery method) (biotite.database.rcsb.Grouping method) (biotite.database.rcsb.IdentityGrouping method) (biotite.database.rcsb.MotifQuery method) (biotite.database.rcsb.Query method) (biotite.database.rcsb.SequenceQuery method) (biotite.database.rcsb.SingleQuery method) (biotite.database.rcsb.Sorting method) (biotite.database.rcsb.StructureQuery method) (biotite.database.rcsb.UniprotGrouping method) get_coord() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.pdb.PDBFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) get_coordinates() (biotite.application.viennarna.RNAplotApp method) get_covariance_energy() (biotite.application.viennarna.RNAalifoldApp method) get_database_name() (in module biotite.database.entrez) get_db_link() (in module biotite.sequence.io.genbank) get_definition() (in module biotite.sequence.io.genbank) get_distance() (biotite.sequence.phylo.Tree method) get_distance_matrix() (biotite.application.clustalo.ClustalOmegaApp method) get_dot_bracket() (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) get_energies() (biotite.application.autodock.VinaApp method) get_exit_code() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) get_fasta() (biotite.application.sra.FastaDumpApp method) get_fastq() (biotite.application.sra.FastqDumpApp method) get_fastq_dump_options() (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) get_features() (biotite.sequence.Annotation method) get_fields() (biotite.sequence.io.genbank.GenBankFile method) get_file_paths() (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) get_files() (biotite.database.pubchem.FormulaQuery method) (biotite.database.pubchem.IdentityQuery method) (biotite.database.pubchem.InchiKeyQuery method) (biotite.database.pubchem.InchiQuery method) (biotite.database.pubchem.NameQuery method) (biotite.database.pubchem.Query method) (biotite.database.pubchem.SimilarityQuery method) (biotite.database.pubchem.SmilesQuery method) (biotite.database.pubchem.SubstructureQuery method) (biotite.database.pubchem.SuperstructureQuery method) get_flexible_residue_models() (biotite.application.autodock.VinaApp method) get_free_energy() (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) get_gapped_sequences() (biotite.application.blast.BlastAlignment method) (biotite.sequence.align.Alignment method) get_gi() (in module biotite.sequence.io.genbank) get_guide_tree() (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.mafft.MafftApp method) (biotite.application.muscle.MuscleApp method) get_in_layout() (biotite.AdaptiveFancyArrow method) get_indices() (biotite.sequence.io.genbank.GenBankFile method) (biotite.sequence.phylo.TreeNode method) get_input_file_path() (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) get_input_url_path() (biotite.database.pubchem.FormulaQuery method) (biotite.database.pubchem.IdentityQuery method) (biotite.database.pubchem.InchiKeyQuery method) (biotite.database.pubchem.InchiQuery method) (biotite.database.pubchem.NameQuery method) (biotite.database.pubchem.Query method) (biotite.database.pubchem.SimilarityQuery method) (biotite.database.pubchem.SmilesQuery method) (biotite.database.pubchem.SubstructureQuery method) (biotite.database.pubchem.SuperstructureQuery method) get_kmers() (biotite.sequence.align.BucketKmerTable method) (biotite.sequence.align.KmerTable method) get_leaf_count() (biotite.sequence.phylo.TreeNode method) get_leaves() (biotite.sequence.phylo.TreeNode method) get_ligand_coord() (biotite.application.autodock.VinaApp method) get_ligand_models() (biotite.application.autodock.VinaApp method) get_location_range() (biotite.sequence.Annotation method) (biotite.sequence.Feature method) get_locus() (in module biotite.sequence.io.genbank) get_mask() (biotite.application.tantan.TantanApp method) get_matrix_file_path() (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) get_model_count() (biotite.structure.io.gro.GROFile method) (biotite.structure.io.pdb.PDBFile method) (in module biotite.structure.io.pdb) (in module biotite.structure.io.pdbx) get_molecular_weight() (biotite.sequence.ProteinSequence method) get_molecule_indices() (in module biotite.structure) get_molecule_masks() (in module biotite.structure) get_output_file_path() (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) get_pairwise_sequence_identity() (in module biotite.sequence.align) get_params() (biotite.database.pubchem.FormulaQuery method) (biotite.database.pubchem.IdentityQuery method) (biotite.database.pubchem.InchiKeyQuery method) (biotite.database.pubchem.InchiQuery method) (biotite.database.pubchem.NameQuery method) (biotite.database.pubchem.Query method) (biotite.database.pubchem.SimilarityQuery method) (biotite.database.pubchem.SmilesQuery method) (biotite.database.pubchem.SubstructureQuery method) (biotite.database.pubchem.SuperstructureQuery method) get_prefetch_options() (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) get_process() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) get_quality() (biotite.sequence.io.fastq.FastqFile method) get_raw_sequence() (in module biotite.sequence.io.genbank) get_receptor_coord() (biotite.application.autodock.VinaApp method) get_remark() (biotite.structure.io.pdb.PDBFile method) get_remarks() (biotite.structure.io.pdbqt.PDBQTFile method) get_residue_count() (in module biotite.structure) get_residue_masks() (in module biotite.structure) get_residue_positions() (in module biotite.structure) get_residue_starts() (in module biotite.structure) get_residue_starts_for() (in module biotite.structure) get_residues() (in module biotite.structure) get_score() (biotite.sequence.align.SubstitutionMatrix method) get_score_by_code() (biotite.sequence.align.SubstitutionMatrix method) get_seq_string() (biotite.sequence.io.fastq.FastqFile method) get_seqtype() (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) get_sequence() (in module biotite.sequence.io.fasta) (in module biotite.sequence.io.fastq) (in module biotite.sequence.io.genbank) (in module biotite.structure.io.pdbx) get_sequence_identity() (in module biotite.sequence.align) get_sequences() (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (in module biotite.sequence.io.fasta) (in module biotite.sequence.io.fastq) get_sequences_and_scores() (biotite.application.sra.FastqDumpApp method) get_source() (in module biotite.sequence.io.genbank) get_sse() (biotite.application.dssp.DsspApp method) get_stderr() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) get_stdout() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) get_structure() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.gro.GROFile method) (biotite.structure.io.mol.MOLFile method) (biotite.structure.io.mol.SDRecord method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.pdb.PDBFile method) (biotite.structure.io.pdbqt.PDBQTFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) (in module biotite.structure.io.mol) (in module biotite.structure.io.pdb) (in module biotite.structure.io.pdbqt) (in module biotite.structure.io.pdbx) get_symbol_frequency() (biotite.sequence.GeneralSequence method) (biotite.sequence.NucleotideSequence method) (biotite.sequence.ProteinSequence method) (biotite.sequence.Sequence method) get_symbols() (biotite.sequence.align.KmerAlphabet method) (biotite.sequence.Alphabet method) (biotite.sequence.LetterAlphabet method) (in module biotite.sequence.align) get_symmetry_mates() (biotite.structure.io.pdb.PDBFile method) (in module biotite.structure.io.pdb) get_time() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) get_version() (in module biotite.sequence.io.genbank) get_xml_response() (biotite.application.blast.BlastWebApp method) GFFFile (class in biotite.sequence.io.gff) GlycosidicBond (class in biotite.structure) GROFile (class in biotite.structure.io.gro) Grouping (class in biotite.database.rcsb) gyration_radius() (in module biotite.structure) H HARD_CLIP (biotite.sequence.align.CigarOp attribute) hbond() (in module biotite.structure) hbond_frequency() (in module biotite.structure) Header (class in biotite.structure.io.mol) HOOGSTEEN (biotite.structure.Edge attribute) I IdentityGrouping (class in biotite.database.rcsb) IdentityQuery (class in biotite.database.pubchem) INAPPLICABLE (biotite.structure.io.pdbx.MaskValue attribute) InchiKeyQuery (class in biotite.database.pubchem) InchiQuery (class in biotite.database.pubchem) IncompleteStructureWarning (class in biotite.structure) index_angle() (in module biotite.structure) index_dihedral() (in module biotite.structure) index_displacement() (in module biotite.structure) index_distance() (in module biotite.structure) infer_elements() (in module biotite.structure) insert() (biotite.sequence.io.genbank.GenBankFile method) (biotite.sequence.io.gff.GFFFile method) INSERTION (biotite.sequence.align.CigarOp attribute) INT16 (biotite.structure.io.pdbx.TypeCode attribute) INT32 (biotite.structure.io.pdbx.TypeCode attribute) INT8 (biotite.structure.io.pdbx.TypeCode attribute) IntegerPackingEncoding (class in biotite.structure.io.pdbx) IntervalQuantizationEncoding (class in biotite.structure.io.pdbx) INTRON (biotite.sequence.align.CigarOp attribute) INVALID (biotite.structure.Edge attribute) (biotite.structure.GlycosidicBond attribute) InvalidFileError (class in biotite) is_compatible_return_type() (biotite.database.rcsb.DepositGrouping method) (biotite.database.rcsb.Grouping method) (biotite.database.rcsb.IdentityGrouping method) (biotite.database.rcsb.UniprotGrouping method) is_finished() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) is_leaf() (biotite.sequence.phylo.TreeNode method) is_letter_alphabet() (biotite.sequence.align.KmerAlphabet method) (biotite.sequence.Alphabet method) (biotite.sequence.LetterAlphabet method) is_orthogonal() (in module biotite.structure) is_root() (biotite.sequence.phylo.TreeNode method) is_start_codon() (biotite.sequence.CodonTable method) is_symmetric() (biotite.sequence.align.SubstitutionMatrix method) is_valid() (biotite.sequence.GeneralSequence method) (biotite.sequence.NucleotideSequence method) (biotite.sequence.ProteinSequence method) (biotite.sequence.Sequence method) J join() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) JOINED (biotite.application.AppState attribute) K kmer_array_length() (biotite.sequence.align.KmerAlphabet method) KmerAlphabet (class in biotite.sequence.align) KmerTable (class in biotite.sequence.align) L LetterAlphabet (class in biotite.sequence) LetterPlotter (class in biotite.sequence.graphics) LetterSimilarityPlotter (class in biotite.sequence.graphics) LetterTypePlotter (class in biotite.sequence.graphics) link_type() (in module biotite.structure.info) list_assemblies() (biotite.structure.io.pdb.PDBFile method) (in module biotite.structure.io.pdb) (in module biotite.structure.io.pdbx) list_color_scheme_names() (in module biotite.sequence.graphics) list_db() (biotite.sequence.align.SubstitutionMatrix static method) load() (biotite.sequence.CodonTable static method) load_color_scheme() (in module biotite.sequence.graphics) load_sequence() (in module biotite.sequence.io) load_sequences() (in module biotite.sequence.io) load_structure() (in module biotite.structure.io) LocalApp (class in biotite.application) Location (class in biotite.sequence) Location.Defect (class in biotite.sequence) Location.Strand (class in biotite.sequence) log_evalue() (biotite.sequence.align.EValueEstimator method) log_odds_matrix() (biotite.sequence.SequenceProfile method) lowest_common_ancestor() (biotite.sequence.phylo.TreeNode method) M MafftApp (class in biotite.application.mafft) map_codon_codes() (biotite.sequence.CodonTable method) map_nucleotide() (in module biotite.structure) mask_repeats() (biotite.application.tantan.TantanApp static method) MaskValue (class in biotite.structure.io.pdbx) mass() (in module biotite.structure.info) mass_center() (in module biotite.structure) MATCH (biotite.sequence.align.CigarOp attribute) match() (biotite.sequence.align.BucketKmerTable method) (biotite.sequence.align.KmerTable method) match_kmer_selection() (biotite.sequence.align.BucketKmerTable method) (biotite.sequence.align.KmerTable method) match_table() (biotite.sequence.align.BucketKmerTable method) (biotite.sequence.align.KmerTable method) matches() (biotite.sequence.graphics.CodingPlotter method) (biotite.sequence.graphics.FeaturePlotter method) (biotite.sequence.graphics.MiscFeaturePlotter method) (biotite.sequence.graphics.PromoterPlotter method) (biotite.sequence.graphics.RBSPlotter method) (biotite.sequence.graphics.TerminatorPlotter method) merge() (biotite.structure.BondList method) Metadata (class in biotite.structure.io.mol) Metadata.Key (class in biotite.structure.io.mol) MincodeSelector (class in biotite.sequence.align) MinimizerSelector (class in biotite.sequence.align) MiscFeaturePlotter (class in biotite.sequence.graphics) MISS_LEFT (biotite.sequence.Location.Defect attribute) MISS_RIGHT (biotite.sequence.Location.Defect attribute) MISSING (biotite.structure.io.pdbx.MaskValue attribute) module biotite biotite.application biotite.application.autodock biotite.application.blast biotite.application.clustalo biotite.application.dssp biotite.application.mafft biotite.application.muscle biotite.application.sra biotite.application.tantan biotite.application.viennarna biotite.database biotite.database.entrez biotite.database.pubchem biotite.database.rcsb biotite.database.uniprot biotite.sequence biotite.sequence.align biotite.sequence.graphics biotite.sequence.io biotite.sequence.io.fasta biotite.sequence.io.fastq biotite.sequence.io.genbank biotite.sequence.io.gff biotite.sequence.phylo biotite.structure biotite.structure.graphics biotite.structure.info biotite.structure.io biotite.structure.io.dcd biotite.structure.io.gro biotite.structure.io.mol biotite.structure.io.netcdf biotite.structure.io.pdb biotite.structure.io.pdbqt biotite.structure.io.pdbx biotite.structure.io.trr biotite.structure.io.xtc molecule_iter() (in module biotite.structure) MOLFile (class in biotite.structure.io.mol) MotifQuery (class in biotite.database.rcsb) move_inside_box() (in module biotite.structure) MSAApp (class in biotite.application) MultiFile (class in biotite.sequence.io.genbank) Muscle5App (class in biotite.application.muscle) MuscleApp (class in biotite.application.muscle) N NameQuery (class in biotite.database.pubchem) NAVIEW (biotite.application.viennarna.RNAplotApp.Layout attribute) neighbor_joining() (in module biotite.sequence.phylo) NetCDFFile (class in biotite.structure.io.netcdf) NONE (biotite.sequence.Location.Defect attribute) nucleotide_names() (in module biotite.structure.info) NucleotideSequence (class in biotite.sequence) O offset_indices() (biotite.structure.BondList method) one_letter_code() (in module biotite.structure.info) orient_principal_components() (in module biotite.structure) P PADDING (biotite.sequence.align.CigarOp attribute) partial_charges() (in module biotite.structure) PDBFile (class in biotite.structure.io.pdb) PDBQTFile (class in biotite.structure.io.pdbqt) Permutation (class in biotite.sequence.align) permute() (biotite.sequence.align.FrequencyPermutation method) (biotite.sequence.align.Permutation method) (biotite.sequence.align.RandomPermutation method) plot_alignment() (in module biotite.sequence.graphics) plot_alignment_array() (in module biotite.sequence.graphics) plot_alignment_similarity_based() (in module biotite.sequence.graphics) plot_alignment_type_based() (in module biotite.sequence.graphics) plot_atoms() (in module biotite.structure.graphics) plot_ball_and_stick_model() (in module biotite.structure.graphics) plot_dendrogram() (in module biotite.sequence.graphics) plot_feature_map() (in module biotite.sequence.graphics) plot_nucleotide_secondary_structure() (in module biotite.structure.graphics) plot_plasmid_map() (in module biotite.sequence.graphics) plot_sequence_logo() (in module biotite.sequence.graphics) plot_symbol() (biotite.sequence.graphics.ArrayPlotter method) (biotite.sequence.graphics.LetterPlotter method) (biotite.sequence.graphics.LetterSimilarityPlotter method) (biotite.sequence.graphics.LetterTypePlotter method) (biotite.sequence.graphics.SymbolPlotter method) prepare_write_values() (biotite.structure.io.dcd.DCDFile class method) (biotite.structure.io.netcdf.NetCDFFile class method) (biotite.structure.io.TrajectoryFile class method) (biotite.structure.io.trr.TRRFile class method) (biotite.structure.io.xtc.XTCFile class method) PRESENT (biotite.structure.io.pdbx.MaskValue attribute) probability_matrix() (biotite.sequence.SequenceProfile method) process_read_values() (biotite.structure.io.dcd.DCDFile class method) (biotite.structure.io.netcdf.NetCDFFile class method) (biotite.structure.io.TrajectoryFile class method) (biotite.structure.io.trr.TRRFile class method) (biotite.structure.io.xtc.XTCFile class method) PromoterPlotter (class in biotite.sequence.graphics) ProteinSequence (class in biotite.sequence) pseudoknots() (in module biotite.structure) Python Enhancement Proposals PEP 8 Q QUADRUPLE (biotite.structure.BondType attribute) Query (class in biotite.database.entrez) (class in biotite.database.pubchem) (class in biotite.database.rcsb) (class in biotite.database.uniprot) R RADIAL (biotite.application.viennarna.RNAplotApp.Layout attribute) RandomPermutation (class in biotite.sequence.align) RBSPlotter (class in biotite.sequence.graphics) rdf() (in module biotite.structure) read() (biotite.File class method) (biotite.sequence.io.fasta.FastaFile class method) (biotite.sequence.io.fastq.FastqFile class method) (biotite.sequence.io.genbank.GenBankFile class method) (biotite.sequence.io.genbank.MultiFile class method) (biotite.sequence.io.gff.GFFFile class method) (biotite.structure.io.dcd.DCDFile class method) (biotite.structure.io.gro.GROFile class method) (biotite.structure.io.mol.MOLFile class method) (biotite.structure.io.mol.SDFile class method) (biotite.structure.io.netcdf.NetCDFFile class method) (biotite.structure.io.pdb.PDBFile class method) (biotite.structure.io.pdbqt.PDBQTFile class method) (biotite.structure.io.pdbx.BinaryCIFFile class method) (biotite.structure.io.pdbx.CIFFile class method) (biotite.structure.io.TrajectoryFile class method) (biotite.structure.io.trr.TRRFile class method) (biotite.structure.io.xtc.XTCFile class method) (biotite.TextFile class method) read_alignment_from_cigar() (in module biotite.sequence.align) read_iter() (biotite.sequence.io.fasta.FastaFile static method) (biotite.sequence.io.fastq.FastqFile static method) (biotite.sequence.io.genbank.GenBankFile static method) (biotite.sequence.io.genbank.MultiFile static method) (biotite.sequence.io.gff.GFFFile static method) (biotite.structure.io.dcd.DCDFile class method) (biotite.structure.io.gro.GROFile static method) (biotite.structure.io.mol.MOLFile static method) (biotite.structure.io.netcdf.NetCDFFile class method) (biotite.structure.io.pdb.PDBFile static method) (biotite.structure.io.pdbqt.PDBQTFile static method) (biotite.structure.io.TrajectoryFile class method) (biotite.structure.io.trr.TRRFile class method) (biotite.structure.io.xtc.XTCFile class method) (biotite.TextFile static method) read_iter_structure() (biotite.structure.io.dcd.DCDFile class method) (biotite.structure.io.netcdf.NetCDFFile class method) (biotite.structure.io.TrajectoryFile class method) (biotite.structure.io.trr.TRRFile class method) (biotite.structure.io.xtc.XTCFile class method) remove_aromaticity() (biotite.structure.BondList method) remove_bond() (biotite.structure.BondList method) remove_bond_order() (biotite.structure.BondList method) remove_bonds() (biotite.structure.BondList method) remove_bonds_to() (biotite.structure.BondList method) remove_pbc() (in module biotite.structure) remove_pbc_from_coord() (in module biotite.structure) remove_stops() (biotite.sequence.ProteinSequence method) remove_terminal_gaps() (in module biotite.sequence.align) repeat() (in module biotite.structure) repeat_box() (in module biotite.structure) repeat_box_coord() (in module biotite.structure) RequestError (class in biotite.database) requires_state() (in module biotite.application) residue() (in module biotite.structure.info) residue_iter() (in module biotite.structure) REVERSE (biotite.sequence.Location.Strand attribute) reverse() (biotite.sequence.GeneralSequence method) (biotite.sequence.NucleotideSequence method) (biotite.sequence.ProteinSequence method) (biotite.sequence.Sequence method) reverse_complement() (biotite.sequence.AnnotatedSequence method) rmsd() (in module biotite.structure) rmsf() (in module biotite.structure) rmspd() (in module biotite.structure) RNAalifoldApp (class in biotite.application.viennarna) RNAfoldApp (class in biotite.application.viennarna) RNAplotApp (class in biotite.application.viennarna) RNAplotApp.Layout (class in biotite.application.viennarna) RNAPUZZLER (biotite.application.viennarna.RNAplotApp.Layout attribute) RNATURTLE (biotite.application.viennarna.RNAplotApp.Layout attribute) rotate() (in module biotite.structure) rotate_about_axis() (in module biotite.structure) rotate_centered() (in module biotite.structure) RuleViolationError (class in biotite.application) run() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) RunLengthEncoding (class in biotite.structure.io.pdbx) RUNNING (biotite.application.AppState attribute) S sasa() (in module biotite.structure) save_sequence() (in module biotite.sequence.io) save_sequences() (in module biotite.sequence.io) save_structure() (in module biotite.structure.io) score() (in module biotite.sequence.align) score_matrix() (biotite.sequence.align.SubstitutionMatrix method) ScoreThresholdRule (class in biotite.sequence.align) SDFile (class in biotite.structure.io.mol) SDRecord (class in biotite.structure.io.mol) search() (in module biotite.database.entrez) (in module biotite.database.pubchem) (in module biotite.database.rcsb) (in module biotite.database.uniprot) search_options() (biotite.database.pubchem.IdentityQuery method) (biotite.database.pubchem.SimilarityQuery method) (biotite.database.pubchem.SubstructureQuery method) (biotite.database.pubchem.SuperstructureQuery method) search_type() (biotite.database.pubchem.IdentityQuery method) (biotite.database.pubchem.SimilarityQuery method) (biotite.database.pubchem.SubstructureQuery method) (biotite.database.pubchem.SuperstructureQuery method) select() (biotite.sequence.align.CachedSyncmerSelector method) (biotite.sequence.align.MincodeSelector method) (biotite.sequence.align.MinimizerSelector method) (biotite.sequence.align.SyncmerSelector method) select_from_kmers() (biotite.sequence.align.CachedSyncmerSelector method) (biotite.sequence.align.MincodeSelector method) (biotite.sequence.align.MinimizerSelector method) (biotite.sequence.align.SyncmerSelector method) Sequence (class in biotite.sequence) sequence_probability() (biotite.sequence.SequenceProfile method) sequence_score() (biotite.sequence.SequenceProfile method) SequenceProfile (class in biotite.sequence) SequenceQuery (class in biotite.database.rcsb) SerializationError (class in biotite) serialize() (biotite.structure.io.mol.Header method) (biotite.structure.io.mol.Metadata method) (biotite.structure.io.mol.Metadata.Key method) (biotite.structure.io.mol.SDFile method) (biotite.structure.io.mol.SDRecord method) (biotite.structure.io.pdbx.BinaryCIFBlock method) (biotite.structure.io.pdbx.BinaryCIFCategory method) (biotite.structure.io.pdbx.BinaryCIFColumn method) (biotite.structure.io.pdbx.BinaryCIFData method) (biotite.structure.io.pdbx.BinaryCIFFile method) (biotite.structure.io.pdbx.ByteArrayEncoding method) (biotite.structure.io.pdbx.CIFBlock method) (biotite.structure.io.pdbx.CIFCategory method) (biotite.structure.io.pdbx.CIFFile method) (biotite.structure.io.pdbx.DeltaEncoding method) (biotite.structure.io.pdbx.FixedPointEncoding method) (biotite.structure.io.pdbx.IntegerPackingEncoding method) (biotite.structure.io.pdbx.IntervalQuantizationEncoding method) (biotite.structure.io.pdbx.RunLengthEncoding method) (biotite.structure.io.pdbx.StringArrayEncoding method) set_alignment() (in module biotite.sequence.io.fasta) set_annotated_sequence() (in module biotite.sequence.io.genbank) set_annotation() (biotite.structure.AtomArray method) (biotite.structure.AtomArrayStack method) (in module biotite.sequence.io.genbank) (in module biotite.sequence.io.gff) set_api_key() (in module biotite.database.entrez) set_arguments() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) set_box() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) set_color() (biotite.sequence.graphics.LetterSimilarityPlotter method) set_component() (in module biotite.structure.io.pdbx) set_constraints() (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) set_coord() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) set_distance_matrix() (biotite.application.clustalo.ClustalOmegaApp method) set_energy_range() (biotite.application.autodock.VinaApp method) set_entrez_query() (biotite.application.blast.BlastWebApp method) set_exec_dir() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) set_exhaustiveness() (biotite.application.autodock.VinaApp method) set_field() (biotite.sequence.io.genbank.GenBankFile method) set_font_size_in_coord() (in module biotite) set_gap_penalty() (biotite.application.blast.BlastWebApp method) (biotite.application.muscle.MuscleApp method) set_guide_tree() (biotite.application.clustalo.ClustalOmegaApp method) set_in_layout() (biotite.AdaptiveFancyArrow method) set_iterations() (biotite.application.muscle.Muscle5App method) set_layout_type() (biotite.application.viennarna.RNAplotApp method) set_locus() (in module biotite.sequence.io.genbank) set_match_reward() (biotite.application.blast.BlastWebApp method) set_max_expect_value() (biotite.application.blast.BlastWebApp method) set_max_number_of_models() (biotite.application.autodock.VinaApp method) set_max_results() (biotite.application.blast.BlastWebApp method) set_mismatch_penalty() (biotite.application.blast.BlastWebApp method) set_seed() (biotite.application.autodock.VinaApp method) set_sequence() (in module biotite.sequence.io.fasta) (in module biotite.sequence.io.fastq) (in module biotite.sequence.io.genbank) set_sequences() (in module biotite.sequence.io.fasta) (in module biotite.sequence.io.fastq) set_stdin() (biotite.application.autodock.VinaApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) set_structure() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.gro.GROFile method) (biotite.structure.io.mol.MOLFile method) (biotite.structure.io.mol.SDRecord method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.pdb.PDBFile method) (biotite.structure.io.pdbqt.PDBQTFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) (in module biotite.structure.io.mol) (in module biotite.structure.io.pdb) (in module biotite.structure.io.pdbqt) (in module biotite.structure.io.pdbx) set_substitution_matrix() (biotite.application.blast.BlastWebApp method) set_temperature() (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) set_thread_number() (biotite.application.muscle.Muscle5App method) set_threshold() (biotite.application.blast.BlastWebApp method) set_time() (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) set_word_size() (biotite.application.blast.BlastWebApp method) shape() (biotite.sequence.align.SubstitutionMatrix method) similar_kmers() (biotite.sequence.align.ScoreThresholdRule method) (biotite.sequence.align.SimilarityRule method) SimilarityQuery (class in biotite.database.pubchem) SimilarityRule (class in biotite.sequence.align) SimpleQuery (class in biotite.database.entrez) (class in biotite.database.uniprot) SINGLE (biotite.structure.BondType attribute) SingleQuery (class in biotite.database.rcsb) SmilesQuery (class in biotite.database.pubchem) SOFT_CLIP (biotite.sequence.align.CigarOp attribute) Sorting (class in biotite.database.rcsb) split() (biotite.sequence.align.KmerAlphabet method) spread_chain_wise() (in module biotite.structure) spread_residue_wise() (in module biotite.structure) src_type (biotite.structure.io.pdbx.FixedPointEncoding attribute) (biotite.structure.io.pdbx.IntervalQuantizationEncoding attribute) stack() (in module biotite.structure) stack_depth() (biotite.structure.AtomArrayStack method) standardize_order() (in module biotite.structure.info) start() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) start_codons() (biotite.sequence.CodonTable method) std_nucleotide_matrix() (biotite.sequence.align.SubstitutionMatrix static method) std_protein_matrix() (biotite.sequence.align.SubstitutionMatrix static method) StringArrayEncoding (class in biotite.structure.io.pdbx) StructureQuery (class in biotite.database.rcsb) subcomponent_class() (biotite.structure.io.pdbx.BinaryCIFBlock static method) (biotite.structure.io.pdbx.BinaryCIFCategory static method) (biotite.structure.io.pdbx.BinaryCIFColumn static method) (biotite.structure.io.pdbx.BinaryCIFData static method) (biotite.structure.io.pdbx.BinaryCIFFile static method) (biotite.structure.io.pdbx.ByteArrayEncoding static method) (biotite.structure.io.pdbx.CIFBlock static method) (biotite.structure.io.pdbx.CIFCategory static method) (biotite.structure.io.pdbx.CIFColumn static method) (biotite.structure.io.pdbx.CIFData static method) (biotite.structure.io.pdbx.CIFFile static method) (biotite.structure.io.pdbx.DeltaEncoding static method) (biotite.structure.io.pdbx.FixedPointEncoding static method) (biotite.structure.io.pdbx.IntegerPackingEncoding static method) (biotite.structure.io.pdbx.IntervalQuantizationEncoding static method) (biotite.structure.io.pdbx.RunLengthEncoding static method) (biotite.structure.io.pdbx.StringArrayEncoding static method) SubstitutionMatrix (class in biotite.sequence.align) SubstructureQuery (class in biotite.database.pubchem) SUGAR (biotite.structure.Edge attribute) supercomponent_class() (biotite.structure.io.pdbx.BinaryCIFBlock static method) (biotite.structure.io.pdbx.BinaryCIFCategory static method) (biotite.structure.io.pdbx.BinaryCIFColumn static method) (biotite.structure.io.pdbx.BinaryCIFData static method) (biotite.structure.io.pdbx.BinaryCIFFile static method) (biotite.structure.io.pdbx.ByteArrayEncoding static method) (biotite.structure.io.pdbx.CIFBlock static method) (biotite.structure.io.pdbx.CIFCategory static method) (biotite.structure.io.pdbx.CIFColumn static method) (biotite.structure.io.pdbx.CIFData static method) (biotite.structure.io.pdbx.CIFFile static method) (biotite.structure.io.pdbx.DeltaEncoding static method) (biotite.structure.io.pdbx.FixedPointEncoding static method) (biotite.structure.io.pdbx.IntegerPackingEncoding static method) (biotite.structure.io.pdbx.IntervalQuantizationEncoding static method) (biotite.structure.io.pdbx.RunLengthEncoding static method) (biotite.structure.io.pdbx.StringArrayEncoding static method) superimpose() (in module biotite.structure) superimpose_homologs() (in module biotite.structure) superimpose_without_outliers() (in module biotite.structure) SuperstructureQuery (class in biotite.database.pubchem) supports_custom_nucleotide_matrix() (biotite.application.clustalo.ClustalOmegaApp static method) (biotite.application.mafft.MafftApp static method) (biotite.application.MSAApp static method) (biotite.application.muscle.Muscle5App static method) (biotite.application.muscle.MuscleApp static method) supports_custom_protein_matrix() (biotite.application.clustalo.ClustalOmegaApp static method) (biotite.application.mafft.MafftApp static method) (biotite.application.MSAApp static method) (biotite.application.muscle.Muscle5App static method) (biotite.application.muscle.MuscleApp static method) supports_nucleotide() (biotite.application.clustalo.ClustalOmegaApp static method) (biotite.application.mafft.MafftApp static method) (biotite.application.MSAApp static method) (biotite.application.muscle.Muscle5App static method) (biotite.application.muscle.MuscleApp static method) supports_protein() (biotite.application.clustalo.ClustalOmegaApp static method) (biotite.application.mafft.MafftApp static method) (biotite.application.MSAApp static method) (biotite.application.muscle.Muscle5App static method) (biotite.application.muscle.MuscleApp static method) SymbolPlotter (class in biotite.sequence.graphics) SyncmerSelector (class in biotite.sequence.align) T table_names() (biotite.sequence.CodonTable static method) TantanApp (class in biotite.application.tantan) TerminatorPlotter (class in biotite.sequence.graphics) TextFile (class in biotite) ThrottleStatus (class in biotite.database.pubchem) TimeoutError (class in biotite.application) to_cigar_symbol() (biotite.sequence.align.CigarOp method) to_consensus() (biotite.sequence.SequenceProfile method) to_dtype() (biotite.structure.io.pdbx.TypeCode method) to_newick() (biotite.sequence.phylo.Tree method) (biotite.sequence.phylo.TreeNode method) to_sequence() (in module biotite.structure) trace_from_strings() (biotite.application.blast.BlastAlignment static method) (biotite.sequence.align.Alignment static method) traj_type() (biotite.structure.io.dcd.DCDFile class method) (biotite.structure.io.netcdf.NetCDFFile class method) (biotite.structure.io.TrajectoryFile class method) (biotite.structure.io.trr.TRRFile class method) (biotite.structure.io.xtc.XTCFile class method) TrajectoryFile (class in biotite.structure.io) TRANS (biotite.structure.GlycosidicBond attribute) translate() (biotite.sequence.NucleotideSequence method) (in module biotite.structure) transpose() (biotite.sequence.align.SubstitutionMatrix method) Tree (class in biotite.sequence.phylo) TreeError (class in biotite.sequence.phylo) TreeNode (class in biotite.sequence.phylo) TRIPLE (biotite.structure.BondType attribute) TRRFile (class in biotite.structure.io.trr) TypeCode (class in biotite.structure.io.pdbx) U UINT16 (biotite.structure.io.pdbx.TypeCode attribute) UINT32 (biotite.structure.io.pdbx.TypeCode attribute) UINT8 (biotite.structure.io.pdbx.TypeCode attribute) unambiguous_alphabet() (biotite.sequence.NucleotideSequence static method) UnexpectedStructureWarning (class in biotite.structure) UniprotGrouping (class in biotite.database.rcsb) unitcell_from_vectors() (in module biotite.structure) UNK_LOC (biotite.sequence.Location.Defect attribute) upgma() (in module biotite.sequence.phylo) use_super5() (biotite.application.muscle.Muscle5App method) V vdw_radius_protor() (in module biotite.structure.info) vdw_radius_single() (in module biotite.structure.info) vectors_from_unitcell() (in module biotite.structure) VersionError (class in biotite.application) VinaApp (class in biotite.application.autodock) violate_rule() (biotite.application.blast.BlastWebApp method) (biotite.application.WebApp method) W wait_if_busy() (biotite.database.pubchem.ThrottleStatus method) wait_interval() (biotite.application.Application method) (biotite.application.autodock.VinaApp method) (biotite.application.blast.BlastWebApp method) (biotite.application.clustalo.ClustalOmegaApp method) (biotite.application.dssp.DsspApp method) (biotite.application.LocalApp method) (biotite.application.mafft.MafftApp method) (biotite.application.MSAApp method) (biotite.application.muscle.Muscle5App method) (biotite.application.muscle.MuscleApp method) (biotite.application.sra.FastaDumpApp method) (biotite.application.sra.FastqDumpApp method) (biotite.application.tantan.TantanApp method) (biotite.application.viennarna.RNAalifoldApp method) (biotite.application.viennarna.RNAfoldApp method) (biotite.application.viennarna.RNAplotApp method) (biotite.application.WebApp method) WATSON_CRICK (biotite.structure.Edge attribute) WebApp (class in biotite.application) with_codon_mappings() (biotite.sequence.CodonTable method) with_start_codons() (biotite.sequence.CodonTable method) without_aromaticity() (biotite.structure.BondType method) write() (biotite.File method) (biotite.sequence.io.fasta.FastaFile method) (biotite.sequence.io.fastq.FastqFile method) (biotite.sequence.io.genbank.GenBankFile method) (biotite.sequence.io.genbank.MultiFile method) (biotite.sequence.io.gff.GFFFile method) (biotite.structure.io.dcd.DCDFile method) (biotite.structure.io.gro.GROFile method) (biotite.structure.io.mol.MOLFile method) (biotite.structure.io.mol.SDFile method) (biotite.structure.io.netcdf.NetCDFFile method) (biotite.structure.io.pdb.PDBFile method) (biotite.structure.io.pdbqt.PDBQTFile method) (biotite.structure.io.pdbx.BinaryCIFFile method) (biotite.structure.io.pdbx.CIFFile method) (biotite.structure.io.TrajectoryFile method) (biotite.structure.io.trr.TRRFile method) (biotite.structure.io.xtc.XTCFile method) (biotite.TextFile method) write_alignment_to_cigar() (in module biotite.sequence.align) write_iter() (biotite.sequence.io.fasta.FastaFile static method) (biotite.sequence.io.fastq.FastqFile static method) (biotite.sequence.io.genbank.GenBankFile static method) (biotite.sequence.io.genbank.MultiFile static method) (biotite.sequence.io.gff.GFFFile static method) (biotite.structure.io.dcd.DCDFile class method) (biotite.structure.io.gro.GROFile static method) (biotite.structure.io.mol.MOLFile static method) (biotite.structure.io.netcdf.NetCDFFile class method) (biotite.structure.io.pdb.PDBFile static method) (biotite.structure.io.pdbqt.PDBQTFile static method) (biotite.structure.io.TrajectoryFile class method) (biotite.structure.io.trr.TRRFile class method) (biotite.structure.io.xtc.XTCFile class method) (biotite.TextFile static method) X XTCFile (class in biotite.structure.io.xtc)
