Section Navigation
biotite
File
TextFile
plot_scaled_text
AdaptiveFancyArrow
Copyable
DeserializationError
InvalidFileError
SerializationError
set_font_size_in_coord
biotite.application
Application
WebApp
LocalApp
MSAApp
AppState
AppStateError
RuleViolationError
TimeoutError
VersionError
requires_state
biotite.application.autodock
VinaApp
biotite.application.blast
BlastAlignment
BlastWebApp
biotite.application.clustalo
ClustalOmegaApp
biotite.application.dssp
DsspApp
biotite.application.mafft
MafftApp
biotite.application.muscle
Muscle5App
MuscleApp
biotite.application.sra
FastaDumpApp
FastqDumpApp
biotite.application.tantan
TantanApp
biotite.application.viennarna
RNAalifoldApp
RNAfoldApp
RNAplotApp
biotite.application_v2
CLIArgument
CLIFlag
CLIOption
CancelledError
CommandSetup
CompositeFuture
Future
LocalProcessFuture
MSAInput
PostprocessFuture
command
resolve_gap_penalty
biotite.application_v2.autodock
VinaResult
biotite.application_v2.clustalo
ClustalOmegaResult
biotite.application_v2.dssp
biotite.application_v2.mafft
MafftResult
biotite.application_v2.mmseqs
AlignmentDatabase
AlignmentFormatMode
AlignmentMode
ClusterDatabase
ClusterMode
CoverageMode
Database
DatabaseType
FoldseekApp
MMseqsApp
MSADatabase
MSAFormatMode
ProfileDatabase
ProfileMatchMode
SearchType
SequenceDatabase
SequenceIdentityMode
StructureAlignmentType
UnpackNameMode
VerbosityLevel
create_database_from_msa
create_database_from_sequences
create_database_from_structures
get_alignment_table
get_alignments
get_clusters
get_matrix_from_profile
get_msa_from_database
get_multimer_report
get_sequences_from_database
link_to_ss_database
biotite.application_v2.muscle
Muscle3App
Muscle3Result
Muscle5Result
biotite.application_v2.sra
FastaResult
FastqResult
PrefetchApp
PrefetchDirectory
biotite.application_v2.tantan
biotite.application_v2.viennarna
FoldApp
SuboptApp
PKplexApp
LfoldApp
CofoldApp
MultifoldApp
DuplexApp
PlexApp
AlifoldApp
LalifoldApp
AliduplexApp
EvalApp
PlotApp
FoldedRNA
CofoldedRNA
FoldedAlignment
CofoldedAlignment
biotite.database
RequestError
biotite.database.afdb
fetch
biotite.database.entrez
Query
CompositeQuery
SimpleQuery
get_database_name
search
fetch_single_file
set_api_key
get_api_key
biotite.database.pubchem
NameQuery
SmilesQuery
InchiQuery
InchiKeyQuery
FormulaQuery
SuperstructureQuery
SubstructureQuery
SimilarityQuery
IdentityQuery
fetch_property
ThrottleStatus
biotite.database.rcsb
SingleQuery
BasicQuery
FieldQuery
SequenceQuery
MotifQuery
StructureQuery
Sorting
Grouping
DepositGrouping
IdentityGrouping
UniprotGrouping
count
biotite.database.uniprot
biotite.interface
LossyConversionWarning
biotite.interface.openmm
from_context
from_state
from_states
from_topology
require_package
to_system
to_topology
biotite.interface.pymol
launch_pymol
launch_interactive_pymol
reset
setup_parameters
DuplicatePyMOLError
PyMOLObject
to_model
from_model
draw_cgo
get_cylinder_cgo
get_cone_cgo
get_sphere_cgo
get_point_cgo
get_line_cgo
get_multiline_cgo
draw_arrows
draw_box
show
play
Any
ModifiedObjectError
NonexistentObjectError
RenderError
biotite.interface.rdkit
from_mol
to_mol
biotite.sequence
Sequence
NucleotideSequence
ProteinSequence
GeneralSequence
Alphabet
LetterAlphabet
AlphabetMapper
AlphabetError
common_alphabet
Feature
Location
Annotation
AnnotatedSequence
find_subsequence
find_symbol
find_symbol_first
find_symbol_last
CodonTable
PositionalSequence
PurePositionalSequence
SequenceProfile
biotite.sequence.align
SubstitutionMatrix
align_ungapped
align_optimal
SeedExtension
align_local_ungapped
align_local_gapped
align_banded
align_multiple
Alignment
get_codes
get_symbols
get_sequence_identity
get_pairwise_sequence_identity
score
KmerAlphabet
KmerTable
BucketKmerTable
SimilarityRule
ScoreThresholdRule
bucket_number
MinimizerSelector
SyncmerSelector
CachedSyncmerSelector
MincodeSelector
Permutation
RandomPermutation
FrequencyPermutation
CigarOp
read_alignment_from_cigar
write_alignment_to_cigar
EValueEstimator
Selector
find_terminal_gaps
remove_gaps
remove_terminal_gaps
biotite.sequence.graphics
plot_feature_map
plot_sequence_logo
plot_alignment
plot_alignment_similarity_based
plot_alignment_type_based
plot_dendrogram
SymbolPlotter
LetterPlotter
LetterSimilarityPlotter
LetterTypePlotter
FeaturePlotter
CodingPlotter
PromoterPlotter
TerminatorPlotter
RBSPlotter
MiscFeaturePlotter
load_color_scheme
get_color_scheme
list_color_scheme_names
ArrayPlotter
plot_alignment_array
plot_plasmid_map
biotite.sequence.io
load_sequence
load_sequences
save_sequence
save_sequences
biotite.sequence.io.clustal
ClustalFile
get_alignment
set_alignment
biotite.sequence.io.fasta
FastaFile
get_a3m_alignments
get_sequence
get_sequences
set_a3m_alignments
set_sequence
set_sequences
biotite.sequence.io.fastq
FastqFile
biotite.sequence.io.genbank
GenBankFile
MultiFile
get_accession
get_annotated_sequence
get_annotation
get_db_link
get_definition
get_gi
get_locus
get_raw_sequence
get_source
get_version
set_annotated_sequence
set_annotation
set_locus
biotite.sequence.io.gff
GFFFile
biotite.sequence.phylo
Tree
TreeNode
TreeError
as_binary
upgma
neighbor_joining
biotite.structure
Atom
AtomArray
AtomArrayStack
concatenate
array
stack
repeat
from_template
space_group_transforms
vectors_from_unitcell
unitcell_from_vectors
box_volume
repeat_box
repeat_box_coord
move_inside_box
remove_pbc
remove_pbc_from_coord
coord_to_fraction
fraction_to_coord
is_orthogonal
BondList
BondType
connect_via_residue_names
connect_via_distances
find_connected
find_rotatable_bonds
infer_bond_types
displacement
index_displacement
distance
index_distance
angle
index_angle
dihedral
index_dihedral
centroid
mass_center
gyration_radius
rdf
AffineTransformation
translate
rotate
rotate_centered
rotate_about_axis
align_vectors
orient_principal_components
superimpose
superimpose_without_outliers
superimpose_homologs
superimpose_structural_homologs
filter_canonical_nucleotides
filter_nucleotides
filter_canonical_amino_acids
filter_amino_acids
filter_carbohydrates
filter_peptide_backbone
filter_phosphate_backbone
filter_linear_bond_continuity
filter_polymer
filter_solvent
filter_monoatomic_ions
filter_heavy
filter_intersection
filter_first_altloc
filter_highest_occupancy_altloc
check_atom_id_continuity
check_res_id_continuity
check_backbone_continuity
check_duplicate_atoms
check_linear_continuity
check_in_box
create_continuous_res_ids
infer_elements
create_atom_names
get_residue_starts
get_residues
apply_residue_wise
spread_residue_wise
get_residue_masks
get_residue_starts_for
get_residue_positions
get_all_residue_positions
get_residue_count
residue_iter
get_atom_name_indices
get_chain_starts
apply_chain_wise
spread_chain_wise
get_chain_masks
get_chain_starts_for
get_chain_positions
get_all_chain_positions
get_chains
get_chain_count
chain_iter
get_molecule_indices
get_molecule_masks
molecule_iter
average
rmsd
rmspd
rmsf
lddt
tm_score
sasa
hbond
hbond_frequency
partial_charges
density
dihedral_backbone
dihedral_side_chain
annotate_sse
Edge
GlycosidicBond
map_nucleotide
base_pairs
base_stacking
pseudoknots
base_pairs_edge
base_pairs_glycosidic_bond
dot_bracket
dot_bracket_from_structure
base_pairs_from_dot_bracket
nucleotide_dihedral_backbone
nucleotide_dihedral_side_chain
find_aromatic_rings
find_stacking_interactions
find_pi_cation_interactions
PiStacking
BadStructureError
CellList
IncompleteStructureWarning
InconsistentBondTypeWarning
UnexpectedStructureWarning
coord
set_print_limits
to_sequence
biotite.structure.alphabet
I3DSequence
ProteinBlocksSequence
ClepapsSequence
to_3di
to_protein_blocks
to_clepaps
biotite.structure.graphics
plot_atoms
plot_ball_and_stick_model
plot_nucleotide_secondary_structure
biotite.structure.info
residue
bond_type
bonds_in_residue
amino_acid_names
nucleotide_names
carbohydrate_names
vdw_radius_single
vdw_radius_protor
get_ccd
get_from_ccd
set_ccd_path
all_residues
atomic_number
full_name
ion_names
link_type
mass
one_letter_code
standardize_order
biotite.structure.io
TrajectoryFile
load_structure
save_structure
biotite.structure.io.dcd
DCDFile
biotite.structure.io.gro
GROFile
biotite.structure.io.mol
Header
MOLFile
Metadata
SDFile
SDRecord
get_structure
set_structure
biotite.structure.io.netcdf
NetCDFFile
biotite.structure.io.pdb
PDBFile
SpaceGroupInfo
get_assembly
get_model_count
get_symmetry_mates
get_unit_cell
list_assemblies
biotite.structure.io.pdbqt
PDBQTFile
biotite.structure.io.pdbx
get_component
set_component
get_sse
CIFFile
CIFBlock
CIFCategory
CIFColumn
CIFData
BinaryCIFFile
BinaryCIFBlock
BinaryCIFCategory
BinaryCIFColumn
BinaryCIFData
ByteArrayEncoding
FixedPointEncoding
IntervalQuantizationEncoding
RunLengthEncoding
DeltaEncoding
IntegerPackingEncoding
StringArrayEncoding
TypeCode
MaskValue
compress
biotite.structure.io.trr
TRRFile
biotite.structure.io.xtc
XTCFile
Bases: Error
Error
The Future was cancelled.
