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.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
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
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
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
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.fasta
FastaFile
get_alignment
get_sequence
get_sequences
set_alignment
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
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
displacement
index_displacement
distance
index_distance
angle
index_angle
dihedral
index_dihedral
centroid
mass_center
gyration_radius
rdf
translate
rotate
rotate_centered
rotate_about_axis
align_vectors
orient_principal_components
superimpose
superimpose_without_outliers
superimpose_homologs
superimpose_structural_homologs
AffineTransformation
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_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
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_residue_count
residue_iter
get_chain_starts
apply_chain_wise
spread_chain_wise
get_chain_masks
get_chain_starts_for
get_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
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
find_aromatic_rings
find_stacking_interactions
PiStacking
BadStructureError
CellList
IncompleteStructureWarning
UnexpectedStructureWarning
coord
to_sequence
biotite.structure.alphabet
I3DSequence
ProteinBlocksSequence
to_3di
to_protein_blocks
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
full_name
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
get_assembly
get_model_count
get_symmetry_mates
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: Exception
Exception
