Releases: biotite-dev/biotite
Releases · biotite-dev/biotite
Biotite 0.36.1
Biotite 0.36.0
Changelog
Additions
- Added Python 3.11 build
- Better support for macromolecular assemblies and symmetry mates (#450)
biotite.structure.io.pdb
andbiotite.structure.io.mmtf
now support parsing of assemblies vialist_assemblies()
andget_assembly()
biotite.structure.io.pdb
is able to parse all atoms within a single unit cell viaget_symmetry_mates()
- Added
structure.rmspd()
to compute the root-mean-square-pairwise-deviation- This is a method to determine deviations between to models without the need of prior structure superimposition
- Refactored
structure.annotate_sse()
(#448)- Higher performance due to more vectorization
- Multiple chains can be processed at once
- More granular macromolecule filters in
structure
subpackage (#436)- Added
filter_peptide_backbone()
andfilter_phosphate_backbone()
to filter backbone atoms of proteins and nucleotides, respectively - Added
filter_linear_bond_continuity()
that filters atoms that are within distance boundaries to the next atom - Added
filter_polymer()
that filters biomacromolecules of the given type (peptide, nucleotide, carbohydrate) and minimum length
- Added
- More integrity checks in
structure
subpackage (#436)check_linear_continuity()
gives positions in a structure where atoms are not within distance boundaries to the next atomcheck_backbone_continuity()
does the same exclusively for peptide/nucleotide backbone atoms
- Added
sequence.common_alphabet()
to determine theAlphabet
from a list of alphabets that extends all other alphabets from this list (#446) sequence.phylo.Tree.to_newick()
andsequence.phylo.TreeNode.to_newick()
allow rounding of distance labels (#439)application.TantanApp
is able to process multiple sequences in a single call (#446)- This significantly improves the performance especially for short sequences
Changes
structure.filter_backbone()
is deprecated and replaced byfilter_peptide_backbone()
(#436)structure.check_bond_continuity()
is deprecated and replaced bycheck_backbone_continuity()
(#436)- Deprecated
chain_id
parameter instructure.annotate_sse()
, multiple chains can now be processed at once (#448)
Fixes
structure.CellList
accepts empty query coordinates inget_atoms()
andget_atoms_in_cells()
(#448)- Fixed padding of
CRYST1
records to 80 instead of 70 characters (#453) - Fixed issue, where
application.dssp.DSSPApp
did not give correct number of secondary structure elements for multi-chain structures (#444) - Resolved
MemoryError
instructure.repeat_box()
(#450)
Biotite 0.35.0
Changelog
Additions
- Support stack-wise iteration over trajectory files (#420)
- Support
Path
objects inFile.read()
- Improved filters for different types of residues in structure
subpackage
(#425)filter_amino_acids()
now also filters for non-canonical amino acidsfilter_nucleotides()
uses an updated list of nucleotides- New
filter_carbohydrates()
filters for saccharides filter_canonical_amino_acids()
andfilter_canonical_nucleotides()
filter the respective canonical residues- New
structure.info.carbohydrate_names()
andstructure.info.amino_acid_names()
give a list of residue names considered as carbohydrates and amino acids, respectively
application.LocalApp
now supports input to STDIN- Improved ViennaRNA interfaces (#435)
- Added
application.viennarna.RNAalifoldApp
interface to RNAalifold - Secondary structure constraints can be given to
application.viennarna.RNAfoldApp
andapplication.viennarna.RNAalifoldApp
- Added
Changes
- The residues that are recognized by
structure.filter_amino_acids()
have changed (see above) - Deprecated
application.viennarna.RNAfoldApp.get_mfe()
and replaced it byapplication.viennarna.RNAfoldApp.get_free_energy()
Fixes
- Support PDB format dialect with inverted charge column (
X+
instead of+X
)
instructure.io.PDBFile
(#421) - Fixed erroneous atom parsing in
strutcure.io.mmtf.MMTFFile
, if an MMTF file
has multiple differentgroupType
entries for the same residue name and the same number of atoms (#426) - Fixed angle condition in
structure.base_stacking()
(#432) - Fixed
TypeError
indatabase.muscle.Muscle5App
- Fixed
bond_line_style
parameter instructure.graphics.plot_secondary_structure()
- Fixed error in
pseudoknots()
andbase_pairs_from_dot_bracket()
in cases the secondary structure had no base pairs - Update identification of error messages from server in
database.entrez.fetch()
Biotite 0.34.1
Biotite 0.34.0
Changelog
Additions
- Support for new RCSB search API (#408)
- Added
case_sensitive
parameter indatabase.rcsb.FieldQuery
- Added
structure.info.mass()
support deuteriumstructure.connect_via_distances()
can connect atoms over periodic boundaries- Added more chain-level utilities consistent with residue-level utilities
structure.apply_chain_wise()
structure.spread_chain_wise()
structure.get_chain_masks()
structure.get_chain_starts_for()
structure.get_chain_positions()
structure.superimpose()
supports also pure coordinates
Changes
structure.hbond()
uses an associatedstructure.BondList
to find hydrogen atoms to potential hydrogen bond donors- Lines depicting bonds in
structure.graphics.plot_atoms()
andstructure.graphics.plot_ball_and_stick_model()
use rounded tips
Fixes
- Fixed
structure.io.pdbx.get_assembly
missing chains in some structures (#387) - Added a more meaningful error, if Matplotlib is required, but not installed (#302)
- Added more descriptive error, if a
structure.io.pdb.PDBFile
has erroneous atom IDs (#379) structure.io.pdb.PDBFile
pads lines always to 80 characters- Allow empty attribute string in
sequence.io.GFFFile
- Fixed wrong similarity scores, if a
sequence.align.SubstitutionMatrix
with two different alphabets is read from string or file - Fixed
application.mafft.MafftApp
runs for more than 10 sequences.
Biotite 0.33.0
Changelog
Additions
- Added
application.muscle.Muscle5App
to support the changed CLI of Muscle 5 - Added
structure.orient_principal_components()
to orient atom coordinates
to the given axes biotite.structure.io.pdbx.get_structure()
useslabel_xxx
orauth_xxx
field as fallback, if the respective other one is not available- Added
default_bond_type
parameter to
biotite.structure.io.write_structure_to_ctab()
and
biotite.structure.connect_via_distances
to allow the user to change the
BondType
in the generatedBondList
Fixes
sequence.io.gff.GFFFile.read()
is now able to read GFF records with trailing
tabs- Fixed
DeprecationWarning
instructure.align_vectors()
(#295) - Fixed alignment in atom name column in
structure.io.pdb.PDBFile.write()
- Fixed error handling in
structure.index_xxx()
functions, if invalid input
shape is given - Ensured quoted values in looped categories will not be truncated in
structure.io.pdbx.PDBxFile.set_category()
Biotite 0.32.0
Changelog
Additions
- Add Python 3.10 build
- Add
writer_iter()
to someFile
classes- Allows entry-wise writing into a file to reduce memory consumption, as
there is no longer the need to keep the entire file content in memory - Implemented for
sequence.io.FastaFile
,sequence.io.FastqFile
and all
classes inheriting fromstructure.io.TrajectoryFile
- Allows entry-wise writing into a file to reduce memory consumption, as
- Add
symbol_spacing
parameter tosequence.graphics.plot_alignment
- If the parameter is given, a small gap is introduced every n
symbols in the alignment - Also added to
sequence.graphics.plot_alignment_similarity_based
and
sequence.graphics.plot_alignment_types_based
- If the parameter is given, a small gap is introduced every n
Changes
- Python 3.7 builds are discontinued
Fixes
- Now the simulation time for each frame is returned in
structure.io.NetCDFFile
, previously it was alwaysNone
Biotite 0.31.0
Changelog
Additions
- New functionalities for
sequence.SequenceProfile
- Added method
probability_matrix()
to compute the symbol probabilities
from total frequencies - Added method
log_odds_matrix()
to calculate a position weight matrix - Added methods
sequence_probability()
andsequence_score()
to assess the
adherence of a given sequence to a profile
- Added method
- New functionalities for
structure.BondList
- New bond type
structure.BondType.AROMATIC_TRIPLE
to support triple bonds
in aromatic systems - Added
structure.BondList.without_aromaticity()
to convert bonds with
structure.BondType.AROMATIC_<order>
tostructure.BondType.<order>
- New bond type
- Added
structure.info.bond_order()
- Used to get the
structure.BondType
of the bond between two atoms in a
residue - Replaces
structure.info.bond_order()
- Initial loading of bond dataset is much faster
- Used to get the
Changes
- Deprecated
structure.info.bond_order()
Fixes
- Fixed
structure.io.pdb.PDBFile.get_structure()
raising an exception,
if the PDB file contains an invalidCRYST1
record, now a warning is printed - Fixed
CONECT
records written bystructure.io.pdb.PDBFile.set_structure()
- Previously, an empty second
CONECT
record was created, if a atom has 4
bond partners
- Previously, an empty second
- Fixed installation of Biotite source distribution with Python 3.10 (#356)
- Fixed running
application.muscle.MuscleApp
with nucleotide sequences
Biotite 0.30.0
Changelog
Changes
sequence.graphics.plot_sequence_logo()
requires now a
sequence.SequenceProfile
, usage ofsequence.align.Alignment
still works,
but is deprecateddatabase.rcsb.FieldQuery
has now an optionalmolecular_definition
parameter to allow searches in molecule related fields.
Fixes
- The new RCSB search API is now supported (#347)
- More than two
database.rcsb.Query
objects can be combined with logical
operators application.blast.BlastWebApp
now also reports hit sequences containing
selenocysteine without errors (#344)Atom
,AtomArray
andAtomArrayStack
can be unpickled (#349)sequence.graphics.plot_sequence_logo()
supports now all Matplotlib backends
(#345)
Biotite 0.29.0
Changelog
Additions
- Extended functionalities for homology searches
- Added
application.tantan.TantanApp
for sequence repeat masking with
Tantan
sequence.align.KmerAlphabet
andsequence.align.KmerTable
support spaced
k-mers- Added
sequence.align.local_gapped()
andsequence.align.local_ungapped()
for aligning sequences locally with X-drop heuristic - Added
EValueEstimator
for calculation of expect values (E-values)
from alignment scores - Increased performance of
sequence.LetterAlphabet.extends()
- Added
- Added
sequence.SequenceProfile
for representing sequence profiles by means
of a symbol frequency tablesequence.SequenceProfile.from_alignment()
creates a profile from an
alignmentsequence.SequenceProfile.to_consenus()
creates a consensus sequence
- Increased performance of
sequence.align.get_codes()
and
sequence.align.get_symbols()
- Bonds can be read from and written to
CONECT
records in
structure.io.pdb.PDBFile
(#329)
Changes
- Documentation now uses sphinxcontrib-bibtex for citations
- Citations include DOI with link to publication