Changelog
Additions
- Support for Numpy
2.0
(#529)1.x
versions are still compatible.
- Trajectory file interfaces in
structure.io
do not requiremdtraj
as extra dependency anymore (#627).- Instead the much smaller
biotraj
package is now a mandatory dependency of Biotite.
- Instead the much smaller
- New documentation website (#552).
- Improved performance of multiple auxiliary methods in
sequence.Alphabet
.
Changes
sequence.graphics
usesflower
color scheme as default instead ofrainbow
. (#617).- It represents similarity of amino acids better.
structure.io.pdbx.get_sequence()
returns dict mapping chain IDs to sequences (#611).- Previously deprecated functionality was removed. (#624)
read()
instance method ofFile
classes: Useread()
class method instead.temp_file()
andtemp_dir()
: Use corresponding functionality fromtempfile
instead.application.viennarna.RNAfoldApp.get_mfe()
: Useapplication.viennarna.RNAfoldApp.get_free_energy()
instead.atom_mask
parameter ofstructure.connect_via_distances()
andstructure.connect_via_residue_names()
: Filter the atoms before instead.- Support for
Alignment
objects as input tosequence.graphics.plot_sequence_logo()
: Input aProfile
instead. sequence.io.fastq.FastqFile.get_sequence()
: Usesequence.io.fastq.FastqFile.get_seq_string()
orsequence.io.fastq.get_sequence()
instead.structure.filter_backbone()
: Usestructure.filter_peptide_backbone()
instead.structure.check_id_continuity()
: Usestructure.check_res_id_continuity()
instead.structure.check_bond_continuity()
: Usestructure.check_backbone_continuity()
instead.structure.renumber_atom_ids()
: Set theatom_id
annotation withnumpy.arange()
instead.structure.renumber_res_ids()
: Usestructure.create_continuous_res_ids()
instead.chain_id
parameter ofstructure.annotate_sse()
: Filter theAtomArray
before instead.structure.superimpose_apply()
: Usestructure.AffineTransformation.apply()
instead.structure.io.read_structure_from_ctab()
andstructure.io.write_structure_to_ctab()
: Use corresponding functions fromstructure.io.mol
.structure.io.mol.MolFile.get_header()
andstructure.io.mol.MolFile.set_header()
: Use theheader
attribute instead.structure.io.npz
: Internal.npz
format is not used anymore.structure.io.pdbx.PDBxFile
: Usestructure.io.pdbx.CIFFile
instead.structure.io.mmtf
:.mmtf
was superseded by.bcif
accessible withstructure.io.pdbx.BinaryCIFFile
.