This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has
also been tested on PyPy3.7 v7.3.5.
Functions read, parse, and write were added to Bio.Align to
read and write Alignment objects. String formatting and printing output
of Alignment objects from Bio.Align were changed to support these new
functions. To obtain a string showing the aligned sequence with the appropriate
gap characters (as previously shown when calling format on an alignment),
use alignment[i], where alignment is an Alignment object and i
is the index of the aligned sequence.
Because dict retains the item order by default since Python3.6, all instances
of collections.OrderedDict have been replaced by either standard dict
or where appropriate by collections.defaultsdict.
Robert Miller has updated the Bio.PDB.internal_coords module to
make better use of Numpy for lossless structure assembly from dihedral
angles and related internal coordinates. In addition to speeding the
assembly step by ~30%, this adds distance plot support (including
re-generating structures from distance plot data), coordinate space
transforms for superimposing residues and their environments, a
per-chain all-atom array for Atom coordinates, and optional default
values for all internal coordinates. The internal coordinates module
continues to support extracting dihedral angle, bond angle and bond
length (internal coordinates) data, reading/writing structure files of
internal coordinates, and OpenSCAD output of structures for 3D CAD/3D
printing work.
The Bio.motifs.jaspar.db now returns tf_family and tf_class as a
string array since the JASPAR 2018 release.
The Local Composition Complexity functions from Bio.SeqUtils now uses
base 4 log instead of 2 as stated in the original reference Konopka (2005),
Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260
Append mode is now supported in Bio.bgzf (and a bug parsing blocked GZIP
files with an internal empty block fixed).
The experimental warning was dropped from Bio.phenotype (which was new in
Biopython 1.67).
Sequences now have a defined attribute that returns a boolean indicating
if the underlying data is defined or not.
The Bio.PDB module now includes a structural alignment module, using the
combinatorial extension algorithm of Shindyalov and Bourne, commonly known as
CEAlign. The module allows for two structures to be aligned based solely on
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dependabot[bot]
commented
1 year ago
Bumps biopython from 1.79 to 1.80.
Changelog
Sourced from biopython's changelog.
... (truncated)
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