Releases
v0.27.0
Changelog
Additions
Added interface to AutoDock Vina
application.autodock.VinaApp
uses vina
executable to perform
docking of ligand to a receptor molecule
Uses new structure.io.pdbqt.PDBQTFile
class for writing input for
and reading output from vina
An MGLTools installation is not necessary
By default the receptor is handled as rigid structure, however,
flexible side chains can be defined
Added modular system for fast k-mer based sequence searches/mappings
sequence.align.KmerAlphabet
encodes a sequence.Sequence
into
k-mers
sequence.align.KmerTable
is able to find k-mer matches between
sequence in an efficient manner
sequence.align.SimilarityRule
allows matching similar instead of
exact k-mer matches via a sequence.align.KmerTable
sequence.align.align_banded()
performs a heuristic local or
semi-global sequence alignment within a defined diagonal band
Added sequence.align.remove_terminal_gaps()
function
Added application.sra.FastqDumpApp.get_file_paths()
method
Increased performance of sequence.Sequence.get_symbol_frequency()
Increased performance of sequence.NucleotideSequence.complement()
sequence.Sequence.reverse()
can optionally create an array view
instead of a copy
Changes
application.sra.FastqDumpApp.get_file_paths()
only parses
downloaded PDBQT files, if required
Running pytest automatically recompiles changed Cython source code
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