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

application.sra.FastqDumpApp.get_file_paths() only parses
downloaded PDBQT files, if required
Running pytest automatically recompiles changed Cython source code