Changelog

Additions

• Utility functions for sequence.align.Alignment objects
  • Read/write functionality for alignments from FASTA files
  • get_codes(), get_symbols(), get_sequence_identity(), score()

Changes

• Renamed structure.AdjacencyMap to structure.CellList
• Renamed sequence.align.simple_score() to sequence.align.align_ungapped()
  • By default the new function returns an alignment, optionally only the score is returned
• Slightly increased performance of structure.sasa()
• Default point_number in structure.sasa() increased to 1000
• Boolean mask replaces the inflexible ca_only parameter in structure.superimpose()

Fixes

• Fixed occasional wrong alphabet when loading as protein seqence from FASTA file (#29)
• Fixed deallocation issue in structure.CellList objects, when an exception is raised in the constructor
• Iteration over alignments is forbidden now, yielded empty generator before

Notes

Currently no wheels are provided for Python 3.5 on Windows due to issues with openssl in the install process.