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Biotite 0.19.1

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@padix-key padix-key released this 24 Dec 11:59
fb0f96a

Changelog

Additions

  • FASTA files can be downloaded from RCSB PDB via database.rcsb
  • Added structure.rotate_about_axis() and structure.align_vectors()
  • Added shape property and copy() method to structure.Atom
  • All array-like objects can be used to set an annotation array in an atom array (stack)
  • Added structure.info.residue() for getting the standard atoms and their coordinates for a given residue name
  • Added structure.graphics.plot_atoms() for interactive molecular visualization
  • Added exclusive_stop parameter to structure.get_residue_starts and structure.get_chain_starts
  • Added connect_via_residue_names() and connect_via_distances() for calculating a structure.BondList for a structure.AtomArray

Changes

  • structure.rotate() does not rotate the box of an atom array (stack) anymore
  • structure.BondList equality is not order dependent

Fixes

  • structure.BondList accepts all dtypes for integer arrays
  • structure.BondList accepts negative integers as indices
  • sequence.io.fasta.FastaFile: Tests for invalid or empty files
  • structure.io.pdb.PDBFile: Exception is raised if an invalid field in extra_fields is given
  • structure.rotate(): Fixed rotation direction