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