Changelog
Additions
- Support for new RCSB search API (#408)
- Added
case_sensitive
parameter indatabase.rcsb.FieldQuery
- Added
structure.info.mass()
support deuteriumstructure.connect_via_distances()
can connect atoms over periodic boundaries- Added more chain-level utilities consistent with residue-level utilities
structure.apply_chain_wise()
structure.spread_chain_wise()
structure.get_chain_masks()
structure.get_chain_starts_for()
structure.get_chain_positions()
structure.superimpose()
supports also pure coordinates
Changes
structure.hbond()
uses an associatedstructure.BondList
to find hydrogen atoms to potential hydrogen bond donors- Lines depicting bonds in
structure.graphics.plot_atoms()
andstructure.graphics.plot_ball_and_stick_model()
use rounded tips
Fixes
- Fixed
structure.io.pdbx.get_assembly
missing chains in some structures (#387) - Added a more meaningful error, if Matplotlib is required, but not installed (#302)
- Added more descriptive error, if a
structure.io.pdb.PDBFile
has erroneous atom IDs (#379) structure.io.pdb.PDBFile
pads lines always to 80 characters- Allow empty attribute string in
sequence.io.GFFFile
- Fixed wrong similarity scores, if a
sequence.align.SubstitutionMatrix
with two different alphabets is read from string or file - Fixed
application.mafft.MafftApp
runs for more than 10 sequences.