Changelog
Additions
- Better support for macromolecular assemblies and symmetry mates (#450)
biotite.structure.io.pdb
andbiotite.structure.io.mmtf
now support parsing of assemblies vialist_assemblies()
andget_assembly()
biotite.structure.io.pdb
is able to parse all atoms within a single unit cell viaget_symmetry_mates()
- Added
structure.rmspd()
to compute the root-mean-square-pairwise-deviation- This is a method to determine deviations between to models without the need of prior structure superimposition
- Refactored
structure.annotate_sse()
(#448)- Higher performance due to more vectorization
- Multiple chains can be processed at once
- More granular macromolecule filters in
structure
subpackage (#436)- Added
filter_peptide_backbone()
andfilter_phosphate_backbone()
to filter backbone atoms of proteins and nucleotides, respectively - Added
filter_linear_bond_continuity()
that filters atoms that are within distance boundaries to the next atom - Added
filter_polymer()
that filters biomacromolecules of the given type (peptide, nucleotide, carbohydrate) and minimum length
- Added
- More integrity checks in
structure
subpackage (#436)check_linear_continuity()
gives positions in a structure where atoms are not within distance boundaries to the next atomcheck_backbone_continuity()
does the same exclusively for peptide/nucleotide backbone atoms
- Added
sequence.common_alphabet()
to determine theAlphabet
from a list of alphabets that extends all other alphabets from this list (#446) sequence.phylo.Tree.to_newick()
andsequence.phylo.TreeNode.to_newick()
allow rounding of distance labels (#439)application.TantanApp
is able to process multiple sequences in a single call (#446)- This significantly improves the performance especially for short sequences
Changes
structure.filter_backbone()
is deprecated and replaced byfilter_peptide_backbone()
(#436)structure.check_bond_continuity()
is deprecated and replaced bycheck_backbone_continuity()
(#436)- Deprecated
chain_id
parameter instructure.annotate_sse()
, multiple chains can now be processed at once (#448)
Fixes
structure.CellList
accepts empty query coordinates inget_atoms()
andget_atoms_in_cells()
(#448)- Fixed padding of
CRYST1
records to 80 instead of 70 characters (#453) - Fixed issue, where
application.dssp.DSSPApp
did not give correct number of secondary structure elements for multi-chain structures (#444) - Resolved
MemoryError
instructure.repeat_box()
(#450)