Changelog
Additions
- Added support for Python 3.7
- Discontinued support for Python 3.4 and 3.5
- Added type hints for public API via stub files (PEP 484)
- Revamped documentation
- New sidebar
- New main page
- Summaries in API documentation
- New layout of class attributes in API documentation
- Function signatues of C-extension functions are shown
- Documentation of decorated functions are correctly shown
- Cross references in tutorial
- Tutorial output is dynamically generated using
sphinx-gallery
- Specified version number for dependencies
- Created
environment.yaml
for convenient creation of a development
environment in conda - Improvements to
structure.CellList
- Improved perfromance
get_atoms()
andget_atoms_in_cells()
can be used in a vectorized
manner (replacingefficient mode
)get_atoms()
andget_atoms_in_cells()
have optionalas_mask
parameter- Added
create_adjacency_matrix()
method
- Added hydrogen bond detection (
structure.hbond()
) - Missing element names in
structure.io.pdb.PDBFile
are automatically
inferred (Gromacs support) - Added support for Gromacs'
.gro
file format (structure.io.gro
). - Color schemes can bes loaded from custom files
File
objects can read/write from/to a file object- Temporary files automastically generate a file name
- STDOUT adn STDERR are accessible from
application.Application
runs
Changes
- Changes in
Enum
typessequence.Location.Strand
is anEnum
sequence.Location.Defect
is aFlag
structure.BondType
is anEnum
application.AppState
is aFlag
- Usage of f-strings for exception messages (and some other places)
res_id
is read fromauth_seq_id
instead oflabel_seq_id
in mmCIF files
Fixes
- Fixed custom color schemes in
sequence.graphics.AlignmentSimilarityVisualizer
- All integral types can be used as indices, instead of only
int
- Installing Biotite from a
.whl
no longer requiresCython
to be installed