PyPI - biotite - Versions diffs - 1.0.1__cp310-cp310-macosx_11_0_arm64.whl → 1.1.0__cp310-cp310-macosx_11_0_arm64.whl - Mend

biotite 1.0.1__cp310-cp310-macosx_11_0_arm64.whl → 1.1.0__cp310-cp310-macosx_11_0_arm64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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Files changed (90) hide show

biotite/application/dssp/app.py +13 -3
biotite/application/localapp.py +34 -0
biotite/application/muscle/app3.py +2 -15
biotite/application/muscle/app5.py +2 -2
biotite/application/util.py +1 -1
biotite/application/viennarna/rnaplot.py +6 -2
biotite/database/rcsb/query.py +6 -6
biotite/database/uniprot/check.py +20 -15
biotite/database/uniprot/download.py +1 -1
biotite/database/uniprot/query.py +1 -1
biotite/sequence/align/alignment.py +16 -3
biotite/sequence/align/banded.cpython-310-darwin.so +0 -0
biotite/sequence/align/banded.pyx +5 -5
biotite/sequence/align/kmeralphabet.cpython-310-darwin.so +0 -0
biotite/sequence/align/kmeralphabet.pyx +17 -0
biotite/sequence/align/kmersimilarity.cpython-310-darwin.so +0 -0
biotite/sequence/align/kmertable.cpython-310-darwin.so +0 -0
biotite/sequence/align/kmertable.pyx +52 -42
biotite/sequence/align/localgapped.cpython-310-darwin.so +0 -0
biotite/sequence/align/localungapped.cpython-310-darwin.so +0 -0
biotite/sequence/align/matrix.py +273 -55
biotite/sequence/align/matrix_data/3Di.mat +24 -0
biotite/sequence/align/matrix_data/PB.license +21 -0
biotite/sequence/align/matrix_data/PB.mat +18 -0
biotite/sequence/align/multiple.cpython-310-darwin.so +0 -0
biotite/sequence/align/pairwise.cpython-310-darwin.so +0 -0
biotite/sequence/align/permutation.cpython-310-darwin.so +0 -0
biotite/sequence/align/selector.cpython-310-darwin.so +0 -0
biotite/sequence/align/tracetable.cpython-310-darwin.so +0 -0
biotite/sequence/alphabet.py +3 -0
biotite/sequence/codec.cpython-310-darwin.so +0 -0
biotite/sequence/graphics/color_schemes/3di_flower.json +48 -0
biotite/sequence/graphics/color_schemes/pb_flower.json +2 -1
biotite/sequence/graphics/colorschemes.py +44 -11
biotite/sequence/phylo/nj.cpython-310-darwin.so +0 -0
biotite/sequence/phylo/tree.cpython-310-darwin.so +0 -0
biotite/sequence/phylo/upgma.cpython-310-darwin.so +0 -0
biotite/sequence/profile.py +86 -4
biotite/sequence/seqtypes.py +124 -3
biotite/setup_ccd.py +197 -0
biotite/structure/__init__.py +4 -3
biotite/structure/alphabet/__init__.py +25 -0
biotite/structure/alphabet/encoder.py +332 -0
biotite/structure/alphabet/encoder_weights_3di.kerasify +0 -0
biotite/structure/alphabet/i3d.py +110 -0
biotite/structure/alphabet/layers.py +86 -0
biotite/structure/alphabet/pb.license +21 -0
biotite/structure/alphabet/pb.py +171 -0
biotite/structure/alphabet/unkerasify.py +122 -0
biotite/structure/atoms.py +129 -40
biotite/structure/bonds.cpython-310-darwin.so +0 -0
biotite/structure/bonds.pyx +72 -21
biotite/structure/celllist.cpython-310-darwin.so +0 -0
biotite/structure/charges.cpython-310-darwin.so +0 -0
biotite/structure/geometry.py +60 -113
biotite/structure/info/__init__.py +1 -0
biotite/structure/info/atoms.py +13 -13
biotite/structure/info/bonds.py +12 -6
biotite/structure/info/ccd.py +125 -32
biotite/structure/info/{ccd/components.bcif → components.bcif} +0 -0
biotite/structure/info/groups.py +63 -17
biotite/structure/info/masses.py +9 -6
biotite/structure/info/misc.py +15 -21
biotite/structure/info/standardize.py +3 -2
biotite/structure/io/mol/sdf.py +41 -40
biotite/structure/io/pdb/convert.py +2 -0
biotite/structure/io/pdb/file.py +74 -3
biotite/structure/io/pdb/hybrid36.cpython-310-darwin.so +0 -0
biotite/structure/io/pdbqt/file.py +32 -32
biotite/structure/io/pdbx/__init__.py +1 -0
biotite/structure/io/pdbx/bcif.py +32 -8
biotite/structure/io/pdbx/cif.py +72 -59
biotite/structure/io/pdbx/component.py +9 -4
biotite/structure/io/pdbx/compress.py +321 -0
biotite/structure/io/pdbx/convert.py +194 -48
biotite/structure/io/pdbx/encoding.cpython-310-darwin.so +0 -0
biotite/structure/io/pdbx/encoding.pyx +98 -17
biotite/structure/molecules.py +141 -141
biotite/structure/sasa.cpython-310-darwin.so +0 -0
biotite/structure/segments.py +1 -2
biotite/structure/util.py +73 -1
biotite/version.py +2 -2
{biotite-1.0.1.dist-info → biotite-1.1.0.dist-info}/METADATA +3 -1
{biotite-1.0.1.dist-info → biotite-1.1.0.dist-info}/RECORD +86 -76
biotite/structure/info/ccd/README.rst +0 -8
biotite/structure/info/ccd/amino_acids.txt +0 -1663
biotite/structure/info/ccd/carbohydrates.txt +0 -1135
biotite/structure/info/ccd/nucleotides.txt +0 -798
{biotite-1.0.1.dist-info → biotite-1.1.0.dist-info}/WHEEL +0 -0
{biotite-1.0.1.dist-info → biotite-1.1.0.dist-info}/licenses/LICENSE.rst +0 -0

biotite/structure/info/ccd/carbohydrates.txt DELETED Viewed

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