biotite 0.39.0__cp312-cp312-macosx_11_0_arm64.whl → 0.40.0__cp312-cp312-macosx_11_0_arm64.whl
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- biotite/__init__.py +3 -3
- biotite/application/dssp/app.py +18 -18
- biotite/database/rcsb/download.py +19 -14
- biotite/sequence/align/banded.c +256 -235
- biotite/sequence/align/banded.cpython-312-darwin.so +0 -0
- biotite/sequence/align/kmeralphabet.c +241 -220
- biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
- biotite/sequence/align/kmersimilarity.c +213 -194
- biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
- biotite/sequence/align/kmertable.cpp +231 -203
- biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
- biotite/sequence/align/localgapped.c +256 -235
- biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
- biotite/sequence/align/localungapped.c +233 -212
- biotite/sequence/align/localungapped.cpython-312-darwin.so +0 -0
- biotite/sequence/align/multiple.c +253 -232
- biotite/sequence/align/multiple.cpython-312-darwin.so +0 -0
- biotite/sequence/align/pairwise.c +272 -251
- biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
- biotite/sequence/align/permutation.c +213 -194
- biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
- biotite/sequence/align/selector.c +215 -195
- biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
- biotite/sequence/align/tracetable.c +213 -193
- biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
- biotite/sequence/codec.c +233 -212
- biotite/sequence/codec.cpython-312-darwin.so +0 -0
- biotite/sequence/phylo/nj.c +213 -194
- biotite/sequence/phylo/nj.cpython-312-darwin.so +0 -0
- biotite/sequence/phylo/tree.c +225 -200
- biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
- biotite/sequence/phylo/upgma.c +213 -194
- biotite/sequence/phylo/upgma.cpython-312-darwin.so +0 -0
- biotite/structure/basepairs.py +7 -12
- biotite/structure/bonds.c +1173 -1224
- biotite/structure/bonds.cpython-312-darwin.so +0 -0
- biotite/structure/celllist.c +215 -195
- biotite/structure/celllist.cpython-312-darwin.so +0 -0
- biotite/structure/charges.c +1050 -1099
- biotite/structure/charges.cpython-312-darwin.so +0 -0
- biotite/structure/filter.py +30 -37
- biotite/structure/info/__init__.py +5 -8
- biotite/structure/info/atoms.py +25 -67
- biotite/structure/info/bonds.py +46 -100
- biotite/structure/info/ccd/README.rst +8 -0
- biotite/structure/info/ccd/amino_acids.txt +1646 -0
- biotite/structure/info/ccd/carbohydrates.txt +1133 -0
- biotite/structure/info/ccd/components.bcif +0 -0
- biotite/structure/info/ccd/nucleotides.txt +797 -0
- biotite/structure/info/ccd.py +95 -0
- biotite/structure/info/groups.py +90 -0
- biotite/structure/info/masses.py +21 -20
- biotite/structure/info/misc.py +11 -22
- biotite/structure/info/standardize.py +17 -12
- biotite/structure/io/__init__.py +2 -4
- biotite/structure/io/ctab.py +1 -1
- biotite/structure/io/general.py +37 -43
- biotite/structure/io/mmtf/__init__.py +3 -0
- biotite/structure/io/mmtf/convertarray.c +217 -196
- biotite/structure/io/mmtf/convertarray.cpython-312-darwin.so +0 -0
- biotite/structure/io/mmtf/convertfile.c +215 -195
- biotite/structure/io/mmtf/convertfile.cpython-312-darwin.so +0 -0
- biotite/structure/io/mmtf/decode.c +223 -202
- biotite/structure/io/mmtf/decode.cpython-312-darwin.so +0 -0
- biotite/structure/io/mmtf/encode.c +213 -194
- biotite/structure/io/mmtf/encode.cpython-312-darwin.so +0 -0
- biotite/structure/io/mmtf/file.py +34 -26
- biotite/structure/io/npz/__init__.py +3 -0
- biotite/structure/io/npz/file.py +21 -18
- biotite/structure/io/pdb/__init__.py +3 -3
- biotite/structure/io/pdb/file.py +5 -3
- biotite/structure/io/pdb/hybrid36.c +63 -43
- biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so +0 -0
- biotite/structure/io/pdbqt/file.py +32 -32
- biotite/structure/io/pdbx/__init__.py +13 -6
- biotite/structure/io/pdbx/bcif.py +649 -0
- biotite/structure/io/pdbx/cif.py +1028 -0
- biotite/structure/io/pdbx/component.py +243 -0
- biotite/structure/io/pdbx/convert.py +707 -359
- biotite/structure/io/pdbx/encoding.c +112803 -0
- biotite/structure/io/pdbx/encoding.cpython-312-darwin.so +0 -0
- biotite/structure/io/pdbx/error.py +14 -0
- biotite/structure/io/pdbx/legacy.py +267 -0
- biotite/structure/molecules.py +151 -151
- biotite/structure/sasa.c +213 -194
- biotite/structure/sasa.cpython-312-darwin.so +0 -0
- biotite/structure/superimpose.py +158 -115
- {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/METADATA +2 -2
- {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/RECORD +92 -90
- {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/WHEEL +1 -1
- biotite/structure/info/amino_acids.json +0 -1556
- biotite/structure/info/amino_acids.py +0 -42
- biotite/structure/info/carbohydrates.json +0 -1122
- biotite/structure/info/carbohydrates.py +0 -39
- biotite/structure/info/intra_bonds.msgpack +0 -0
- biotite/structure/info/link_types.msgpack +0 -1
- biotite/structure/info/nucleotides.json +0 -772
- biotite/structure/info/nucleotides.py +0 -39
- biotite/structure/info/residue_masses.msgpack +0 -0
- biotite/structure/info/residue_names.msgpack +0 -3
- biotite/structure/info/residues.msgpack +0 -0
- biotite/structure/io/pdbx/file.py +0 -652
- {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/LICENSE.rst +0 -0
- {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/top_level.txt +0 -0
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