PyPI - biotite - Versions diffs - 0.39.0__cp312-cp312-win_amd64.whl → 0.41.0__cp312-cp312-win_amd64.whl - Mend

biotite 0.39.0__cp312-cp312-win_amd64.whl → 0.41.0__cp312-cp312-win_amd64.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 (121) hide show

biotite/__init__.py +3 -3
biotite/application/dssp/app.py +18 -18
biotite/database/pubchem/download.py +23 -23
biotite/database/pubchem/query.py +7 -7
biotite/database/rcsb/download.py +19 -14
biotite/file.py +17 -9
biotite/sequence/align/banded.c +256 -235
biotite/sequence/align/banded.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/cigar.py +60 -15
biotite/sequence/align/kmeralphabet.c +241 -220
biotite/sequence/align/kmeralphabet.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/kmersimilarity.c +213 -194
biotite/sequence/align/kmersimilarity.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.cpp +231 -203
biotite/sequence/align/localgapped.c +256 -235
biotite/sequence/align/localgapped.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/localungapped.c +233 -212
biotite/sequence/align/localungapped.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/multiple.c +253 -232
biotite/sequence/align/multiple.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/pairwise.c +272 -251
biotite/sequence/align/pairwise.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/permutation.c +213 -194
biotite/sequence/align/permutation.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/selector.c +215 -195
biotite/sequence/align/selector.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/tracetable.c +213 -193
biotite/sequence/align/tracetable.cp312-win_amd64.pyd +0 -0
biotite/sequence/annotation.py +2 -2
biotite/sequence/codec.c +233 -212
biotite/sequence/codec.cp312-win_amd64.pyd +0 -0
biotite/sequence/io/fasta/convert.py +27 -24
biotite/sequence/phylo/nj.c +213 -194
biotite/sequence/phylo/nj.cp312-win_amd64.pyd +0 -0
biotite/sequence/phylo/tree.c +225 -200
biotite/sequence/phylo/tree.cp312-win_amd64.pyd +0 -0
biotite/sequence/phylo/upgma.c +213 -194
biotite/sequence/phylo/upgma.cp312-win_amd64.pyd +0 -0
biotite/structure/__init__.py +2 -0
biotite/structure/basepairs.py +7 -12
biotite/structure/bonds.c +1435 -1277
biotite/structure/bonds.cp312-win_amd64.pyd +0 -0
biotite/structure/celllist.c +215 -195
biotite/structure/celllist.cp312-win_amd64.pyd +0 -0
biotite/structure/charges.c +1050 -1099
biotite/structure/charges.cp312-win_amd64.pyd +0 -0
biotite/structure/dotbracket.py +2 -0
biotite/structure/filter.py +30 -37
biotite/structure/info/__init__.py +5 -8
biotite/structure/info/atoms.py +31 -68
biotite/structure/info/bonds.py +47 -101
biotite/structure/info/ccd/README.rst +8 -0
biotite/structure/info/ccd/amino_acids.txt +1663 -0
biotite/structure/info/ccd/carbohydrates.txt +1135 -0
biotite/structure/info/ccd/components.bcif +0 -0
biotite/structure/info/ccd/nucleotides.txt +798 -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 +78 -25
biotite/structure/info/standardize.py +17 -12
biotite/structure/integrity.py +19 -70
biotite/structure/io/__init__.py +2 -4
biotite/structure/io/ctab.py +12 -106
biotite/structure/io/general.py +167 -181
biotite/structure/io/gro/file.py +16 -16
biotite/structure/io/mmtf/__init__.py +3 -0
biotite/structure/io/mmtf/convertarray.c +217 -196
biotite/structure/io/mmtf/convertarray.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/convertfile.c +215 -195
biotite/structure/io/mmtf/convertfile.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/decode.c +223 -202
biotite/structure/io/mmtf/decode.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/encode.c +213 -194
biotite/structure/io/mmtf/encode.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/file.py +34 -26
biotite/structure/io/mol/__init__.py +4 -2
biotite/structure/io/mol/convert.py +71 -7
biotite/structure/io/mol/ctab.py +414 -0
biotite/structure/io/mol/header.py +116 -0
biotite/structure/io/mol/{file.py → mol.py} +69 -82
biotite/structure/io/mol/sdf.py +909 -0
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 +89 -34
biotite/structure/io/pdb/hybrid36.c +63 -43
biotite/structure/io/pdb/hybrid36.cp312-win_amd64.pyd +0 -0
biotite/structure/io/pdbqt/file.py +32 -32
biotite/structure/io/pdbx/__init__.py +12 -6
biotite/structure/io/pdbx/bcif.py +648 -0
biotite/structure/io/pdbx/cif.py +1032 -0
biotite/structure/io/pdbx/component.py +246 -0
biotite/structure/io/pdbx/convert.py +858 -386
biotite/structure/io/pdbx/encoding.c +112803 -0
biotite/structure/io/pdbx/encoding.cp312-win_amd64.pyd +0 -0
biotite/structure/io/pdbx/legacy.py +267 -0
biotite/structure/molecules.py +151 -151
biotite/structure/repair.py +253 -0
biotite/structure/sasa.c +213 -194
biotite/structure/sasa.cp312-win_amd64.pyd +0 -0
biotite/structure/sequence.py +112 -0
biotite/structure/superimpose.py +618 -116
{biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/METADATA +3 -3
{biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/RECORD +109 -103
{biotite-0.39.0.dist-info → biotite-0.41.0.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-0.41.0.dist-info}/LICENSE.rst +0 -0
{biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/top_level.txt +0 -0

biotite/structure/info/nucleotides.json DELETED Viewed

@@ -1,772 +0,0 @@
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- "TPG",
- "TS",
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- "VC7",
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- "WC7",
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- "X4A",
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- "XGA",
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- "XGR",
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- "XNY",
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- "XTF",
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- "XTL",
- "XTR",
- "XTS",
- "XTY",
- "XUA",
- "XUG",
- "Y",
- "Y5P",
- "YA4",
- "YCO",
- "YG",
- "YRR",
- "YYG",
- "Z",
- "ZAD",
- "ZBC",
- "ZBU",
- "ZCY",
- "ZDU",
- "ZGU",
- "ZHP"
-]