PyPI - biotite - Versions diffs - 0.39.0__cp311-cp311-win_amd64.whl → 0.41.0__cp311-cp311-win_amd64.whl - Mend

biotite 0.39.0__cp311-cp311-win_amd64.whl → 0.41.0__cp311-cp311-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 +258 -237
biotite/sequence/align/banded.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/cigar.py +60 -15
biotite/sequence/align/kmeralphabet.c +243 -222
biotite/sequence/align/kmeralphabet.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/kmersimilarity.c +215 -196
biotite/sequence/align/kmersimilarity.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.cpp +233 -205
biotite/sequence/align/localgapped.c +258 -237
biotite/sequence/align/localgapped.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/localungapped.c +235 -214
biotite/sequence/align/localungapped.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/multiple.c +255 -234
biotite/sequence/align/multiple.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/pairwise.c +274 -253
biotite/sequence/align/pairwise.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/permutation.c +215 -196
biotite/sequence/align/permutation.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/selector.c +217 -197
biotite/sequence/align/selector.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/tracetable.c +215 -195
biotite/sequence/align/tracetable.cp311-win_amd64.pyd +0 -0
biotite/sequence/annotation.py +2 -2
biotite/sequence/codec.c +235 -214
biotite/sequence/codec.cp311-win_amd64.pyd +0 -0
biotite/sequence/io/fasta/convert.py +27 -24
biotite/sequence/phylo/nj.c +215 -196
biotite/sequence/phylo/nj.cp311-win_amd64.pyd +0 -0
biotite/sequence/phylo/tree.c +227 -202
biotite/sequence/phylo/tree.cp311-win_amd64.pyd +0 -0
biotite/sequence/phylo/upgma.c +215 -196
biotite/sequence/phylo/upgma.cp311-win_amd64.pyd +0 -0
biotite/structure/__init__.py +2 -0
biotite/structure/basepairs.py +7 -12
biotite/structure/bonds.c +1437 -1279
biotite/structure/bonds.cp311-win_amd64.pyd +0 -0
biotite/structure/celllist.c +217 -197
biotite/structure/celllist.cp311-win_amd64.pyd +0 -0
biotite/structure/charges.c +1052 -1101
biotite/structure/charges.cp311-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 +219 -198
biotite/structure/io/mmtf/convertarray.cp311-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/convertfile.c +217 -197
biotite/structure/io/mmtf/convertfile.cp311-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/decode.c +225 -204
biotite/structure/io/mmtf/decode.cp311-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/encode.c +215 -196
biotite/structure/io/mmtf/encode.cp311-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.cp311-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 +112813 -0
biotite/structure/io/pdbx/encoding.cp311-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 +215 -196
biotite/structure/sasa.cp311-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/ccd/amino_acids.txt ADDED Viewed

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