biotite 1.1.0__cp313-cp313-macosx_11_0_arm64.whl → 1.3.0__cp313-cp313-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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- biotite/application/application.py +3 -3
- biotite/application/autodock/app.py +1 -1
- biotite/application/blast/webapp.py +1 -1
- biotite/application/clustalo/app.py +1 -1
- biotite/application/localapp.py +2 -2
- biotite/application/msaapp.py +10 -10
- biotite/application/muscle/app3.py +3 -3
- biotite/application/muscle/app5.py +3 -3
- biotite/application/sra/app.py +0 -5
- biotite/application/util.py +21 -1
- biotite/application/viennarna/rnaalifold.py +8 -8
- biotite/application/viennarna/rnaplot.py +10 -8
- biotite/application/viennarna/util.py +1 -1
- biotite/application/webapp.py +1 -1
- biotite/database/afdb/__init__.py +12 -0
- biotite/database/afdb/download.py +191 -0
- biotite/database/entrez/dbnames.py +10 -0
- biotite/database/entrez/download.py +9 -10
- biotite/database/entrez/key.py +1 -1
- biotite/database/entrez/query.py +5 -4
- biotite/database/pubchem/download.py +6 -6
- biotite/database/pubchem/error.py +10 -0
- biotite/database/pubchem/query.py +12 -23
- biotite/database/rcsb/download.py +3 -2
- biotite/database/rcsb/query.py +2 -3
- biotite/database/uniprot/check.py +2 -2
- biotite/database/uniprot/download.py +2 -5
- biotite/database/uniprot/query.py +3 -4
- biotite/file.py +14 -2
- biotite/interface/__init__.py +19 -0
- biotite/interface/openmm/__init__.py +20 -0
- biotite/interface/openmm/state.py +93 -0
- biotite/interface/openmm/system.py +227 -0
- biotite/interface/pymol/__init__.py +201 -0
- biotite/interface/pymol/cgo.py +346 -0
- biotite/interface/pymol/convert.py +185 -0
- biotite/interface/pymol/display.py +267 -0
- biotite/interface/pymol/object.py +1226 -0
- biotite/interface/pymol/shapes.py +178 -0
- biotite/interface/pymol/startup.py +169 -0
- biotite/interface/rdkit/__init__.py +19 -0
- biotite/interface/rdkit/mol.py +490 -0
- biotite/interface/version.py +94 -0
- biotite/interface/warning.py +19 -0
- biotite/sequence/align/__init__.py +0 -4
- biotite/sequence/align/alignment.py +33 -11
- biotite/sequence/align/banded.cpython-313-darwin.so +0 -0
- biotite/sequence/align/banded.pyx +22 -22
- biotite/sequence/align/cigar.py +2 -2
- biotite/sequence/align/kmeralphabet.cpython-313-darwin.so +0 -0
- biotite/sequence/align/kmeralphabet.pyx +2 -2
- biotite/sequence/align/kmersimilarity.cpython-313-darwin.so +0 -0
- biotite/sequence/align/kmertable.cpython-313-darwin.so +0 -0
- biotite/sequence/align/kmertable.pyx +6 -6
- biotite/sequence/align/localgapped.cpython-313-darwin.so +0 -0
- biotite/sequence/align/localgapped.pyx +47 -47
- biotite/sequence/align/localungapped.cpython-313-darwin.so +0 -0
- biotite/sequence/align/localungapped.pyx +10 -10
- biotite/sequence/align/matrix.py +12 -3
- biotite/sequence/align/multiple.cpython-313-darwin.so +0 -0
- biotite/sequence/align/multiple.pyx +1 -2
- biotite/sequence/align/pairwise.cpython-313-darwin.so +0 -0
- biotite/sequence/align/pairwise.pyx +37 -39
- biotite/sequence/align/permutation.cpython-313-darwin.so +0 -0
- biotite/sequence/align/selector.cpython-313-darwin.so +0 -0
- biotite/sequence/align/selector.pyx +2 -2
- biotite/sequence/align/statistics.py +1 -1
- biotite/sequence/align/tracetable.cpython-313-darwin.so +0 -0
- biotite/sequence/alphabet.py +2 -2
- biotite/sequence/annotation.py +19 -13
- biotite/sequence/codec.cpython-313-darwin.so +0 -0
- biotite/sequence/codon.py +1 -2
- biotite/sequence/graphics/alignment.py +25 -39
- biotite/sequence/graphics/dendrogram.py +4 -2
- biotite/sequence/graphics/features.py +2 -2
- biotite/sequence/graphics/logo.py +10 -12
- biotite/sequence/io/fasta/convert.py +1 -2
- biotite/sequence/io/fasta/file.py +1 -1
- biotite/sequence/io/fastq/file.py +3 -3
- biotite/sequence/io/genbank/file.py +3 -3
- biotite/sequence/io/genbank/sequence.py +2 -0
- biotite/sequence/io/gff/convert.py +1 -1
- biotite/sequence/io/gff/file.py +1 -2
- biotite/sequence/phylo/nj.cpython-313-darwin.so +0 -0
- biotite/sequence/phylo/tree.cpython-313-darwin.so +0 -0
- biotite/sequence/phylo/upgma.cpython-313-darwin.so +0 -0
- biotite/sequence/profile.py +19 -25
- biotite/sequence/search.py +0 -1
- biotite/sequence/seqtypes.py +12 -5
- biotite/sequence/sequence.py +1 -2
- biotite/structure/__init__.py +2 -0
- biotite/structure/alphabet/i3d.py +1 -2
- biotite/structure/alphabet/pb.py +1 -2
- biotite/structure/alphabet/unkerasify.py +8 -2
- biotite/structure/atoms.py +35 -27
- biotite/structure/basepairs.py +39 -40
- biotite/structure/bonds.cpython-313-darwin.so +0 -0
- biotite/structure/bonds.pyx +8 -5
- biotite/structure/box.py +159 -23
- biotite/structure/celllist.cpython-313-darwin.so +0 -0
- biotite/structure/celllist.pyx +83 -68
- biotite/structure/chains.py +17 -55
- biotite/structure/charges.cpython-313-darwin.so +0 -0
- biotite/structure/compare.py +420 -13
- biotite/structure/density.py +1 -1
- biotite/structure/dotbracket.py +31 -32
- biotite/structure/filter.py +8 -8
- biotite/structure/geometry.py +15 -15
- biotite/structure/graphics/rna.py +19 -16
- biotite/structure/hbond.py +18 -21
- biotite/structure/info/atoms.py +11 -2
- biotite/structure/info/ccd.py +0 -2
- biotite/structure/info/components.bcif +0 -0
- biotite/structure/info/groups.py +0 -3
- biotite/structure/info/misc.py +0 -1
- biotite/structure/info/radii.py +92 -22
- biotite/structure/info/standardize.py +1 -2
- biotite/structure/integrity.py +4 -6
- biotite/structure/io/general.py +2 -2
- biotite/structure/io/gro/file.py +8 -9
- biotite/structure/io/mol/convert.py +1 -1
- biotite/structure/io/mol/ctab.py +33 -28
- biotite/structure/io/mol/mol.py +1 -1
- biotite/structure/io/mol/sdf.py +39 -13
- biotite/structure/io/pdb/convert.py +86 -5
- biotite/structure/io/pdb/file.py +90 -24
- biotite/structure/io/pdb/hybrid36.cpython-313-darwin.so +0 -0
- biotite/structure/io/pdbqt/file.py +4 -4
- biotite/structure/io/pdbx/bcif.py +22 -7
- biotite/structure/io/pdbx/cif.py +20 -7
- biotite/structure/io/pdbx/component.py +6 -0
- biotite/structure/io/pdbx/compress.py +71 -34
- biotite/structure/io/pdbx/convert.py +429 -77
- biotite/structure/io/pdbx/encoding.cpython-313-darwin.so +0 -0
- biotite/structure/io/pdbx/encoding.pyx +39 -23
- biotite/structure/io/trajfile.py +9 -6
- biotite/structure/io/util.py +38 -0
- biotite/structure/mechanics.py +0 -1
- biotite/structure/molecules.py +0 -15
- biotite/structure/pseudoknots.py +13 -19
- biotite/structure/repair.py +2 -4
- biotite/structure/residues.py +20 -48
- biotite/structure/rings.py +335 -0
- biotite/structure/sasa.cpython-313-darwin.so +0 -0
- biotite/structure/sasa.pyx +30 -30
- biotite/structure/segments.py +123 -9
- biotite/structure/sequence.py +0 -1
- biotite/structure/spacegroups.json +1567 -0
- biotite/structure/spacegroups.license +26 -0
- biotite/structure/sse.py +0 -2
- biotite/structure/superimpose.py +75 -253
- biotite/structure/tm.py +581 -0
- biotite/structure/transform.py +232 -26
- biotite/structure/util.py +3 -3
- biotite/version.py +9 -4
- biotite/visualize.py +111 -1
- {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/METADATA +8 -36
- {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/RECORD +160 -138
- {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/WHEEL +3 -1
- {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/licenses/LICENSE.rst +0 -0
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biotite/structure/info/bonds.py,sha256=6pXAZPeKPL2pwFi5fhSyTwh_gd5fToIgvwguGffrE-0,4644
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biotite/structure/info/masses.py,sha256=HOdaeFZkd5LSrl00025S1MwXT7im8V-s0bU54tr1te8,4555
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biotite/structure/info/ccd.py,sha256=A3-YomYJS3bbAfntLpvwLkmCgQFjR2suMwFnGQsgPXg,5851
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biotite/structure/graphics/__init__.py,sha256=YwMT8-c2DjrkcwyK6jPeDtAKxQda0OhElnwk8J0y3Hc,353
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biotite/structure/graphics/rna.py,sha256=
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biotite/structure/graphics/atoms.py,sha256=988_URX4hfTE3oBOYgAvZruOrzogMPcFKiTT5RJL01E,8116
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biotite-1.3.0.dist-info/RECORD,,
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biotite-1.3.0.dist-info/WHEEL,sha256=s0cTlxH34_QlWnER2EjFUsHTyO2KntcvTrX9yBtBmNo,133
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biotite-1.3.0.dist-info/METADATA,sha256=gcnHDjnEHlvw3vQKLx2ZpW64zoh-snCRfNU0n0erVEw,5525
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biotite-1.3.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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