PyPI - biotite - Versions diffs - 0.41.1__cp311-cp311-macosx_10_16_x86_64.whl - Mend

biotite 0.41.1__cp311-cp311-macosx_10_16_x86_64.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/__init__.py +19 -0
biotite/application/__init__.py +43 -0
biotite/application/application.py +265 -0
biotite/application/autodock/__init__.py +12 -0
biotite/application/autodock/app.py +505 -0
biotite/application/blast/__init__.py +14 -0
biotite/application/blast/alignment.py +83 -0
biotite/application/blast/webapp.py +421 -0
biotite/application/clustalo/__init__.py +12 -0
biotite/application/clustalo/app.py +238 -0
biotite/application/dssp/__init__.py +12 -0
biotite/application/dssp/app.py +152 -0
biotite/application/localapp.py +306 -0
biotite/application/mafft/__init__.py +12 -0
biotite/application/mafft/app.py +122 -0
biotite/application/msaapp.py +374 -0
biotite/application/muscle/__init__.py +13 -0
biotite/application/muscle/app3.py +254 -0
biotite/application/muscle/app5.py +171 -0
biotite/application/sra/__init__.py +18 -0
biotite/application/sra/app.py +456 -0
biotite/application/tantan/__init__.py +12 -0
biotite/application/tantan/app.py +222 -0
biotite/application/util.py +59 -0
biotite/application/viennarna/__init__.py +18 -0
biotite/application/viennarna/rnaalifold.py +304 -0
biotite/application/viennarna/rnafold.py +269 -0
biotite/application/viennarna/rnaplot.py +187 -0
biotite/application/viennarna/util.py +72 -0
biotite/application/webapp.py +77 -0
biotite/copyable.py +71 -0
biotite/database/__init__.py +23 -0
biotite/database/entrez/__init__.py +15 -0
biotite/database/entrez/check.py +61 -0
biotite/database/entrez/dbnames.py +89 -0
biotite/database/entrez/download.py +223 -0
biotite/database/entrez/key.py +44 -0
biotite/database/entrez/query.py +223 -0
biotite/database/error.py +15 -0
biotite/database/pubchem/__init__.py +21 -0
biotite/database/pubchem/download.py +260 -0
biotite/database/pubchem/error.py +20 -0
biotite/database/pubchem/query.py +827 -0
biotite/database/pubchem/throttle.py +99 -0
biotite/database/rcsb/__init__.py +13 -0
biotite/database/rcsb/download.py +167 -0
biotite/database/rcsb/query.py +959 -0
biotite/database/uniprot/__init__.py +13 -0
biotite/database/uniprot/check.py +32 -0
biotite/database/uniprot/download.py +134 -0
biotite/database/uniprot/query.py +209 -0
biotite/file.py +251 -0
biotite/sequence/__init__.py +73 -0
biotite/sequence/align/__init__.py +49 -0
biotite/sequence/align/alignment.py +658 -0
biotite/sequence/align/banded.cpython-311-darwin.so +0 -0
biotite/sequence/align/banded.pyx +652 -0
biotite/sequence/align/buckets.py +69 -0
biotite/sequence/align/cigar.py +434 -0
biotite/sequence/align/kmeralphabet.cpython-311-darwin.so +0 -0
biotite/sequence/align/kmeralphabet.pyx +574 -0
biotite/sequence/align/kmersimilarity.cpython-311-darwin.so +0 -0
biotite/sequence/align/kmersimilarity.pyx +233 -0
biotite/sequence/align/kmertable.cpython-311-darwin.so +0 -0
biotite/sequence/align/kmertable.pyx +3400 -0
biotite/sequence/align/localgapped.cpython-311-darwin.so +0 -0
biotite/sequence/align/localgapped.pyx +892 -0
biotite/sequence/align/localungapped.cpython-311-darwin.so +0 -0
biotite/sequence/align/localungapped.pyx +279 -0
biotite/sequence/align/matrix.py +405 -0
biotite/sequence/align/matrix_data/BLOSUM100.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM30.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM35.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM40.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM45.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM50.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM50_13p.mat +25 -0
biotite/sequence/align/matrix_data/BLOSUM50_14.3.mat +25 -0
biotite/sequence/align/matrix_data/BLOSUM50_5.0.mat +25 -0
biotite/sequence/align/matrix_data/BLOSUM55.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM60.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM62.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM62_13p.mat +25 -0
biotite/sequence/align/matrix_data/BLOSUM62_14.3.mat +25 -0
biotite/sequence/align/matrix_data/BLOSUM62_5.0.mat +25 -0
biotite/sequence/align/matrix_data/BLOSUM65.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM70.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM75.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM80.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM85.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUM90.mat +31 -0
biotite/sequence/align/matrix_data/BLOSUMN.mat +31 -0
biotite/sequence/align/matrix_data/CorBLOSUM49_5.0.mat +25 -0
biotite/sequence/align/matrix_data/CorBLOSUM57_13p.mat +25 -0
biotite/sequence/align/matrix_data/CorBLOSUM57_14.3.mat +25 -0
biotite/sequence/align/matrix_data/CorBLOSUM61_5.0.mat +25 -0
biotite/sequence/align/matrix_data/CorBLOSUM66_13p.mat +25 -0
biotite/sequence/align/matrix_data/CorBLOSUM67_14.3.mat +25 -0
biotite/sequence/align/matrix_data/DAYHOFF.mat +32 -0
biotite/sequence/align/matrix_data/GONNET.mat +26 -0
biotite/sequence/align/matrix_data/IDENTITY.mat +25 -0
biotite/sequence/align/matrix_data/MATCH.mat +25 -0
biotite/sequence/align/matrix_data/NUC.mat +25 -0
biotite/sequence/align/matrix_data/PAM10.mat +34 -0
biotite/sequence/align/matrix_data/PAM100.mat +34 -0
biotite/sequence/align/matrix_data/PAM110.mat +34 -0
biotite/sequence/align/matrix_data/PAM120.mat +34 -0
biotite/sequence/align/matrix_data/PAM130.mat +34 -0
biotite/sequence/align/matrix_data/PAM140.mat +34 -0
biotite/sequence/align/matrix_data/PAM150.mat +34 -0
biotite/sequence/align/matrix_data/PAM160.mat +34 -0
biotite/sequence/align/matrix_data/PAM170.mat +34 -0
biotite/sequence/align/matrix_data/PAM180.mat +34 -0
biotite/sequence/align/matrix_data/PAM190.mat +34 -0
biotite/sequence/align/matrix_data/PAM20.mat +34 -0
biotite/sequence/align/matrix_data/PAM200.mat +34 -0
biotite/sequence/align/matrix_data/PAM210.mat +34 -0
biotite/sequence/align/matrix_data/PAM220.mat +34 -0
biotite/sequence/align/matrix_data/PAM230.mat +34 -0
biotite/sequence/align/matrix_data/PAM240.mat +34 -0
biotite/sequence/align/matrix_data/PAM250.mat +34 -0
biotite/sequence/align/matrix_data/PAM260.mat +34 -0
biotite/sequence/align/matrix_data/PAM270.mat +34 -0
biotite/sequence/align/matrix_data/PAM280.mat +34 -0
biotite/sequence/align/matrix_data/PAM290.mat +34 -0
biotite/sequence/align/matrix_data/PAM30.mat +34 -0
biotite/sequence/align/matrix_data/PAM300.mat +34 -0
biotite/sequence/align/matrix_data/PAM310.mat +34 -0
biotite/sequence/align/matrix_data/PAM320.mat +34 -0
biotite/sequence/align/matrix_data/PAM330.mat +34 -0
biotite/sequence/align/matrix_data/PAM340.mat +34 -0
biotite/sequence/align/matrix_data/PAM350.mat +34 -0
biotite/sequence/align/matrix_data/PAM360.mat +34 -0
biotite/sequence/align/matrix_data/PAM370.mat +34 -0
biotite/sequence/align/matrix_data/PAM380.mat +34 -0
biotite/sequence/align/matrix_data/PAM390.mat +34 -0
biotite/sequence/align/matrix_data/PAM40.mat +34 -0
biotite/sequence/align/matrix_data/PAM400.mat +34 -0
biotite/sequence/align/matrix_data/PAM410.mat +34 -0
biotite/sequence/align/matrix_data/PAM420.mat +34 -0
biotite/sequence/align/matrix_data/PAM430.mat +34 -0
biotite/sequence/align/matrix_data/PAM440.mat +34 -0
biotite/sequence/align/matrix_data/PAM450.mat +34 -0
biotite/sequence/align/matrix_data/PAM460.mat +34 -0
biotite/sequence/align/matrix_data/PAM470.mat +34 -0
biotite/sequence/align/matrix_data/PAM480.mat +34 -0
biotite/sequence/align/matrix_data/PAM490.mat +34 -0
biotite/sequence/align/matrix_data/PAM50.mat +34 -0
biotite/sequence/align/matrix_data/PAM500.mat +34 -0
biotite/sequence/align/matrix_data/PAM60.mat +34 -0
biotite/sequence/align/matrix_data/PAM70.mat +34 -0
biotite/sequence/align/matrix_data/PAM80.mat +34 -0
biotite/sequence/align/matrix_data/PAM90.mat +34 -0
biotite/sequence/align/matrix_data/RBLOSUM52_5.0.mat +25 -0
biotite/sequence/align/matrix_data/RBLOSUM59_13p.mat +25 -0
biotite/sequence/align/matrix_data/RBLOSUM59_14.3.mat +25 -0
biotite/sequence/align/matrix_data/RBLOSUM64_5.0.mat +25 -0
biotite/sequence/align/matrix_data/RBLOSUM69_13p.mat +25 -0
biotite/sequence/align/matrix_data/RBLOSUM69_14.3.mat +25 -0
biotite/sequence/align/multiple.cpython-311-darwin.so +0 -0
biotite/sequence/align/multiple.pyx +620 -0
biotite/sequence/align/pairwise.cpython-311-darwin.so +0 -0
biotite/sequence/align/pairwise.pyx +587 -0
biotite/sequence/align/permutation.cpython-311-darwin.so +0 -0
biotite/sequence/align/permutation.pyx +305 -0
biotite/sequence/align/primes.txt +821 -0
biotite/sequence/align/selector.cpython-311-darwin.so +0 -0
biotite/sequence/align/selector.pyx +956 -0
biotite/sequence/align/statistics.py +265 -0
biotite/sequence/align/tracetable.cpython-311-darwin.so +0 -0
biotite/sequence/align/tracetable.pxd +64 -0
biotite/sequence/align/tracetable.pyx +370 -0
biotite/sequence/alphabet.py +566 -0
biotite/sequence/annotation.py +829 -0
biotite/sequence/codec.cpython-311-darwin.so +0 -0
biotite/sequence/codec.pyx +155 -0
biotite/sequence/codon.py +466 -0
biotite/sequence/codon_tables.txt +202 -0
biotite/sequence/graphics/__init__.py +33 -0
biotite/sequence/graphics/alignment.py +1034 -0
biotite/sequence/graphics/color_schemes/autumn.json +51 -0
biotite/sequence/graphics/color_schemes/blossom.json +51 -0
biotite/sequence/graphics/color_schemes/clustalx_dna.json +11 -0
biotite/sequence/graphics/color_schemes/clustalx_protein.json +28 -0
biotite/sequence/graphics/color_schemes/flower.json +51 -0
biotite/sequence/graphics/color_schemes/jalview_buried.json +31 -0
biotite/sequence/graphics/color_schemes/jalview_hydrophobicity.json +31 -0
biotite/sequence/graphics/color_schemes/jalview_prop_helix.json +31 -0
biotite/sequence/graphics/color_schemes/jalview_prop_strand.json +31 -0
biotite/sequence/graphics/color_schemes/jalview_prop_turn.json +31 -0
biotite/sequence/graphics/color_schemes/jalview_taylor.json +28 -0
biotite/sequence/graphics/color_schemes/jalview_zappo.json +28 -0
biotite/sequence/graphics/color_schemes/ocean.json +51 -0
biotite/sequence/graphics/color_schemes/pb_flower.json +39 -0
biotite/sequence/graphics/color_schemes/rainbow_dna.json +11 -0
biotite/sequence/graphics/color_schemes/rainbow_protein.json +30 -0
biotite/sequence/graphics/color_schemes/spring.json +51 -0
biotite/sequence/graphics/color_schemes/sunset.json +51 -0
biotite/sequence/graphics/color_schemes/wither.json +51 -0
biotite/sequence/graphics/colorschemes.py +139 -0
biotite/sequence/graphics/dendrogram.py +184 -0
biotite/sequence/graphics/features.py +510 -0
biotite/sequence/graphics/logo.py +110 -0
biotite/sequence/graphics/plasmid.py +661 -0
biotite/sequence/io/__init__.py +12 -0
biotite/sequence/io/fasta/__init__.py +22 -0
biotite/sequence/io/fasta/convert.py +273 -0
biotite/sequence/io/fasta/file.py +278 -0
biotite/sequence/io/fastq/__init__.py +19 -0
biotite/sequence/io/fastq/convert.py +120 -0
biotite/sequence/io/fastq/file.py +551 -0
biotite/sequence/io/genbank/__init__.py +17 -0
biotite/sequence/io/genbank/annotation.py +277 -0
biotite/sequence/io/genbank/file.py +575 -0
biotite/sequence/io/genbank/metadata.py +324 -0
biotite/sequence/io/genbank/sequence.py +172 -0
biotite/sequence/io/general.py +192 -0
biotite/sequence/io/gff/__init__.py +26 -0
biotite/sequence/io/gff/convert.py +133 -0
biotite/sequence/io/gff/file.py +434 -0
biotite/sequence/phylo/__init__.py +36 -0
biotite/sequence/phylo/nj.cpython-311-darwin.so +0 -0
biotite/sequence/phylo/nj.pyx +221 -0
biotite/sequence/phylo/tree.cpython-311-darwin.so +0 -0
biotite/sequence/phylo/tree.pyx +1169 -0
biotite/sequence/phylo/upgma.cpython-311-darwin.so +0 -0
biotite/sequence/phylo/upgma.pyx +164 -0
biotite/sequence/profile.py +456 -0
biotite/sequence/search.py +116 -0
biotite/sequence/seqtypes.py +556 -0
biotite/sequence/sequence.py +374 -0
biotite/structure/__init__.py +132 -0
biotite/structure/atoms.py +1455 -0
biotite/structure/basepairs.py +1415 -0
biotite/structure/bonds.cpython-311-darwin.so +0 -0
biotite/structure/bonds.pyx +1933 -0
biotite/structure/box.py +592 -0
biotite/structure/celllist.cpython-311-darwin.so +0 -0
biotite/structure/celllist.pyx +849 -0
biotite/structure/chains.py +298 -0
biotite/structure/charges.cpython-311-darwin.so +0 -0
biotite/structure/charges.pyx +520 -0
biotite/structure/compare.py +274 -0
biotite/structure/density.py +114 -0
biotite/structure/dotbracket.py +216 -0
biotite/structure/error.py +31 -0
biotite/structure/filter.py +585 -0
biotite/structure/geometry.py +697 -0
biotite/structure/graphics/__init__.py +13 -0
biotite/structure/graphics/atoms.py +226 -0
biotite/structure/graphics/rna.py +282 -0
biotite/structure/hbond.py +409 -0
biotite/structure/info/__init__.py +25 -0
biotite/structure/info/atom_masses.json +121 -0
biotite/structure/info/atoms.py +82 -0
biotite/structure/info/bonds.py +145 -0
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 +123 -0
biotite/structure/info/misc.py +144 -0
biotite/structure/info/radii.py +197 -0
biotite/structure/info/standardize.py +196 -0
biotite/structure/integrity.py +268 -0
biotite/structure/io/__init__.py +30 -0
biotite/structure/io/ctab.py +72 -0
biotite/structure/io/dcd/__init__.py +13 -0
biotite/structure/io/dcd/file.py +65 -0
biotite/structure/io/general.py +257 -0
biotite/structure/io/gro/__init__.py +14 -0
biotite/structure/io/gro/file.py +343 -0
biotite/structure/io/mmtf/__init__.py +21 -0
biotite/structure/io/mmtf/assembly.py +214 -0
biotite/structure/io/mmtf/convertarray.cpython-311-darwin.so +0 -0
biotite/structure/io/mmtf/convertarray.pyx +341 -0
biotite/structure/io/mmtf/convertfile.cpython-311-darwin.so +0 -0
biotite/structure/io/mmtf/convertfile.pyx +501 -0
biotite/structure/io/mmtf/decode.cpython-311-darwin.so +0 -0
biotite/structure/io/mmtf/decode.pyx +152 -0
biotite/structure/io/mmtf/encode.cpython-311-darwin.so +0 -0
biotite/structure/io/mmtf/encode.pyx +183 -0
biotite/structure/io/mmtf/file.py +233 -0
biotite/structure/io/mol/__init__.py +20 -0
biotite/structure/io/mol/convert.py +115 -0
biotite/structure/io/mol/ctab.py +414 -0
biotite/structure/io/mol/header.py +116 -0
biotite/structure/io/mol/mol.py +193 -0
biotite/structure/io/mol/sdf.py +916 -0
biotite/structure/io/netcdf/__init__.py +13 -0
biotite/structure/io/netcdf/file.py +63 -0
biotite/structure/io/npz/__init__.py +20 -0
biotite/structure/io/npz/file.py +152 -0
biotite/structure/io/pdb/__init__.py +20 -0
biotite/structure/io/pdb/convert.py +293 -0
biotite/structure/io/pdb/file.py +1240 -0
biotite/structure/io/pdb/hybrid36.cpython-311-darwin.so +0 -0
biotite/structure/io/pdb/hybrid36.pyx +242 -0
biotite/structure/io/pdbqt/__init__.py +15 -0
biotite/structure/io/pdbqt/convert.py +107 -0
biotite/structure/io/pdbqt/file.py +640 -0
biotite/structure/io/pdbx/__init__.py +23 -0
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 +1597 -0
biotite/structure/io/pdbx/encoding.cpython-311-darwin.so +0 -0
biotite/structure/io/pdbx/encoding.pyx +950 -0
biotite/structure/io/pdbx/legacy.py +267 -0
biotite/structure/io/tng/__init__.py +13 -0
biotite/structure/io/tng/file.py +46 -0
biotite/structure/io/trajfile.py +710 -0
biotite/structure/io/trr/__init__.py +13 -0
biotite/structure/io/trr/file.py +46 -0
biotite/structure/io/xtc/__init__.py +13 -0
biotite/structure/io/xtc/file.py +46 -0
biotite/structure/mechanics.py +75 -0
biotite/structure/molecules.py +353 -0
biotite/structure/pseudoknots.py +642 -0
biotite/structure/rdf.py +243 -0
biotite/structure/repair.py +253 -0
biotite/structure/residues.py +562 -0
biotite/structure/resutil.py +178 -0
biotite/structure/sasa.cpython-311-darwin.so +0 -0
biotite/structure/sasa.pyx +322 -0
biotite/structure/sequence.py +112 -0
biotite/structure/sse.py +327 -0
biotite/structure/superimpose.py +727 -0
biotite/structure/transform.py +504 -0
biotite/structure/util.py +98 -0
biotite/temp.py +86 -0
biotite/version.py +16 -0
biotite/visualize.py +251 -0
biotite-0.41.1.dist-info/METADATA +187 -0
biotite-0.41.1.dist-info/RECORD +340 -0
biotite-0.41.1.dist-info/WHEEL +4 -0
biotite-0.41.1.dist-info/licenses/LICENSE.rst +30 -0

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

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