biotite 1.5.0__cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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- biotite/__init__.py +18 -0
- biotite/application/__init__.py +69 -0
- biotite/application/application.py +276 -0
- biotite/application/autodock/__init__.py +12 -0
- biotite/application/autodock/app.py +500 -0
- biotite/application/blast/__init__.py +14 -0
- biotite/application/blast/alignment.py +92 -0
- biotite/application/blast/webapp.py +428 -0
- biotite/application/clustalo/__init__.py +12 -0
- biotite/application/clustalo/app.py +223 -0
- biotite/application/dssp/__init__.py +12 -0
- biotite/application/dssp/app.py +216 -0
- biotite/application/localapp.py +342 -0
- biotite/application/mafft/__init__.py +12 -0
- biotite/application/mafft/app.py +116 -0
- biotite/application/msaapp.py +363 -0
- biotite/application/muscle/__init__.py +13 -0
- biotite/application/muscle/app3.py +227 -0
- biotite/application/muscle/app5.py +163 -0
- biotite/application/sra/__init__.py +18 -0
- biotite/application/sra/app.py +447 -0
- biotite/application/tantan/__init__.py +12 -0
- biotite/application/tantan/app.py +199 -0
- biotite/application/util.py +77 -0
- biotite/application/viennarna/__init__.py +18 -0
- biotite/application/viennarna/rnaalifold.py +310 -0
- biotite/application/viennarna/rnafold.py +254 -0
- biotite/application/viennarna/rnaplot.py +208 -0
- biotite/application/viennarna/util.py +77 -0
- biotite/application/webapp.py +76 -0
- biotite/copyable.py +71 -0
- biotite/database/__init__.py +23 -0
- biotite/database/afdb/__init__.py +12 -0
- biotite/database/afdb/download.py +197 -0
- biotite/database/entrez/__init__.py +15 -0
- biotite/database/entrez/check.py +60 -0
- biotite/database/entrez/dbnames.py +101 -0
- biotite/database/entrez/download.py +228 -0
- biotite/database/entrez/key.py +44 -0
- biotite/database/entrez/query.py +263 -0
- biotite/database/error.py +16 -0
- biotite/database/pubchem/__init__.py +21 -0
- biotite/database/pubchem/download.py +258 -0
- biotite/database/pubchem/error.py +30 -0
- biotite/database/pubchem/query.py +819 -0
- biotite/database/pubchem/throttle.py +98 -0
- biotite/database/rcsb/__init__.py +13 -0
- biotite/database/rcsb/download.py +161 -0
- biotite/database/rcsb/query.py +963 -0
- biotite/database/uniprot/__init__.py +13 -0
- biotite/database/uniprot/check.py +40 -0
- biotite/database/uniprot/download.py +126 -0
- biotite/database/uniprot/query.py +292 -0
- biotite/file.py +244 -0
- 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 +1228 -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/__init__.py +84 -0
- biotite/sequence/align/__init__.py +199 -0
- biotite/sequence/align/alignment.py +702 -0
- biotite/sequence/align/banded.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/banded.pyx +652 -0
- biotite/sequence/align/buckets.py +71 -0
- biotite/sequence/align/cigar.py +425 -0
- biotite/sequence/align/kmeralphabet.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/kmeralphabet.pyx +595 -0
- biotite/sequence/align/kmersimilarity.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/kmersimilarity.pyx +233 -0
- biotite/sequence/align/kmertable.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/kmertable.pyx +3411 -0
- biotite/sequence/align/localgapped.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/localgapped.pyx +892 -0
- biotite/sequence/align/localungapped.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/localungapped.pyx +279 -0
- biotite/sequence/align/matrix.py +631 -0
- biotite/sequence/align/matrix_data/3Di.mat +24 -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/PB.license +21 -0
- biotite/sequence/align/matrix_data/PB.mat +18 -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-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/multiple.pyx +619 -0
- biotite/sequence/align/pairwise.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/pairwise.pyx +585 -0
- biotite/sequence/align/permutation.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/permutation.pyx +313 -0
- biotite/sequence/align/primes.txt +821 -0
- biotite/sequence/align/selector.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/selector.pyx +954 -0
- biotite/sequence/align/statistics.py +264 -0
- biotite/sequence/align/tracetable.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/align/tracetable.pxd +64 -0
- biotite/sequence/align/tracetable.pyx +370 -0
- biotite/sequence/alphabet.py +555 -0
- biotite/sequence/annotation.py +836 -0
- biotite/sequence/codec.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/codec.pyx +155 -0
- biotite/sequence/codon.py +476 -0
- biotite/sequence/codon_tables.txt +202 -0
- biotite/sequence/graphics/__init__.py +33 -0
- biotite/sequence/graphics/alignment.py +1101 -0
- biotite/sequence/graphics/color_schemes/3di_flower.json +48 -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 +40 -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 +170 -0
- biotite/sequence/graphics/dendrogram.py +231 -0
- biotite/sequence/graphics/features.py +544 -0
- biotite/sequence/graphics/logo.py +102 -0
- biotite/sequence/graphics/plasmid.py +712 -0
- biotite/sequence/io/__init__.py +12 -0
- biotite/sequence/io/fasta/__init__.py +22 -0
- biotite/sequence/io/fasta/convert.py +283 -0
- biotite/sequence/io/fasta/file.py +265 -0
- biotite/sequence/io/fastq/__init__.py +19 -0
- biotite/sequence/io/fastq/convert.py +117 -0
- biotite/sequence/io/fastq/file.py +507 -0
- biotite/sequence/io/genbank/__init__.py +17 -0
- biotite/sequence/io/genbank/annotation.py +269 -0
- biotite/sequence/io/genbank/file.py +573 -0
- biotite/sequence/io/genbank/metadata.py +336 -0
- biotite/sequence/io/genbank/sequence.py +173 -0
- biotite/sequence/io/general.py +201 -0
- biotite/sequence/io/gff/__init__.py +26 -0
- biotite/sequence/io/gff/convert.py +128 -0
- biotite/sequence/io/gff/file.py +449 -0
- biotite/sequence/phylo/__init__.py +36 -0
- biotite/sequence/phylo/nj.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/phylo/nj.pyx +221 -0
- biotite/sequence/phylo/tree.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/phylo/tree.pyx +1169 -0
- biotite/sequence/phylo/upgma.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/sequence/phylo/upgma.pyx +164 -0
- biotite/sequence/profile.py +561 -0
- biotite/sequence/search.py +117 -0
- biotite/sequence/seqtypes.py +720 -0
- biotite/sequence/sequence.py +373 -0
- biotite/setup_ccd.py +197 -0
- biotite/structure/__init__.py +135 -0
- biotite/structure/alphabet/__init__.py +25 -0
- biotite/structure/alphabet/encoder.py +332 -0
- biotite/structure/alphabet/encoder_weights_3di.kerasify +0 -0
- biotite/structure/alphabet/i3d.py +109 -0
- biotite/structure/alphabet/layers.py +86 -0
- biotite/structure/alphabet/pb.license +21 -0
- biotite/structure/alphabet/pb.py +170 -0
- biotite/structure/alphabet/unkerasify.py +128 -0
- biotite/structure/atoms.py +1562 -0
- biotite/structure/basepairs.py +1403 -0
- biotite/structure/bonds.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/structure/bonds.pyx +2036 -0
- biotite/structure/box.py +724 -0
- biotite/structure/celllist.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/structure/celllist.pyx +864 -0
- biotite/structure/chains.py +310 -0
- biotite/structure/charges.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/structure/charges.pyx +520 -0
- biotite/structure/compare.py +683 -0
- biotite/structure/density.py +109 -0
- biotite/structure/dotbracket.py +213 -0
- biotite/structure/error.py +39 -0
- biotite/structure/filter.py +591 -0
- biotite/structure/geometry.py +817 -0
- biotite/structure/graphics/__init__.py +13 -0
- biotite/structure/graphics/atoms.py +243 -0
- biotite/structure/graphics/rna.py +298 -0
- biotite/structure/hbond.py +425 -0
- biotite/structure/info/__init__.py +24 -0
- biotite/structure/info/atom_masses.json +121 -0
- biotite/structure/info/atoms.py +98 -0
- biotite/structure/info/bonds.py +149 -0
- biotite/structure/info/ccd.py +200 -0
- biotite/structure/info/components.bcif +0 -0
- biotite/structure/info/groups.py +128 -0
- biotite/structure/info/masses.py +121 -0
- biotite/structure/info/misc.py +137 -0
- biotite/structure/info/radii.py +267 -0
- biotite/structure/info/standardize.py +185 -0
- biotite/structure/integrity.py +213 -0
- biotite/structure/io/__init__.py +29 -0
- biotite/structure/io/dcd/__init__.py +13 -0
- biotite/structure/io/dcd/file.py +67 -0
- biotite/structure/io/general.py +243 -0
- biotite/structure/io/gro/__init__.py +14 -0
- biotite/structure/io/gro/file.py +343 -0
- biotite/structure/io/mol/__init__.py +20 -0
- biotite/structure/io/mol/convert.py +112 -0
- biotite/structure/io/mol/ctab.py +420 -0
- biotite/structure/io/mol/header.py +120 -0
- biotite/structure/io/mol/mol.py +149 -0
- biotite/structure/io/mol/sdf.py +940 -0
- biotite/structure/io/netcdf/__init__.py +13 -0
- biotite/structure/io/netcdf/file.py +64 -0
- biotite/structure/io/pdb/__init__.py +20 -0
- biotite/structure/io/pdb/convert.py +389 -0
- biotite/structure/io/pdb/file.py +1380 -0
- biotite/structure/io/pdb/hybrid36.cpython-311-x86_64-linux-gnu.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 +113 -0
- biotite/structure/io/pdbqt/file.py +688 -0
- biotite/structure/io/pdbx/__init__.py +23 -0
- biotite/structure/io/pdbx/bcif.py +674 -0
- biotite/structure/io/pdbx/cif.py +1091 -0
- biotite/structure/io/pdbx/component.py +251 -0
- biotite/structure/io/pdbx/compress.py +362 -0
- biotite/structure/io/pdbx/convert.py +2113 -0
- biotite/structure/io/pdbx/encoding.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/structure/io/pdbx/encoding.pyx +1078 -0
- biotite/structure/io/trajfile.py +696 -0
- biotite/structure/io/trr/__init__.py +13 -0
- biotite/structure/io/trr/file.py +43 -0
- biotite/structure/io/util.py +38 -0
- biotite/structure/io/xtc/__init__.py +13 -0
- biotite/structure/io/xtc/file.py +43 -0
- biotite/structure/mechanics.py +72 -0
- biotite/structure/molecules.py +337 -0
- biotite/structure/pseudoknots.py +622 -0
- biotite/structure/rdf.py +245 -0
- biotite/structure/repair.py +302 -0
- biotite/structure/residues.py +716 -0
- biotite/structure/rings.py +451 -0
- biotite/structure/sasa.cpython-311-x86_64-linux-gnu.so +0 -0
- biotite/structure/sasa.pyx +322 -0
- biotite/structure/segments.py +328 -0
- biotite/structure/sequence.py +110 -0
- biotite/structure/spacegroups.json +1567 -0
- biotite/structure/spacegroups.license +26 -0
- biotite/structure/sse.py +306 -0
- biotite/structure/superimpose.py +511 -0
- biotite/structure/tm.py +581 -0
- biotite/structure/transform.py +736 -0
- biotite/structure/util.py +160 -0
- biotite/version.py +34 -0
- biotite/visualize.py +375 -0
- biotite-1.5.0.dist-info/METADATA +162 -0
- biotite-1.5.0.dist-info/RECORD +354 -0
- biotite-1.5.0.dist-info/WHEEL +6 -0
- biotite-1.5.0.dist-info/licenses/LICENSE.rst +30 -0
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# Pre-computed list of prime numbers, approx. 5% apart,
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# with cheap div/modulo computation.
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# Suitable for efficient hash tables.
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# licensed under MIT license (https://spdx.org/licenses/MIT.html)
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# (c) 2020 Thomas Neumann
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