PyPI - biotite - Versions diffs - 0.41.2__cp311-cp311-win_amd64.whl → 1.0.0__cp311-cp311-win_amd64.whl - Mend

biotite 0.41.2__cp311-cp311-win_amd64.whl → 1.0.0__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 (205) hide show

biotite/__init__.py +2 -3
biotite/application/__init__.py +1 -1
biotite/application/application.py +20 -10
biotite/application/autodock/__init__.py +1 -1
biotite/application/autodock/app.py +74 -79
biotite/application/blast/__init__.py +1 -1
biotite/application/blast/alignment.py +19 -10
biotite/application/blast/webapp.py +92 -85
biotite/application/clustalo/__init__.py +1 -1
biotite/application/clustalo/app.py +46 -61
biotite/application/dssp/__init__.py +1 -1
biotite/application/dssp/app.py +8 -11
biotite/application/localapp.py +62 -60
biotite/application/mafft/__init__.py +1 -1
biotite/application/mafft/app.py +16 -22
biotite/application/msaapp.py +78 -89
biotite/application/muscle/__init__.py +1 -1
biotite/application/muscle/app3.py +50 -64
biotite/application/muscle/app5.py +23 -31
biotite/application/sra/__init__.py +1 -1
biotite/application/sra/app.py +64 -68
biotite/application/tantan/__init__.py +1 -1
biotite/application/tantan/app.py +22 -45
biotite/application/util.py +7 -9
biotite/application/viennarna/rnaalifold.py +34 -28
biotite/application/viennarna/rnafold.py +24 -39
biotite/application/viennarna/rnaplot.py +36 -21
biotite/application/viennarna/util.py +17 -12
biotite/application/webapp.py +13 -14
biotite/copyable.py +13 -13
biotite/database/__init__.py +1 -1
biotite/database/entrez/__init__.py +1 -1
biotite/database/entrez/check.py +2 -3
biotite/database/entrez/dbnames.py +7 -5
biotite/database/entrez/download.py +55 -49
biotite/database/entrez/key.py +1 -1
biotite/database/entrez/query.py +62 -23
biotite/database/error.py +2 -1
biotite/database/pubchem/__init__.py +1 -1
biotite/database/pubchem/download.py +43 -45
biotite/database/pubchem/error.py +2 -2
biotite/database/pubchem/query.py +34 -31
biotite/database/pubchem/throttle.py +3 -4
biotite/database/rcsb/__init__.py +1 -1
biotite/database/rcsb/download.py +44 -52
biotite/database/rcsb/query.py +85 -80
biotite/database/uniprot/check.py +6 -3
biotite/database/uniprot/download.py +6 -11
biotite/database/uniprot/query.py +115 -31
biotite/file.py +12 -31
biotite/sequence/__init__.py +3 -3
biotite/sequence/align/__init__.py +2 -2
biotite/sequence/align/alignment.py +99 -90
biotite/sequence/align/banded.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/buckets.py +12 -10
biotite/sequence/align/cigar.py +43 -52
biotite/sequence/align/kmeralphabet.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/kmeralphabet.pyx +55 -51
biotite/sequence/align/kmersimilarity.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.pyx +3 -2
biotite/sequence/align/localgapped.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/localungapped.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/matrix.py +81 -82
biotite/sequence/align/multiple.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/multiple.pyx +1 -1
biotite/sequence/align/pairwise.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/permutation.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/permutation.pyx +12 -4
biotite/sequence/align/selector.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/selector.pyx +52 -54
biotite/sequence/align/statistics.py +32 -33
biotite/sequence/align/tracetable.cp311-win_amd64.pyd +0 -0
biotite/sequence/alphabet.py +51 -65
biotite/sequence/annotation.py +78 -77
biotite/sequence/codec.cp311-win_amd64.pyd +0 -0
biotite/sequence/codon.py +90 -79
biotite/sequence/graphics/__init__.py +1 -1
biotite/sequence/graphics/alignment.py +184 -103
biotite/sequence/graphics/colorschemes.py +10 -12
biotite/sequence/graphics/dendrogram.py +79 -34
biotite/sequence/graphics/features.py +133 -99
biotite/sequence/graphics/logo.py +22 -28
biotite/sequence/graphics/plasmid.py +229 -178
biotite/sequence/io/fasta/__init__.py +1 -1
biotite/sequence/io/fasta/convert.py +44 -33
biotite/sequence/io/fasta/file.py +42 -55
biotite/sequence/io/fastq/__init__.py +1 -1
biotite/sequence/io/fastq/convert.py +11 -14
biotite/sequence/io/fastq/file.py +68 -112
biotite/sequence/io/genbank/__init__.py +2 -2
biotite/sequence/io/genbank/annotation.py +12 -20
biotite/sequence/io/genbank/file.py +74 -76
biotite/sequence/io/genbank/metadata.py +74 -62
biotite/sequence/io/genbank/sequence.py +13 -14
biotite/sequence/io/general.py +39 -30
biotite/sequence/io/gff/__init__.py +2 -2
biotite/sequence/io/gff/convert.py +10 -15
biotite/sequence/io/gff/file.py +81 -65
biotite/sequence/phylo/__init__.py +1 -1
biotite/sequence/phylo/nj.cp311-win_amd64.pyd +0 -0
biotite/sequence/phylo/tree.cp311-win_amd64.pyd +0 -0
biotite/sequence/phylo/upgma.cp311-win_amd64.pyd +0 -0
biotite/sequence/profile.py +57 -28
biotite/sequence/search.py +17 -15
biotite/sequence/seqtypes.py +200 -164
biotite/sequence/sequence.py +15 -17
biotite/structure/__init__.py +3 -3
biotite/structure/atoms.py +221 -235
biotite/structure/basepairs.py +260 -271
biotite/structure/bonds.cp311-win_amd64.pyd +0 -0
biotite/structure/bonds.pyx +29 -32
biotite/structure/box.py +67 -71
biotite/structure/celllist.cp311-win_amd64.pyd +0 -0
biotite/structure/chains.py +55 -39
biotite/structure/charges.cp311-win_amd64.pyd +0 -0
biotite/structure/compare.py +32 -32
biotite/structure/density.py +13 -18
biotite/structure/dotbracket.py +20 -22
biotite/structure/error.py +10 -2
biotite/structure/filter.py +82 -77
biotite/structure/geometry.py +130 -119
biotite/structure/graphics/atoms.py +60 -43
biotite/structure/graphics/rna.py +81 -68
biotite/structure/hbond.py +112 -93
biotite/structure/info/__init__.py +0 -2
biotite/structure/info/atoms.py +10 -11
biotite/structure/info/bonds.py +41 -43
biotite/structure/info/ccd.py +4 -5
biotite/structure/info/groups.py +1 -3
biotite/structure/info/masses.py +5 -10
biotite/structure/info/misc.py +1 -1
biotite/structure/info/radii.py +20 -20
biotite/structure/info/standardize.py +15 -26
biotite/structure/integrity.py +18 -71
biotite/structure/io/__init__.py +3 -4
biotite/structure/io/dcd/__init__.py +1 -1
biotite/structure/io/dcd/file.py +22 -20
biotite/structure/io/general.py +47 -61
biotite/structure/io/gro/__init__.py +1 -1
biotite/structure/io/gro/file.py +73 -72
biotite/structure/io/mol/__init__.py +1 -1
biotite/structure/io/mol/convert.py +8 -11
biotite/structure/io/mol/ctab.py +37 -36
biotite/structure/io/mol/header.py +14 -10
biotite/structure/io/mol/mol.py +9 -53
biotite/structure/io/mol/sdf.py +47 -50
biotite/structure/io/netcdf/__init__.py +1 -1
biotite/structure/io/netcdf/file.py +24 -23
biotite/structure/io/pdb/__init__.py +1 -1
biotite/structure/io/pdb/convert.py +32 -20
biotite/structure/io/pdb/file.py +151 -172
biotite/structure/io/pdb/hybrid36.cp311-win_amd64.pyd +0 -0
biotite/structure/io/pdbqt/__init__.py +1 -1
biotite/structure/io/pdbqt/convert.py +17 -11
biotite/structure/io/pdbqt/file.py +128 -80
biotite/structure/io/pdbx/__init__.py +1 -2
biotite/structure/io/pdbx/bcif.py +36 -44
biotite/structure/io/pdbx/cif.py +64 -62
biotite/structure/io/pdbx/component.py +10 -16
biotite/structure/io/pdbx/convert.py +235 -246
biotite/structure/io/pdbx/encoding.cp311-win_amd64.pyd +0 -0
biotite/structure/io/trajfile.py +76 -93
biotite/structure/io/trr/__init__.py +1 -1
biotite/structure/io/trr/file.py +12 -15
biotite/structure/io/xtc/__init__.py +1 -1
biotite/structure/io/xtc/file.py +11 -14
biotite/structure/mechanics.py +9 -11
biotite/structure/molecules.py +3 -4
biotite/structure/pseudoknots.py +53 -67
biotite/structure/rdf.py +23 -21
biotite/structure/repair.py +137 -86
biotite/structure/residues.py +26 -16
biotite/structure/sasa.cp311-win_amd64.pyd +0 -0
biotite/structure/{resutil.py → segments.py} +24 -23
biotite/structure/sequence.py +10 -11
biotite/structure/sse.py +100 -119
biotite/structure/superimpose.py +39 -77
biotite/structure/transform.py +97 -71
biotite/structure/util.py +11 -13
biotite/version.py +2 -2
biotite/visualize.py +69 -55
{biotite-0.41.2.dist-info → biotite-1.0.0.dist-info}/METADATA +5 -5
biotite-1.0.0.dist-info/RECORD +322 -0
biotite/structure/io/ctab.py +0 -72
biotite/structure/io/mmtf/__init__.py +0 -21
biotite/structure/io/mmtf/assembly.py +0 -214
biotite/structure/io/mmtf/convertarray.cp311-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/convertarray.pyx +0 -341
biotite/structure/io/mmtf/convertfile.cp311-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/convertfile.pyx +0 -501
biotite/structure/io/mmtf/decode.cp311-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/decode.pyx +0 -152
biotite/structure/io/mmtf/encode.cp311-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/encode.pyx +0 -183
biotite/structure/io/mmtf/file.py +0 -233
biotite/structure/io/npz/__init__.py +0 -20
biotite/structure/io/npz/file.py +0 -152
biotite/structure/io/pdbx/legacy.py +0 -267
biotite/structure/io/tng/__init__.py +0 -13
biotite/structure/io/tng/file.py +0 -46
biotite/temp.py +0 -86
biotite-0.41.2.dist-info/RECORD +0 -340
{biotite-0.41.2.dist-info → biotite-1.0.0.dist-info}/WHEEL +0 -0
{biotite-0.41.2.dist-info → biotite-1.0.0.dist-info}/licenses/LICENSE.rst +0 -0

biotite-0.41.2.dist-info/RECORD DELETED Viewed

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