PyPI - biotite - Versions diffs - 1.0.1__cp311-cp311-win_amd64.whl → 1.2.0__cp311-cp311-win_amd64.whl - Mend

biotite 1.0.1__cp311-cp311-win_amd64.whl → 1.2.0__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 (177) hide show

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/dssp/app.py +13 -3
biotite/application/localapp.py +36 -2
biotite/application/msaapp.py +10 -10
biotite/application/muscle/app3.py +5 -18
biotite/application/muscle/app5.py +5 -5
biotite/application/sra/app.py +0 -5
biotite/application/util.py +22 -2
biotite/application/viennarna/rnaalifold.py +8 -8
biotite/application/viennarna/rnaplot.py +9 -3
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 +8 -9
biotite/database/uniprot/check.py +22 -17
biotite/database/uniprot/download.py +3 -6
biotite/database/uniprot/query.py +4 -5
biotite/file.py +14 -2
biotite/interface/__init__.py +19 -0
biotite/interface/openmm/__init__.py +16 -0
biotite/interface/openmm/state.py +93 -0
biotite/interface/openmm/system.py +227 -0
biotite/interface/pymol/__init__.py +198 -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 +15 -0
biotite/interface/rdkit/mol.py +490 -0
biotite/interface/version.py +71 -0
biotite/interface/warning.py +19 -0
biotite/sequence/align/__init__.py +0 -4
biotite/sequence/align/alignment.py +49 -14
biotite/sequence/align/banded.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/banded.pyx +26 -26
biotite/sequence/align/cigar.py +2 -2
biotite/sequence/align/kmeralphabet.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/kmeralphabet.pyx +19 -2
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 +58 -48
biotite/sequence/align/localgapped.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/localgapped.pyx +47 -47
biotite/sequence/align/localungapped.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/localungapped.pyx +10 -10
biotite/sequence/align/matrix.py +284 -57
biotite/sequence/align/matrix_data/3Di.mat +24 -0
biotite/sequence/align/matrix_data/PB.license +21 -0
biotite/sequence/align/matrix_data/PB.mat +18 -0
biotite/sequence/align/multiple.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/pairwise.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/pairwise.pyx +35 -35
biotite/sequence/align/permutation.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/selector.cp311-win_amd64.pyd +0 -0
biotite/sequence/align/selector.pyx +2 -2
biotite/sequence/align/statistics.py +1 -1
biotite/sequence/align/tracetable.cp311-win_amd64.pyd +0 -0
biotite/sequence/alphabet.py +5 -2
biotite/sequence/annotation.py +19 -13
biotite/sequence/codec.cp311-win_amd64.pyd +0 -0
biotite/sequence/codon.py +1 -2
biotite/sequence/graphics/alignment.py +25 -39
biotite/sequence/graphics/color_schemes/3di_flower.json +48 -0
biotite/sequence/graphics/color_schemes/pb_flower.json +2 -1
biotite/sequence/graphics/colorschemes.py +44 -11
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.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 +105 -29
biotite/sequence/search.py +0 -1
biotite/sequence/seqtypes.py +136 -8
biotite/sequence/sequence.py +1 -2
biotite/setup_ccd.py +197 -0
biotite/structure/__init__.py +6 -3
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 +163 -66
biotite/structure/basepairs.py +26 -26
biotite/structure/bonds.cp311-win_amd64.pyd +0 -0
biotite/structure/bonds.pyx +79 -25
biotite/structure/box.py +19 -21
biotite/structure/celllist.cp311-win_amd64.pyd +0 -0
biotite/structure/celllist.pyx +83 -67
biotite/structure/chains.py +5 -37
biotite/structure/charges.cp311-win_amd64.pyd +0 -0
biotite/structure/compare.py +420 -13
biotite/structure/density.py +1 -1
biotite/structure/dotbracket.py +27 -28
biotite/structure/filter.py +8 -8
biotite/structure/geometry.py +74 -127
biotite/structure/hbond.py +17 -19
biotite/structure/info/__init__.py +1 -0
biotite/structure/info/atoms.py +24 -15
biotite/structure/info/bonds.py +12 -6
biotite/structure/info/ccd.py +125 -34
biotite/structure/info/{ccd/components.bcif → components.bcif} +0 -0
biotite/structure/info/groups.py +62 -19
biotite/structure/info/masses.py +9 -6
biotite/structure/info/misc.py +15 -22
biotite/structure/info/radii.py +92 -22
biotite/structure/info/standardize.py +4 -4
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 +80 -53
biotite/structure/io/pdb/convert.py +4 -3
biotite/structure/io/pdb/file.py +85 -25
biotite/structure/io/pdb/hybrid36.cp311-win_amd64.pyd +0 -0
biotite/structure/io/pdbqt/file.py +36 -36
biotite/structure/io/pdbx/__init__.py +1 -0
biotite/structure/io/pdbx/bcif.py +54 -15
biotite/structure/io/pdbx/cif.py +92 -66
biotite/structure/io/pdbx/component.py +15 -4
biotite/structure/io/pdbx/compress.py +321 -0
biotite/structure/io/pdbx/convert.py +410 -75
biotite/structure/io/pdbx/encoding.cp311-win_amd64.pyd +0 -0
biotite/structure/io/pdbx/encoding.pyx +98 -17
biotite/structure/io/trajfile.py +9 -6
biotite/structure/io/util.py +38 -0
biotite/structure/mechanics.py +0 -1
biotite/structure/molecules.py +141 -156
biotite/structure/pseudoknots.py +7 -13
biotite/structure/repair.py +2 -4
biotite/structure/residues.py +13 -24
biotite/structure/rings.py +335 -0
biotite/structure/sasa.cp311-win_amd64.pyd +0 -0
biotite/structure/sasa.pyx +2 -1
biotite/structure/segments.py +69 -11
biotite/structure/sequence.py +0 -1
biotite/structure/sse.py +0 -2
biotite/structure/superimpose.py +74 -62
biotite/structure/tm.py +581 -0
biotite/structure/transform.py +12 -25
biotite/structure/util.py +76 -4
biotite/version.py +9 -4
biotite/visualize.py +111 -1
{biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/METADATA +6 -2
{biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/RECORD +173 -143
biotite/structure/info/ccd/README.rst +0 -8
biotite/structure/info/ccd/amino_acids.txt +0 -1663
biotite/structure/info/ccd/carbohydrates.txt +0 -1135
biotite/structure/info/ccd/nucleotides.txt +0 -798
{biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/WHEEL +0 -0
{biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/licenses/LICENSE.rst +0 -0

{biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/RECORD RENAMED Viewed

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@@ -164,6 +183,8 @@ biotite/sequence/align/matrix_data/PAM60.mat,sha256=tEP5rtSKfgJt14UAQd1dhHO4BDBz
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@@ -171,12 +192,13 @@ biotite/sequence/align/matrix_data/RBLOSUM64_5.0.mat,sha256=E52mnslKgzhNeB6n3LNT
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@@ -190,7 +212,7 @@ biotite/sequence/graphics/color_schemes/jalview_prop_turn.json,sha256=Iw3f9dAmt9
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biotite/structure/info/ccd/README.rst DELETED Viewed

@@ -1,8 +0,0 @@
-These files are based on the
-`Chemical Component Dictionary <https://www.wwpdb.org/data/ccd>`_
-and were created using ``setup_ccd.py``.
-To keep the size of the repository small, the original commit should be
-rewritten, if the formats of the affected files are compatible with the
-original ones.
-The name of the commit is ``Add CCD dataset``.