biotite 1.0.1__cp312-cp312-win_amd64.whl → 1.1.0__cp312-cp312-win_amd64.whl

{biotite-1.0.1.dist-info → biotite-1.1.0.dist-info}/RECORD

@@ -1,13 +1,14 @@
 biotite/__init__.py,sha256=gzqOy5P7Zf667uYuUwqjLLW0GiBdqc23NLcZaXMuHKw,563
 biotite/copyable.py,sha256=Qnja44k58dAc3WkIUM0svqrbvqO9pSV-Atr9MUJSoCI,1968
 biotite/file.py,sha256=oZdBRv34nrGFJ7ZIrSW9uf4NSk9H3Mg0WxgbQqxibbU,6756
-biotite/version.py,sha256=XglbmfebHuSdifAMbIgy8xq3Isq3dxwcF1ZQoKBpUa0,427
+biotite/setup_ccd.py,sha256=9StRz4qPVdTJNrPUoA_liwvkKnTb8O0U8PDxt1tDVwc,6248
+biotite/version.py,sha256=mLrG-mC5i2vs5IEM3ZgT5S9ZdaqM1wQHESPk1-Rj79o,427
 biotite/visualize.py,sha256=d926kscZJdQKYM9v7CUaAeMial11N8l_NyC7_fVv7wQ,10277
 biotite/application/__init__.py,sha256=Rei3EwlpCnC_cJNQoTJYY_Gw_qLdsqgnRxV5b1slHJU,3148
 biotite/application/application.py,sha256=WKGVuCJ5WTwuoOmSWAklZwAGbEgJaTdf3fFmb4f1Iv8,8374
-biotite/application/localapp.py,sha256=MAhpvSbooc5VqfEgrXyZaRZ8QHs2N7NFX_vXvGIOKvU,9594
+biotite/application/localapp.py,sha256=3WgiDMNXL1T7K5_g1URkLS-OqfBVQE48E7FcwoglfUY,10612
 biotite/application/msaapp.py,sha256=NZJVMWyx7TgiDI5NP7FMZx1ZOUfYJU8wKxBqcle-Pmg,12339
-biotite/application/util.py,sha256=rmtP_KHmP3WuZnfPRT2mpU_BvI9cRaDqWxUlupnaPl4,2152
+biotite/application/util.py,sha256=GgOezqMoxjXeWLwce1HL3gWByZAWmoRhWc3JRjqo2q8,2168
 biotite/application/webapp.py,sha256=zkkMc9zyaDancX24TwUkBSKA2NQR70QQLALVZ9XZKHc,2237
 biotite/application/autodock/__init__.py,sha256=QtcZDgjFXYaHYSoVtnx8Bs2YA9TvwCg0fSkMfrxKK3k,327
 biotite/application/autodock/app.py,sha256=zfqKFYT6K8zKrHN1uotIX-gBAKdj_kzB7klRThxClO8,19186
@@ -17,12 +18,12 @@ biotite/application/blast/webapp.py,sha256=byuSfcaKHKokxUwf2fjT3-DTtqsiSD0gB3lys
 biotite/application/clustalo/__init__.py,sha256=UtEQiS9nDZF9-Sup3kbi06mTjv6YRD9Qbu5A722bNlY,338
 biotite/application/clustalo/app.py,sha256=TMZEHqZc_czqAFtsEg9cYIPTCCLltbgbEqC6zhas2WM,7640
 biotite/application/dssp/__init__.py,sha256=smuKF9_8g5xzY-MFjYXTYa3wbTfQD4g6L3TDCfMTr8w,335
-biotite/application/dssp/app.py,sha256=OvpOBF0H5UKua4bhXv-F2hcHFmWy8P9CMyvrVHH7lVs,4989
+biotite/application/dssp/app.py,sha256=ZBgW5R5Y1nt1D69imUpc_79-XPm9N3yqfdZKxgVc8-M,5482
 biotite/application/mafft/__init__.py,sha256=urPUmmuKAsB9DQeEeaj8EDt3uL0UjgBSo76H2HnLsLs,327
 biotite/application/mafft/app.py,sha256=W_iWXuaO0CaCFpnTyawlmQ1P0wt9pnGnwr-AzAudLM0,3397
 biotite/application/muscle/__init__.py,sha256=26qqctlXpZqoFBD1K_y_Zv7QZfDdMHOodGAXW20r42Q,351
-biotite/application/muscle/app3.py,sha256=b08T6ID4NJ-Pbw_R0NCI2a5lvB-_5alcDM6TBXW5IiY,8325
-biotite/application/muscle/app5.py,sha256=TGIQzz8BCw_R2fqcEFm3P1E-QiYl5OzAvzSvwrzGZZQ,4589
+biotite/application/muscle/app3.py,sha256=OmugKWOwQhI6a7Rg0rOFD4_AHlLJjxG6KfoI_ANzprA,7840
+biotite/application/muscle/app5.py,sha256=KPwqhPjSUPRH0y0wd2Qg9dCEt8KY_lZiJ5MHK2nJYNc,4598
 biotite/application/sra/__init__.py,sha256=GwfAKbOfTTYaLVdTwdkJxCMCY-SUd7WsN7BDAU2Xq7A,571
 biotite/application/sra/app.py,sha256=PIiBIy5wZfzcyDEh2N3oD9I_HwnCDWE4KJ7fy0VB_AY,16316
 biotite/application/tantan/__init__.py,sha256=XivhGt3vpQ7EvRKdxT_jQNXIPnvVxAUXCnHYZkSuiHY,340
@@ -30,7 +31,7 @@ biotite/application/tantan/app.py,sha256=nWE3rlDqf3-jfpIXUw1ddH4ooiD2lZ1GeqBvGXE
 biotite/application/viennarna/__init__.py,sha256=HlvHvgsTdzTbq3e9luAmMP-4DbkiBqx5ru69swdz4ns,491
 biotite/application/viennarna/rnaalifold.py,sha256=sLFebN8_ThaC0r4tBPAsYWHrbSYAhwdr3D6QxSj3dlI,10918
 biotite/application/viennarna/rnafold.py,sha256=skqZzqE-otS6uL38isGpikLUbwf8srsOQirINB6qi-8,8164
-biotite/application/viennarna/rnaplot.py,sha256=C9Nfw6fBDfm2Yz_WCVtdmg_hovXKMUM2pMzMs21Lulw,6529
+biotite/application/viennarna/rnaplot.py,sha256=WOBsfgYZ0pXmpbCc4NFHfdFITfsLhgBKDvZtWSxTqiI,6622
 biotite/application/viennarna/util.py,sha256=rJizJjwn7yw2lfnz93sHNVle04WwpdfskhBkT6gWbsE,2711
 biotite/database/__init__.py,sha256=N3PuLKuEbQ0J55CddwryBGiLfYSazC697F8KnxizrKY,748
 biotite/database/error.py,sha256=L_FvDa-F4XUaCIVo6ZtLXIMn6P-cv783lvxR_Rtluqw,426
@@ -47,32 +48,32 @@ biotite/database/pubchem/query.py,sha256=dPONXpyWc3158KP_7DRxZ2JMEI5qjyoe3atIkcF
 biotite/database/pubchem/throttle.py,sha256=V4RzypMfh1IaBC8yZrH1l8W1k7v2KLpj1_fK94k-__w,3384
 biotite/database/rcsb/__init__.py,sha256=BKYOAhSIX1zb00wp_6bw30M7XGliu64B35Dm2Gf-A14,345
 biotite/database/rcsb/download.py,sha256=Orst9nfBrcDJhUyfj3aS8Tf11N9tdNSpwAoLUfWXgnE,5781
-biotite/database/rcsb/query.py,sha256=ygCFI2JguXbofOlAKKckhC5N_eLV-eXrwkbU2ck7-Eg,33866
+biotite/database/rcsb/query.py,sha256=pSNcDTEBiTAWMDRLV3SKMfNL4s_q4nM4w8gOcpWTRk4,33883
 biotite/database/uniprot/__init__.py,sha256=0U1mt1nphhPZomlauOeMEVDfFx-6Npyi2eGsf6ztH6E,347
-biotite/database/uniprot/check.py,sha256=CLY9XaxuhY6-GkwfY8_mtLJVChsh_tRYTf_AfjFyeoQ,1327
-biotite/database/uniprot/download.py,sha256=pCdJ3ihdlW6tMNQIyniZ1kTBABF7qHxmDZuE_NX1wHk,4449
-biotite/database/uniprot/query.py,sha256=_iqdxWKBIfmFlb7gZw-pQDj-2-KTwFYeyfcHO2n7oiI,7856
+biotite/database/uniprot/check.py,sha256=mcG3V3iVEubQAlGyBKGM1QQ9nhmjLIlVMWPDUa_oYNo,1413
+biotite/database/uniprot/download.py,sha256=7lVV4bZmhw_m7vXdYgYSmNrSkftPzW0a7RXtPLrEy8I,4437
+biotite/database/uniprot/query.py,sha256=jNEsV-EoNQUB7JZC7byMoLuHY_WsVyiosJC55XHPo-A,7844
 biotite/sequence/__init__.py,sha256=fUoOYLTavBTicHu-JCQkvrCAyRfKRspfCItufOBDGGE,3507
-biotite/sequence/alphabet.py,sha256=PM_aKD5ivsU5Ral_z6SuKw6rX-wkB3CWOlZs_9VzMr4,17742
+biotite/sequence/alphabet.py,sha256=CzgnebrYH_zCnBD7arCAUX_46ZzYHMWFKKDoaKVY_cY,17800
 biotite/sequence/annotation.py,sha256=Z-Q03m4EE32wAeaG7ov0BuoG4mH7Vr3EM59v_5qgwJ8,30343
 biotite/sequence/codec.pyx,sha256=JIKPODmlk7RGW1GIhoUSrbfS1XRJa6vbOb5ur-62jIc,5116
 biotite/sequence/codon.py,sha256=zPe7lKcdxM8IvBwF42IBWeaVufMFXbuwViaMBGHgWqs,16869
 biotite/sequence/codon_tables.txt,sha256=knCf-Q8tZToxEr7s4nM9xuq_5BlhL_IYEyNh9rfwWEQ,10411
-biotite/sequence/profile.py,sha256=sEp5UYFykZwjge94xlVmCxJtFVE6LrrCfZ9hnABbjWg,17611
+biotite/sequence/profile.py,sha256=62fXOvouRGuPZ1TD-Y73DI0ui7ZOzSwX1hDCCGtJmrg,19942
 biotite/sequence/search.py,sha256=J6ogMj58ft6bLGUw6IMckwG4nJonIojiICyAvv7mn7w,3207
-biotite/sequence/seqtypes.py,sha256=ACzLqjzrzE0PJSjv-GKDHaNHK_sQ4EHtug-vPl4r5qc,19938
+biotite/sequence/seqtypes.py,sha256=FENMFahEBe86svQa7csx1HZHAHp7DIJ39D_xBSUbVXM,23806
 biotite/sequence/sequence.py,sha256=lRfkfK5r5awT8a4jqEZSn-z3Q1XjcS3BsqxTLBTKWXw,12067
 biotite/sequence/align/__init__.py,sha256=wZEaGdpVi5ei6giroWWphOtfHn_jqBZPNpyAYqqg2gc,4918
-biotite/sequence/align/alignment.py,sha256=aUMXPUrtTmXRhTUX9q2KIHjEwa1rM22t3Ue_q9aoqfg,22018
-biotite/sequence/align/banded.pyx,sha256=LmRd4yR3lozB9usUvvREsbSsHMTFIAMC3RXbUbaawTs,26043
+biotite/sequence/align/alignment.py,sha256=wdqW29Fi_F0se9DJn3_nQmiyAkVgvLYhT-n2Ta2SF9A,22373
+biotite/sequence/align/banded.pyx,sha256=BB41oDfUs4yE7U3Q5CfE66B7BmFTMwOcFnmEJ9xLukA,26044
 biotite/sequence/align/buckets.py,sha256=3QLzBDorc0ZYJv2SNuRn-mWmT3I2XljfCD1AoNV3ldw,2535
 biotite/sequence/align/cigar.py,sha256=DWkAlFL05b3Px0Bek9KNnU6UhvjkXxw7rCRsilREAKU,14710
-biotite/sequence/align/kmeralphabet.pyx,sha256=gNnkUJa1aEIhpxG_pPa6ChcG7PuW5ZJUM3RsnlSXoyw,18693
+biotite/sequence/align/kmeralphabet.pyx,sha256=RSONYcLGOMGbW0qW2dXRlXhGxFVpVie3DDTwRTvU3tI,19231
 biotite/sequence/align/kmersimilarity.pyx,sha256=tmAKKZY2JOvnPjU0PQqInvb_MRo7whUxgX0iVZNWIbg,8665
-biotite/sequence/align/kmertable.pyx,sha256=IkmJgU-3e5qT3TTVfPXWc-Z7L8SqmWWUhwOqe4gOSD0,124735
+biotite/sequence/align/kmertable.pyx,sha256=NmQeOlRTfr7B8hqX7N5lg8VsLLVOsG9MSRjVWsgUhPo,125108
 biotite/sequence/align/localgapped.pyx,sha256=523kib6BGDASd4AYZw4j0AMx7c_TfKr_gO-LTPL2Puo,34277
 biotite/sequence/align/localungapped.pyx,sha256=Uid8_OGa2yLrLeoblEF6VqUanqtvcAMgJHKWBfz9Ppw,9974
-biotite/sequence/align/matrix.py,sha256=Xwc6MKCsy7e9tcJn5pXkWs-5-lvvC_Nv8WIvzoJkqLA,13124
+biotite/sequence/align/matrix.py,sha256=b4dCr6FQGIfwnSBKQ5tbHvxHS55JTTalH1KGQWD9vhI,22725
 biotite/sequence/align/multiple.pyx,sha256=J9MLWqzSvJN-1eWsjCPGlCdr51cSYkkiwyjyyE46qFo,22585
 biotite/sequence/align/pairwise.pyx,sha256=P8aiNasedIZPuTrNfUSkQK_6fK5msdCmvcXAVHnPgP0,23422
 biotite/sequence/align/permutation.pyx,sha256=G9quD4yyP_5BCgVkJE_Xf_9wovn1Bg_MXPtltopaUYw,10340
@@ -81,6 +82,7 @@ biotite/sequence/align/selector.pyx,sha256=xVc2DyA4KHTunzulYaiS225Ghaw3Hm5_44hdS
 biotite/sequence/align/statistics.py,sha256=aAB_RRl7wjUhqlHtRyfrw1XQ91WsZ45fHePnmsL17rQ,9919
 biotite/sequence/align/tracetable.pxd,sha256=JhxS9sl5wV6HD_cJMXaBt1zm_4_y5twsBs5buMVDYI0,2888
 biotite/sequence/align/tracetable.pyx,sha256=ReX5kId42RQqlMZmNRpzMmF3_9Z4laL8dXK88IiW-6c,15824
+biotite/sequence/align/matrix_data/3Di.mat,sha256=-vJKsfx0GvUTWQLn6E4iQqAb17886onYD5277vE0DSc,2044
 biotite/sequence/align/matrix_data/BLOSUM100.mat,sha256=W-q25YSvx6Eh_OMpjlHAxHS1CN2n8pfKvxVzTYeE-ck,2205
 biotite/sequence/align/matrix_data/BLOSUM30.mat,sha256=s5AR5BjhXVly2A900JiriOodp2I5tv95wqw87TUAyOk,2153
 biotite/sequence/align/matrix_data/BLOSUM35.mat,sha256=0PksmPiSphINnKFWBh1jQieLg0F5bIISIwZVwS7trFc,2153
@@ -164,6 +166,8 @@ biotite/sequence/align/matrix_data/PAM60.mat,sha256=tEP5rtSKfgJt14UAQd1dhHO4BDBz
 biotite/sequence/align/matrix_data/PAM70.mat,sha256=hYpO31Doaim0281R8CSaLuN3ufFslxH4sho8ErMpqx4,2700
 biotite/sequence/align/matrix_data/PAM80.mat,sha256=Q6B4P1vT9zLD4zXWpuBUrRfPgmjTLTOcF_yMnKeDgWI,2700
 biotite/sequence/align/matrix_data/PAM90.mat,sha256=kB9YeLnQcIJwSRrIm3Ds961BH44ZTPVFjPZ2ZoJjhXQ,2700
+biotite/sequence/align/matrix_data/PB.license,sha256=rRrKDQMPavU4XuIApytyQgVJLESA4rij074TO2sNijs,1111
+biotite/sequence/align/matrix_data/PB.mat,sha256=uzRYqr9cWWM9aJYyT7n2ZDWRcWLCXTJSj4UvDviB0zI,1711
 biotite/sequence/align/matrix_data/RBLOSUM52_5.0.mat,sha256=x9VzlyYY5EZ8xei0rnQ2ytuG6EGS-hUTxk7h1MSAyII,1875
 biotite/sequence/align/matrix_data/RBLOSUM59_13p.mat,sha256=t2RTYBWH7pD2mr8OGH7KGu8DIs14TI3SDh_OF75YQyM,1875
 biotite/sequence/align/matrix_data/RBLOSUM59_14.3.mat,sha256=ppkCtdb5MiZFF4JNokg3X1gf1mDN4qGV0C_dCHcbsbs,1875
@@ -172,11 +176,12 @@ biotite/sequence/align/matrix_data/RBLOSUM69_13p.mat,sha256=xABdTJkFD8zQKcmyvnt6
 biotite/sequence/align/matrix_data/RBLOSUM69_14.3.mat,sha256=FzdtLvS9xnAvNH_xCZ9P1ydCHCMaFeYC6VkqA844x5Y,1875
 biotite/sequence/graphics/__init__.py,sha256=nQMB_4upyPX-9_f6rThY9-KSRkGtBi_WRxMc92v2A6I,1185
 biotite/sequence/graphics/alignment.py,sha256=pgmbX8R2rHby3ZTq6ER7UZwGjrIPdEhVxSDKHn_TmoY,40645
-biotite/sequence/graphics/colorschemes.py,sha256=BO1Y9VnCTLBcN3XiL6G29oWt8T8D5KWuM8IegC-KOyU,4610
+biotite/sequence/graphics/colorschemes.py,sha256=ISSJvX0c840TJEhnjH-Y57jo8LhHCuaU3DTFNu3nxWI,5687
 biotite/sequence/graphics/dendrogram.py,sha256=txLxITGdxY_iUXwtcxqxMqK00GUR0MPIayVxdTqz2uM,7821
 biotite/sequence/graphics/features.py,sha256=L1RksYnwHy0bHYWNUyeso4krWLrYrxekj9zxp9bYpuQ,17839
 biotite/sequence/graphics/logo.py,sha256=EYaz9h9rSCUn2LLLKBsLon7BA2s1vRfsGdPOQLFoGto,3923
 biotite/sequence/graphics/plasmid.py,sha256=9SZItKWdLSCdTbolBsWDPyVDb-75aYGtTsPKH_9ywio,26714
+biotite/sequence/graphics/color_schemes/3di_flower.json,sha256=O5CIZo3B4kA6ItoEAFCcCwvkFlz5-9GH4fRH-Hh6Ugc,964
 biotite/sequence/graphics/color_schemes/autumn.json,sha256=ykykAiaOGDBaBLXwtjqVBRYmce-8uK4NgtwHgnkLfio,893
 biotite/sequence/graphics/color_schemes/blossom.json,sha256=puHv-OkH37s_6kPSM_Uq6wnbnHdGu08Mdq-QxNu2fv0,894
 biotite/sequence/graphics/color_schemes/clustalx_dna.json,sha256=54lrQvggpxSKGTy4n-yOvFrTwGxucJeo2ruzrghXfSk,259
@@ -190,7 +195,7 @@ biotite/sequence/graphics/color_schemes/jalview_prop_turn.json,sha256=Iw3f9dAmt9
 biotite/sequence/graphics/color_schemes/jalview_taylor.json,sha256=EIjhkViMxbIE67_YUGTi-JYv55bLLGVr9Y5ah_J4cug,729
 biotite/sequence/graphics/color_schemes/jalview_zappo.json,sha256=jzg12_f-7cmxtVKwgqNZCj1NxSKjKCUG2tZdc7ihvqA,728
 biotite/sequence/graphics/color_schemes/ocean.json,sha256=hfQeJFs90GA4q85Is6kE6NROqctuQY_N8TvfbD1FvAU,892
-biotite/sequence/graphics/color_schemes/pb_flower.json,sha256=tFGmH2bKbT1NEtrpKDYVAfU7Qv1FYF6N86bt4FoudBI,702
+biotite/sequence/graphics/color_schemes/pb_flower.json,sha256=0OhKObhab7Oyj8ChVEGdOPz9FshhhPuakwUV5f5mS_4,716
 biotite/sequence/graphics/color_schemes/rainbow_dna.json,sha256=Lw_My4qOSFPRCpiEJWZQU4kUvy30mXx_-YS_gcIWqiU,258
 biotite/sequence/graphics/color_schemes/rainbow_protein.json,sha256=Ulm9UqjT_klqIz93g54qz5VxlKDJNSLi4ywpyElfCzU,782
 biotite/sequence/graphics/color_schemes/spring.json,sha256=Yw49LbAU_TFE_L_mt4wocoiVUHpZEMjrAZi2pWUuR5s,893
@@ -216,10 +221,10 @@ biotite/sequence/phylo/__init__.py,sha256=aNP1B9DNNTXMyiqWkzF6JZFynlcmIg-bDeN-eD
 biotite/sequence/phylo/nj.pyx,sha256=YOseJP7fKCnqhh8w3mK1z3fw6cKF5sU5oRkb1D3X9vI,7501
 biotite/sequence/phylo/tree.pyx,sha256=kmT2kO9cH3svQOxsyuPLfbUsWnTNdfVrx5xaxcmTC3I,40374
 biotite/sequence/phylo/upgma.pyx,sha256=llgc-9fEOU-D1a-ESMSIAoPjHvsd_L0-GnwkL-uzWNc,5376
-biotite/structure/__init__.py,sha256=KwHwWyOA4EETmuAvS894YV7jWXopuCh1CWfKY9rmfCc,5456
-biotite/structure/atoms.py,sha256=6eFRFYTXVokF-0NehXxhxcP_AoWxZKjJGk-UpP-Iig8,48876
+biotite/structure/__init__.py,sha256=YNaoZja9BAB7HA1dEiMpvEg1jFieHUt6mRmpybIGGi0,5582
+biotite/structure/atoms.py,sha256=GV47SmC_BBok1mZEiQBN4lwrSLR9bczWa1V2z42qt-Y,52012
 biotite/structure/basepairs.py,sha256=eZF67fnecHkvDYnIlfeejdJC7sCDWYqOghjbweLoxFE,51163
-biotite/structure/bonds.pyx,sha256=hR_vTYigOv06EdV9TnxdGFSM6WdZrCAV6w9coquSFWg,69917
+biotite/structure/bonds.pyx,sha256=m23KZbTUR-iCso2soKPoURt5Dbqtfcaej5VpJBxt89U,71518
 biotite/structure/box.py,sha256=zp80_Q4Xv5t2KIfrSK-SachkIbbK1mctl91mVrk5T3A,19186
 biotite/structure/celllist.pyx,sha256=gGv_j-jVdoC6K-8Dw38Tc5Xq_KbEdFO5ZnvHZl__htA,35310
 biotite/structure/chains.py,sha256=GjacD8hgSZemI7Bs8Y8zHpPy8I-iGUOoUSYpJ5cLuJY,9141
@@ -229,40 +234,44 @@ biotite/structure/density.py,sha256=jlWog4xJcaHRvtMiLQueeJJwzIH3ZnRiZSb-ZCDq9B8,
 biotite/structure/dotbracket.py,sha256=MjJf6x67jME_tdFhKGhQtGUpwsgJkHKjmNL77bpxG7c,7048
 biotite/structure/error.py,sha256=NaQBi7CGUYpa7-Y9t0We8iVEJwqpsNWLXkr1PTBKlxQ,822
 biotite/structure/filter.py,sha256=e3xLwZobrhRJ-7uX4HeerstE5sC8b7RpIJ_mg9TTPEM,18557
-biotite/structure/geometry.py,sha256=1myUT4HVwMzcz6e_CA2yf6BOKPx5ZFK4xCykA_wLHm0,25766
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 biotite/structure/hbond.py,sha256=7eULKwg94uQY2G-3ea8M0yOOHi0-tl_2TV-Ia2lzLhI,15646
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biotite/structure/info/ccd/README.rst

@@ -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``.