biotite 0.41.2__cp311-cp311-win_amd64.whl → 1.0.1__cp311-cp311-win_amd64.whl

{biotite-0.41.2.dist-info → biotite-1.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biotite
-Version: 0.41.2
+Version: 1.0.1
 Summary: A comprehensive library for computational molecular biology
 Project-URL: homepage, https://www.biotite-python.org
 Project-URL: repository, https://github.com/biotite-dev/biotite
@@ -37,7 +37,7 @@ License: BSD 3-Clause License
         (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
         SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 License-File: LICENSE.rst
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
@@ -49,12 +49,14 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.10
+Requires-Dist: biotraj<2.0,>=1.0
 Requires-Dist: msgpack>=0.5.6
 Requires-Dist: networkx>=2.0
-Requires-Dist: numpy<2.0,>=1.14.5
+Requires-Dist: numpy>=1.25
 Requires-Dist: requests>=2.12
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-codspeed; extra == 'test'
 Description-Content-Type: text/x-rst
 
 .. image:: https://img.shields.io/pypi/v/biotite.svg
@@ -80,7 +82,7 @@ This package bundles popular tasks in computational molecular biology
 into a uniform *Python* library.
 It can handle a major part of the typical workflow
 for sequence and biomolecular structure data:
-   
+
    - Searching and fetching data from biological databases
    - Reading and writing popular sequence/structure file formats
    - Analyzing and editing sequence/structure data
@@ -116,7 +118,6 @@ Installation
 
 Some functions require some extra packages:
 
-   - **mdtraj** - Required for trajetory file I/O operations.
    - **matplotlib** - Required for plotting purposes.
 
 *Biotite* can be installed via *Conda*...

biotite-1.0.1.dist-info/RECORD

@@ -0,0 +1,322 @@
+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/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/msaapp.py,sha256=NZJVMWyx7TgiDI5NP7FMZx1ZOUfYJU8wKxBqcle-Pmg,12339
+biotite/application/util.py,sha256=rmtP_KHmP3WuZnfPRT2mpU_BvI9cRaDqWxUlupnaPl4,2152
+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
+biotite/application/blast/__init__.py,sha256=90FNcYrxTkEGlzf8RSR1uQkSp4BF42S99XK6FXnmUY4,380
+biotite/application/blast/alignment.py,sha256=aPbMz_qyH8Izl_g24BQKgvh6McYXyx0tPsGcocwQ4E8,3209
+biotite/application/blast/webapp.py,sha256=byuSfcaKHKokxUwf2fjT3-DTtqsiSD0gB3lysGi7Wg8,14891
+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/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/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
+biotite/application/tantan/app.py,sha256=nWE3rlDqf3-jfpIXUw1ddH4ooiD2lZ1GeqBvGXEXtsI,7637
+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/util.py,sha256=rJizJjwn7yw2lfnz93sHNVle04WwpdfskhBkT6gWbsE,2711
+biotite/database/__init__.py,sha256=N3PuLKuEbQ0J55CddwryBGiLfYSazC697F8KnxizrKY,748
+biotite/database/error.py,sha256=L_FvDa-F4XUaCIVo6ZtLXIMn6P-cv783lvxR_Rtluqw,426
+biotite/database/entrez/__init__.py,sha256=88kXhS1XqXb4exnfZIaKD98t3RH3gEZBiNR-aBhl-OE,403
+biotite/database/entrez/check.py,sha256=3JQZshjekA1woJll6UefEsUZ8kMw-MG1uh86jGgDomQ,1913
+biotite/database/entrez/dbnames.py,sha256=k3FbpMP5No8m0Gq_PR4TWZkzFFXHiNrQahXcXYAqCvo,2711
+biotite/database/entrez/download.py,sha256=qblZk-OZ3UQWTO4ECpyIVNCTUU12qSK9hvieSK1h-lM,7605
+biotite/database/entrez/key.py,sha256=sH-RU0oEDG-u5RaZyr506acSBpwAfeScE8HA34QZhR0,1156
+biotite/database/entrez/query.py,sha256=7jRFZ4aUXlMiACd5RXEBlQA718lg0_BWHPBKaaW0S0w,7636
+biotite/database/pubchem/__init__.py,sha256=YvB4_HXgHto_Jw6PdsSNea-sFoh0HtEUWD7ByyxH2Xg,690
+biotite/database/pubchem/download.py,sha256=wzKlu9LhUcVVJ-tVmBF5sOPlKbopO55DnnBiG9pUpIA,10125
+biotite/database/pubchem/error.py,sha256=ebfAx3Q3-qlmhA4vRkPG9OD9MEKM0cSsTVUkHH7bx5c,733
+biotite/database/pubchem/query.py,sha256=dPONXpyWc3158KP_7DRxZ2JMEI5qjyoe3atIkcFQElE,27278
+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/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/sequence/__init__.py,sha256=fUoOYLTavBTicHu-JCQkvrCAyRfKRspfCItufOBDGGE,3507
+biotite/sequence/alphabet.py,sha256=PM_aKD5ivsU5Ral_z6SuKw6rX-wkB3CWOlZs_9VzMr4,17742
+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/search.py,sha256=J6ogMj58ft6bLGUw6IMckwG4nJonIojiICyAvv7mn7w,3207
+biotite/sequence/seqtypes.py,sha256=ACzLqjzrzE0PJSjv-GKDHaNHK_sQ4EHtug-vPl4r5qc,19938
+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/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/kmersimilarity.pyx,sha256=tmAKKZY2JOvnPjU0PQqInvb_MRo7whUxgX0iVZNWIbg,8665
+biotite/sequence/align/kmertable.pyx,sha256=IkmJgU-3e5qT3TTVfPXWc-Z7L8SqmWWUhwOqe4gOSD0,124735
+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/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
+biotite/sequence/align/primes.txt,sha256=XcNX2_hYQI4H-8MPvZH1oiYeQ1lfxU8rBvuwMlcQa3Y,10961
+biotite/sequence/align/selector.pyx,sha256=xVc2DyA4KHTunzulYaiS225Ghaw3Hm5_44hdSBxdNd4,34425
+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/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
+biotite/sequence/align/matrix_data/BLOSUM40.mat,sha256=mqc0rBUGlBSW8valFG4GSp9sWhJGRw0j9-3gCiCX6Jo,2153
+biotite/sequence/align/matrix_data/BLOSUM45.mat,sha256=cld3hS0GR6A32UQYixIkOYo_Ntyel4bEpXVjARpNm7o,2153
+biotite/sequence/align/matrix_data/BLOSUM50.mat,sha256=jrNEGAggP_gpUggGMkyemzyUogSXX48ykoqM5kBMHjU,2153
+biotite/sequence/align/matrix_data/BLOSUM50_13p.mat,sha256=8q22VeYCDIPnRM474MRDdmrSowgUhclt7IG0kW_4WyA,1875
+biotite/sequence/align/matrix_data/BLOSUM50_14.3.mat,sha256=6VAYKFu1hyvH4TlUvKzpitWNhLxFKie0PwUSN3vrNVA,1875
+biotite/sequence/align/matrix_data/BLOSUM50_5.0.mat,sha256=uQnHlhJPr34ETMroukHG32is8Y8Ij7FHyovgpM9ewBo,1875
+biotite/sequence/align/matrix_data/BLOSUM55.mat,sha256=esaCloPHgElMqbDeM6cG1V4eAAy0DuAoIto7W2RZmIE,2153
+biotite/sequence/align/matrix_data/BLOSUM60.mat,sha256=PQ_0xnQZ9wvEJDu3AAVeqtOWY4FPzHL-IoO7zgdGflE,2153
+biotite/sequence/align/matrix_data/BLOSUM62.mat,sha256=_rmVwPd02hfykIVtqK9HVrkXi10ns9AlNexxZUWZvDI,2153
+biotite/sequence/align/matrix_data/BLOSUM62_13p.mat,sha256=mID-XPFLoDyu4E_UKgN4vRjBGR745fBAsTegyoyhT2M,1875
+biotite/sequence/align/matrix_data/BLOSUM62_14.3.mat,sha256=R7QFP9TwclNXUG-VoOBNWxR616k1IRwSQdeMLbCqoOI,1875
+biotite/sequence/align/matrix_data/BLOSUM62_5.0.mat,sha256=lukNF3Usljvt1F7tp8nTErTS-KmgOM5nacUNIP7svNo,1875
+biotite/sequence/align/matrix_data/BLOSUM65.mat,sha256=OVfRPcz1Tt-Xd8rgi5C7BBcZkz_rkznxDLghEWZCKIM,2153
+biotite/sequence/align/matrix_data/BLOSUM70.mat,sha256=o0C1o5I0WD0rylKba_-WEDWTdhGzKU1ke8qJQHEdR1Q,2153
+biotite/sequence/align/matrix_data/BLOSUM75.mat,sha256=eKtqmYGwYNAIx5VjHlciapubqef3Fj-_FbFfaYqP3TU,2153
+biotite/sequence/align/matrix_data/BLOSUM80.mat,sha256=iDNgcsVFZrGF0Ksx6TbbtZDgXS8VrwKsr-Wa91NLq9w,2155
+biotite/sequence/align/matrix_data/BLOSUM85.mat,sha256=oaJKauPQ6m2Z8-lXL6QKW4rm-kQ8SbKZ2VHfxoDZpJ0,2153
+biotite/sequence/align/matrix_data/BLOSUM90.mat,sha256=E-byBZiX9-KoHU-Rns5-fQTeKcE4H7OX4HcP9LC-DRE,2153
+biotite/sequence/align/matrix_data/BLOSUMN.mat,sha256=2e2wYW20_PmJzFoFgd0NeNZ-dpTASqobXupnwB-ZPa8,2152
+biotite/sequence/align/matrix_data/CorBLOSUM49_5.0.mat,sha256=cMtXxZlPBLb5xK0gaeeh6tPxEjINyy5CFzjsyKdh6lc,1875
+biotite/sequence/align/matrix_data/CorBLOSUM57_13p.mat,sha256=AhADYOEOJa_2Z3Vk_A7nf179IEvEVNnFRN3Izw0w1Aw,1875
+biotite/sequence/align/matrix_data/CorBLOSUM57_14.3.mat,sha256=e0mN-lYiDEhVRCJ4M6SM0vDe0v_GzRZxvFEgBRhl3qM,1875
+biotite/sequence/align/matrix_data/CorBLOSUM61_5.0.mat,sha256=cHb4Xgfs1ClvlLprxkMhAaYoqJw6-doKB-gvuYdoKsg,1875
+biotite/sequence/align/matrix_data/CorBLOSUM66_13p.mat,sha256=CNxG720EeLp4Q92TZjiLlk3hxW7PJFtnvFN6beSfhsw,1875
+biotite/sequence/align/matrix_data/CorBLOSUM67_14.3.mat,sha256=SqvZBwB7M7QKn2urlHrV2roG9GYK6j6tgR-hTKWUiz0,1875
+biotite/sequence/align/matrix_data/DAYHOFF.mat,sha256=uvYbLTdwac9DgOswGoCHQwesPDH-IaJtXTkSVDgTF4M,2113
+biotite/sequence/align/matrix_data/GONNET.mat,sha256=TVzc43DX6QWdU5fcRCcd-2x5TDqLHorS4B_TXLs7kyg,1705
+biotite/sequence/align/matrix_data/IDENTITY.mat,sha256=JyqbeAE05T3JrM4azvLuvyeL3ZtYLOTmtBApzy3-A0o,4082
+biotite/sequence/align/matrix_data/MATCH.mat,sha256=GErmlX4HbkLO6-JasT3CJFIMLT4tBjF0T3OEGHPcdhw,1875
+biotite/sequence/align/matrix_data/NUC.mat,sha256=B5LFCFoqbX5dHBrM_A0zFKraQixVioBUYUx_gLiV2uk,1196
+biotite/sequence/align/matrix_data/PAM10.mat,sha256=Q5SCwzP1JP8WV6LK3yplYic-9Hlb16RjB0xxnePYCRU,2700
+biotite/sequence/align/matrix_data/PAM100.mat,sha256=rMMayRLjhCbCfkXqR3SrKsaEqo_A3uqVdeQNhXscqKE,2100
+biotite/sequence/align/matrix_data/PAM110.mat,sha256=ZOgBVcFHbf7LYxOOhD4lOZ1CRmjpI57ncVt6PQ4_4EQ,2100
+biotite/sequence/align/matrix_data/PAM120.mat,sha256=BL__IVzN0taPMX6OrbUBqCM_cx0wQsEVXY4Q3wzKeUc,2101
+biotite/sequence/align/matrix_data/PAM130.mat,sha256=S5kfwlOUYWzdpgBcCxP-VYigZlxPbsSpgMZsLg-YX0s,2101
+biotite/sequence/align/matrix_data/PAM140.mat,sha256=lrUkyXHLLI-diGiwz7mXODMSGvZMnbchPnoHqi80Wzo,2101
+biotite/sequence/align/matrix_data/PAM150.mat,sha256=sb_UBf1D75MBocAxvsS_brC-71DJG4LX6eR5lgcImKE,2101
+biotite/sequence/align/matrix_data/PAM160.mat,sha256=FsF5lVpwSWYYT-VxYgTdw4sR9g_GaWLtVc90cYhzLgg,2101
+biotite/sequence/align/matrix_data/PAM170.mat,sha256=u_FrksvWr_93JoPHcq98kbiL_criHpkmMlP0JEzkRqw,2702
+biotite/sequence/align/matrix_data/PAM180.mat,sha256=cB7ObBcyQRdkL6TwNSLZC56JWdckmgE_aDXgdKwxjC4,2702
+biotite/sequence/align/matrix_data/PAM190.mat,sha256=OjGFjUBnY8bS3hCRkrsJX609JzIayS12PJaAF01GnsI,2101
+biotite/sequence/align/matrix_data/PAM20.mat,sha256=zwMcwCrUtGBovoFD5ZwU-u_69uaNCm3kEC87yaLkQFE,2700
+biotite/sequence/align/matrix_data/PAM200.mat,sha256=3SQbSCLtN2EjOqNtW1h2g91Lm_B60Gv9k0AUbvH9xUI,2101
+biotite/sequence/align/matrix_data/PAM210.mat,sha256=dLHMDY3p04HX0ggxEBsIXH6VCaKMzYFb50FnQnIATvQ,2101
+biotite/sequence/align/matrix_data/PAM220.mat,sha256=4WyRwlIHzpAm_kSbZPTuGDllYqf5Fx7MmawJ4fa-AiA,2101
+biotite/sequence/align/matrix_data/PAM230.mat,sha256=01wKWPEzBWgnZBmhlTpDk0R8Et0dWeA7oxpLs1KXnAA,2102
+biotite/sequence/align/matrix_data/PAM240.mat,sha256=9jC0cjrdkYc-f13XWJkFif4cRsKMXaAukUdabaImBak,2102
+biotite/sequence/align/matrix_data/PAM250.mat,sha256=y9MQhrrBchLJ99xKGsQFxAyQV5U3umC_JaT6hTt5cIM,2102
+biotite/sequence/align/matrix_data/PAM260.mat,sha256=QL2Jc2wNcxJaknyJeB_Ug-E6lsxnCgxsKIFytRrZMzc,2102
+biotite/sequence/align/matrix_data/PAM270.mat,sha256=SDuy9ZgiyOxuwLXI5rMNrdEqxIEOJrqshrtKrHFcIMI,2703
+biotite/sequence/align/matrix_data/PAM280.mat,sha256=RSEQWeyNtEqU5gWgUGPXprMj-Q9tyMVgPHpOMkuVxVY,2102
+biotite/sequence/align/matrix_data/PAM290.mat,sha256=CMM9FqtFqXCGZggUJ5N2qp9NWJozwVDvhvqeOMCKHfQ,2102
+biotite/sequence/align/matrix_data/PAM30.mat,sha256=RVyaISQizjROVMC_40_uLKuxmkFJFbO0LSWwaZuNmkg,2700
+biotite/sequence/align/matrix_data/PAM300.mat,sha256=neWuBVsuGUQgQ8pfCtF0HgTG9uCSyKZAHJq7-SfhdlE,2102
+biotite/sequence/align/matrix_data/PAM310.mat,sha256=Xn05ov6o7431yPJJ-XW9z0fVs-TBuKWlq2nQWEwXgS0,2102
+biotite/sequence/align/matrix_data/PAM320.mat,sha256=2T270mwuV95gGOJ5IJlKIeXYwDAaEUIBQ4-9yzENxn8,2102
+biotite/sequence/align/matrix_data/PAM330.mat,sha256=6Sj0fVGaFSREgiv6SzIRs0NF4-2GiSfltVj33_cW5uU,2102
+biotite/sequence/align/matrix_data/PAM340.mat,sha256=oqHYGm5OCMaCkEsc0wb0KRCKhVaOEe-Ql0KOhbFdOgY,2102
+biotite/sequence/align/matrix_data/PAM350.mat,sha256=KPkW_qQgiCb2VwUz3FuqBb2f5NcA16tDiMMHTOsT02g,2703
+biotite/sequence/align/matrix_data/PAM360.mat,sha256=J0N57KI05sGuaDKc8ImknGa4OPs-NVC1BRt6cQNNE0g,2102
+biotite/sequence/align/matrix_data/PAM370.mat,sha256=C591IaeROpL3CuS7QgijAXTLJ_jMpenXR0KQY-irvr8,2102
+biotite/sequence/align/matrix_data/PAM380.mat,sha256=QV3SnTK4yzqcGKKzGEBLOCdVVQ0EcyMgDjRQ5oE7wG0,2102
+biotite/sequence/align/matrix_data/PAM390.mat,sha256=jserXJqS6aZ-93c4L3vB07EcBrOHUcNc5SOC1qfbjxc,2102
+biotite/sequence/align/matrix_data/PAM40.mat,sha256=NSYI8cKFFIMktbejssnHNmcG4ohKplzp9_-SpB4fVoU,2700
+biotite/sequence/align/matrix_data/PAM400.mat,sha256=L7WknkJVDNs2RryikJN4Dz3DoGpgHeELcAht9fmsQxs,2102
+biotite/sequence/align/matrix_data/PAM410.mat,sha256=kwCJCXg2UoSqewmmuggFlEQfQ4-_CenFCuuqzSZZssk,2703
+biotite/sequence/align/matrix_data/PAM420.mat,sha256=HoANpnh-_iz-gbBrC5P79V1R8xuqvK0FVPwfOA-d98w,2703
+biotite/sequence/align/matrix_data/PAM430.mat,sha256=AvubENvc01eSMC3uJAigBnNVmnAn6nWBHqesmJrjsvg,2102
+biotite/sequence/align/matrix_data/PAM440.mat,sha256=32Gm35V0mb2C0U02AyojfUQ1vJw_Mw2JhOwgVoJMZLw,2102
+biotite/sequence/align/matrix_data/PAM450.mat,sha256=FGLj7yWNvEsP2qLGKw9xIjYnodHrzw0VLa6IVVk0k74,2102
+biotite/sequence/align/matrix_data/PAM460.mat,sha256=ZPifNWXnIRDrHJrE78rCPhUvdwdbf0VjDLjNKgTnfQY,2103
+biotite/sequence/align/matrix_data/PAM470.mat,sha256=FkQrvmy0i7BQ6RtwWSuCtieYFL8QuWn2bOYFKw40su0,2705
+biotite/sequence/align/matrix_data/PAM480.mat,sha256=S-lQRy2v8kZzvHaEQk8XyWK2ZA3B4DD9m4pE-kChO2A,2705
+biotite/sequence/align/matrix_data/PAM490.mat,sha256=NK3ktYiytB3N1xZOAPFrluohm7RAxmBGAVaEvSG-MAA,2104
+biotite/sequence/align/matrix_data/PAM50.mat,sha256=eZmmjxqsG46xR-lfxbS-M-WPyiMxQwM_P1hCgZZgw84,2700
+biotite/sequence/align/matrix_data/PAM500.mat,sha256=eMHkixX5TRiq7V4nLdYvXfTN-acJ_A_rUVAnawrNThM,2104
+biotite/sequence/align/matrix_data/PAM60.mat,sha256=tEP5rtSKfgJt14UAQd1dhHO4BDBzlUibpq1NQpR4BsE,2700
+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/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
+biotite/sequence/align/matrix_data/RBLOSUM64_5.0.mat,sha256=E52mnslKgzhNeB6n3LNTr_ITc2Wnv_59PySCPd6-au4,1875
+biotite/sequence/align/matrix_data/RBLOSUM69_13p.mat,sha256=xABdTJkFD8zQKcmyvnt6jL3saEP0o9CF7EcP3KM9aU8,1875
+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/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/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
+biotite/sequence/graphics/color_schemes/clustalx_protein.json,sha256=k4Ree6wofz9WnOUOvqHmP0nBv-sqC6TYG1gX8U75NY0,731
+biotite/sequence/graphics/color_schemes/flower.json,sha256=GCtQFSSwsCWRLFDCfkW3t3hX1Z8yT2Tgz2SuTa8U5vY,893
+biotite/sequence/graphics/color_schemes/jalview_buried.json,sha256=wGL4cJkizB3miiMOcnde36kl81NAWdg3PFtIHVa1nvE,807
+biotite/sequence/graphics/color_schemes/jalview_hydrophobicity.json,sha256=k_iWsZjBpjXbnwFbnt__WQWnFmktZraYwvmBxz7V9fc,815
+biotite/sequence/graphics/color_schemes/jalview_prop_helix.json,sha256=rRf4rpqdIiMMZj9fVOdRdaEkzcS74cI1snTFpZv8Gvg,810
+biotite/sequence/graphics/color_schemes/jalview_prop_strand.json,sha256=yVz0kIvv1q0hXj1v9taxG2Ff-dk60csTQLSzFhBKK3E,811
+biotite/sequence/graphics/color_schemes/jalview_prop_turn.json,sha256=Iw3f9dAmt9vEDj0TqP1ogXjCn8QN50pdEEC-KzidN5w,809
+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/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
+biotite/sequence/graphics/color_schemes/sunset.json,sha256=LQTsAQIuH1vIn2479AlLZwrBqySEE9aQSBpUKN74XAs,893
+biotite/sequence/graphics/color_schemes/wither.json,sha256=SawwzITBHvhS4XYf6CkNDOnK-i-yj-Yx4aQEGnUycjQ,893
+biotite/sequence/io/__init__.py,sha256=MbsrDuoq0Cxd77d9m0ueUvI0lsftNt5EibJIYUo6a0M,326
+biotite/sequence/io/general.py,sha256=7JQBPcp0gVblaGUwYW05dYreyOG9J5LFUz-v6XGGX-k,6895
+biotite/sequence/io/fasta/__init__.py,sha256=6aXOhuGVn4FJoJMop3HedLQ6IRrZiuEOWCrC-sGtu28,742
+biotite/sequence/io/fasta/convert.py,sha256=aBD3anuhtaUNtIKQCFuz4X5WiCXVjD0MiD8R32qmOKI,9705
+biotite/sequence/io/fasta/file.py,sha256=yzyREJeOBIcfz20eWr1f5PDGsjeirA3mTj8ikL_bkvc,9320
+biotite/sequence/io/fastq/__init__.py,sha256=p3dmgI_ytFxai_tdrqpRhkTUzBkQMM5J2cNQ1p9-JXI,607
+biotite/sequence/io/fastq/convert.py,sha256=BKZ3_wHFeynAfDLNKDctI2Amfl5-F0wNyV6qv_uctMs,3749
+biotite/sequence/io/fastq/file.py,sha256=MVuaOL7pHk1NAOdRtOSDSONfIe8ovknZ-b3uBXDF870,18323
+biotite/sequence/io/genbank/__init__.py,sha256=DVTqOI2ilzlo2O-IyfUv-7WxsxVIBPPtoEjZ1MNV3Pk,490
+biotite/sequence/io/genbank/annotation.py,sha256=J8_DODOqNcPvj_le5md3-9nttlNV3ViXCNtGAdNtSBk,9700
+biotite/sequence/io/genbank/file.py,sha256=BbefCk8q9XQafbpqY1kKgN4_XYQ4Jlofq9sNnnYAdb0,20939
+biotite/sequence/io/genbank/metadata.py,sha256=bF3fttJMmFa6eELvQ9UqzFVSgGkVUqLfVsgiLz01LBA,9687
+biotite/sequence/io/genbank/sequence.py,sha256=81q3memdbZkI63ljhDLGEkJtKrpfpRzflGb_WcDNbns,5590
+biotite/sequence/io/gff/__init__.py,sha256=-m--LdBhi8sDWD0mbjxoxU_hRPSeJ7APYCYFKkpb448,949
+biotite/sequence/io/gff/convert.py,sha256=ojfSlrFuQZB1EEeZ2iK6duOSCQQtOU2glvsA4qkqXFg,4742
+biotite/sequence/io/gff/file.py,sha256=BspHz4_hUrY88qlBml5glkymoX6_RKv16kh5BUI3Xys,16546
+biotite/sequence/phylo/__init__.py,sha256=aNP1B9DNNTXMyiqWkzF6JZFynlcmIg-bDeN-eDKakgQ,1297
+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/basepairs.py,sha256=eZF67fnecHkvDYnIlfeejdJC7sCDWYqOghjbweLoxFE,51163
+biotite/structure/bonds.pyx,sha256=hR_vTYigOv06EdV9TnxdGFSM6WdZrCAV6w9coquSFWg,69917
+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
+biotite/structure/charges.pyx,sha256=ZqQeMaSr0kjgBWRN_mYWBXV6wYtglADRrvY4ZQ0KKSU,19341
+biotite/structure/compare.py,sha256=jf4L3xuPz_ZBNhdMHpxNaEu27qVgy5z1mXRz-dfoyFc,9711
+biotite/structure/density.py,sha256=jlWog4xJcaHRvtMiLQueeJJwzIH3ZnRiZSb-ZCDq9B8,4305
+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
+biotite/structure/hbond.py,sha256=7eULKwg94uQY2G-3ea8M0yOOHi0-tl_2TV-Ia2lzLhI,15646
+biotite/structure/integrity.py,sha256=ubkv2vA5yhb-3GIsX4ZHsAGiB-zQ30Pr_hUlpWHJcHw,7041
+biotite/structure/mechanics.py,sha256=fjNrK0BDTyKDgnxK-hMG2P8uTnqSZWSFrZi6s0RBEeo,2661
+biotite/structure/molecules.py,sha256=sFXmT-i-nJPjMLI_YUr9-xESzDu8QRC_jfFkEtp_2zw,15856
+biotite/structure/pseudoknots.py,sha256=29mW6yDiJ4_NYMH9sFWZEN7gfWHYmQpvOkXuG5DD5uk,22852
+biotite/structure/rdf.py,sha256=XAkbnbfk0wx_cIlrDYXBMUzzShgICUCpyPPfTNviWBQ,8349
+biotite/structure/repair.py,sha256=wAxye1HguqSqhELWEpuxIkaTkv3ZswDXTOhkEZhdchc,7300
+biotite/structure/residues.py,sha256=iuVK2pVfU8qRCf7kmCbO8lfH4O4PfrECmbOjCk3B2sU,23026
+biotite/structure/sasa.pyx,sha256=4G_5jJGRsUenLtVPr9mD9KlbYfmP4WnDY_iHXjJE_pw,13305
+biotite/structure/segments.py,sha256=7qTacvlpheHHo_WgHcSIN_aZ-FN97ksGuNwwS_cC9xw,5725
+biotite/structure/sequence.py,sha256=Hpt5FvDJG1tBY0eQJNri-DboeZ3BoADy9I_MzWlzOq8,4357
+biotite/structure/sse.py,sha256=w_ww5JwImQKDlLQiaDZLEr49viP7WZyYg_p5n59Eguw,11714
+biotite/structure/superimpose.py,sha256=37elE1zeY7cAAnF77B6zerQDqtnHZanpqjB_xcWlDSk,25813
+biotite/structure/transform.py,sha256=7yuzqo0y4fVDOIYk_fhOuaeBIzPAL9HyMqYn4r9JJxQ,20179
+biotite/structure/util.py,sha256=C5nrQ6la_MMT8-dURLDnylvMnpYaAb-1WvTJcsyzkAc,2296
+biotite/structure/graphics/__init__.py,sha256=crwq14wVv4ttDEecmExvEyh5Z1LCafb3wznZWB7HOhA,366
+biotite/structure/graphics/atoms.py,sha256=acZXrWVRblk83FfLePe3pHoMcjJJH2eEDyZFmqmw-xs,8359
+biotite/structure/graphics/rna.py,sha256=7PSX9JHfo1840k8HqKcC8UXX-rxP8YwFtN_VLgUilbE,12311
+biotite/structure/info/__init__.py,sha256=Sp3hhSL45bNtaoAMue1CuHwOcC8D39zMzuCispcrNLA,702
+biotite/structure/info/atom_masses.json,sha256=DJ2YMCN4Fvn0zzT91N6TotoLMPm_EkeOF23Yjb5mvGg,2504
+biotite/structure/info/atoms.py,sha256=u0nuWmTFhxtXjOsOQQIf0gH3zahGt5oEyrNEtX9AGZI,2703
+biotite/structure/info/bonds.py,sha256=BwfXvRBUYboNLeFzUEeKdSG0mJWiBRijJv1RTIhKPgI,4644
+biotite/structure/info/ccd.py,sha256=NnaaMLNb3gDbgABYqA9Rn_qZynL-Cn6DCjUolQ_MEZE,3111
+biotite/structure/info/groups.py,sha256=8SGEC4SNAULcrYCPx_olpESbx13aa0dYAu8HvCiTlGs,2068
+biotite/structure/info/masses.py,sha256=VQ4kOKtcBgx5UiZVP6PC14PQcdwmNiTH_YQCtyTQoq8,4601
+biotite/structure/info/misc.py,sha256=aUImiOGxWuMDMSu_YJW3AiSlPPFoougDSHsev8OH5Rc,3656
+biotite/structure/info/radii.py,sha256=NIy1knADXUw5zx6dMX08LHqXlfS62e98rsA6r3E8wWA,5807
+biotite/structure/info/standardize.py,sha256=3G1pPjnJruBARwe5P4YuQuLSWfNHMKHzWB6_rmHfReY,7898
+biotite/structure/info/ccd/README.rst,sha256=GeRC_rNZkw9mmGBjSwiy6pgyzzYZEPh0IX5pMIjCruQ,349
+biotite/structure/info/ccd/amino_acids.txt,sha256=l1yE8BcddZ8aJtMhDr0wfn_zRHy-am39xuMm80DIsuA,8332
+biotite/structure/info/ccd/carbohydrates.txt,sha256=R6WD5xRqmmiYAQp6QrdtlSBF6IBVC4BeMPPl5keEMeA,5679
+biotite/structure/info/ccd/components.bcif,sha256=xgvErxils9GNg5s0sGI33B7w4lWeUBZRksPer3japnE,35649254
+biotite/structure/info/ccd/nucleotides.txt,sha256=rVTN65IGs1rfwDzjdhiaIZQ3mCGg3WvllNPSUWCBsoY,3934
+biotite/structure/io/__init__.py,sha256=d9zsCIGeTRQ_R8n5xBwi5jrfanRMEeCIh9E9xjmnqVQ,1027
+biotite/structure/io/general.py,sha256=uZPbBq35Mp4TuqxAEMWFhUztvolzUzAxSKXXdMI6Pb8,8691
+biotite/structure/io/trajfile.py,sha256=XnLmQ7AvD9mIbSclgQqAev069qqCL0hBRBG6mXtUO8k,25877
+biotite/structure/io/dcd/__init__.py,sha256=oy8P1khM60o8M5grpSoGNZkudTBrTUPF33xuLub5sNQ,401
+biotite/structure/io/dcd/file.py,sha256=zLvngfNmF8pBM6J6kw-i_-rtFiJj1Bh4HSCAmN0EegI,2291
+biotite/structure/io/gro/__init__.py,sha256=jPh0RWv2vbpmgB0U0lZ6yo7SkVZycYfx2UQqKWCkOHg,422
+biotite/structure/io/gro/file.py,sha256=DlRBWIMl8VEA4kW1HS_Z73DayBfMzWZ5DV8-IIeA7C8,13076
+biotite/structure/io/mol/__init__.py,sha256=s1_xplK-Grhil2LLZiNiLU39wLvYr0LB1Vrn66BOmrU,602
+biotite/structure/io/mol/convert.py,sha256=_jGauQH97v_RJi9wHqiKdRusSTw2KN1R4kbkmyhiNFM,3901
+biotite/structure/io/mol/ctab.py,sha256=xHhXPLnoVAl06_FQetwCYRXewmQiJjolk2pwjiD8acs,13885
+biotite/structure/io/mol/header.py,sha256=Ee78HGDy6DHQEaOh2AGyG0gQGsoMfqLPnfoCo0CwsyY,3545
+biotite/structure/io/mol/mol.py,sha256=cY0wBIboaC-o-Mr270pJv-gSErAikFXZJhYpNYyBSoE,5610
+biotite/structure/io/mol/sdf.py,sha256=kERmWpbzjnkPafWHU1PZI2zGk-GT3aWdJ_5TbaTeOI8,33158
+biotite/structure/io/netcdf/__init__.py,sha256=BVUimn1EklpgdoCFE5sC-H4E47exDe_xIviMeGnn_tk,363
+biotite/structure/io/netcdf/file.py,sha256=8jht6qCgw0Q7q1-WaQ1iCBjc1QLzjrwpppe3uBZhZ1Y,2256
+biotite/structure/io/pdb/__init__.py,sha256=UqePAxP48oww8SEexxr6JlugRua8wgOryAvxmHd58f4,753
+biotite/structure/io/pdb/convert.py,sha256=a0W8kqzuuHegPnue-a3Ds7BZErU5EfE3qG8LhE-GMI8,10907
+biotite/structure/io/pdb/file.py,sha256=IHzDyyXuIuVRhcmUz-KJOdLrkhf-owtc3PA2aoSmpsI,49115
+biotite/structure/io/pdb/hybrid36.pyx,sha256=-feGX_k9H7uAfbqmy37PvlWbuij-mknpbCR2ot1l4kk,8277
+biotite/structure/io/pdbqt/__init__.py,sha256=JiBnbhNHevtmVIwEeYBubOzK5xu1d9dSny7Zf3Aas74,456
+biotite/structure/io/pdbqt/convert.py,sha256=M2SytCYO2ihvpcUQCqz4PD4DAKwCPxcjGbhFhJjbDZY,4121
+biotite/structure/io/pdbqt/file.py,sha256=aXhDPIkoDrQEoZm5-iPCF0JwRdrsHocezLNUzHjPO2A,27321
+biotite/structure/io/pdbx/__init__.py,sha256=6l-w3pEY3LYCnVC55bFe50K5nEFCk1zxzgacV1sQ4H8,715
+biotite/structure/io/pdbx/bcif.py,sha256=9yoYIW6ea617mz461ps5bqMc36OEjuNi2uk9Cp4odCw,20452
+biotite/structure/io/pdbx/cif.py,sha256=4gZk9mPslZoFEROiCg_8W6Lc6CPcI_yc7S5LybkxUNo,35517
+biotite/structure/io/pdbx/component.py,sha256=B5QxWiaCABuauX4GJiqoaTExAGnzzZQxksj46-AWZQg,8266
+biotite/structure/io/pdbx/convert.py,sha256=F1s2RBcR73ea_RYI36tE6kAGmX4C0k6_Tq2woFJXVtA,61807
+biotite/structure/io/pdbx/encoding.pyx,sha256=fjob-qQN3qiIo6KfmKla6401oIM5zjMaeK4LqdJbmU4,29674
+biotite/structure/io/trr/__init__.py,sha256=xp4FpuAy_ESqzVWyugRXUHZ0iF8j5ox6EfCxSWhkcUY,372
+biotite/structure/io/trr/file.py,sha256=XcdYOf9M2tjRXMM87p9U7jMdQb0PlTFvDHXHgSdjbl8,1278
+biotite/structure/io/xtc/__init__.py,sha256=P17UBQnG-KmOlScHp46FXAb5i7d-ZCMlyljcOkFolMw,370
+biotite/structure/io/xtc/file.py,sha256=X4iIDjAWn1ZySg3NjbPeSMNByoyH1y8asmtqcBYycpE,1278
+biotite/sequence/codec.cp311-win_amd64.pyd,sha256=iWwU7xgh7pIDvVZlBdxugJN_IbQQjypWqyZLYNfh08U,248320
+biotite/structure/bonds.cp311-win_amd64.pyd,sha256=U0dSr3wexSHpDisrmRmwl1xIUET7-D1pB1gPpEDeG3g,486912
+biotite/structure/celllist.cp311-win_amd64.pyd,sha256=rXmOyfuYkhARHEDKZH60-3jth_fcvUBRi1ijWuJW4w0,257024
+biotite/structure/charges.cp311-win_amd64.pyd,sha256=TIQ8qUocTSKiV3Dhqr8_VBLqP0mtxo18Igwjw-eB3mQ,223744
+biotite/structure/sasa.cp311-win_amd64.pyd,sha256=6-yqw-zbzNJ7DVernf3MKhZGgqViD66XucYahNeJPlc,193536
+biotite/sequence/align/banded.cp311-win_amd64.pyd,sha256=ekbw2BkBWtMhPqgKZpbVSDiy25LOb46NIzEaQfIdqYU,499200
+biotite/sequence/align/kmeralphabet.cp311-win_amd64.pyd,sha256=8tCuS2CgrPai7B-7g9_EYVY8LxIdQamxmcT_jAyJuyI,316928
+biotite/sequence/align/kmersimilarity.cp311-win_amd64.pyd,sha256=UnUCT1UCvqLnJJRucAO0kjzAetCxG_4A9TEBwdaxoDI,176128
+biotite/sequence/align/kmertable.cp311-win_amd64.pyd,sha256=XBONRa382xLhd4HmXrE-CSoJlYgXNsf2_jxU7unQ5tU,607232
+biotite/sequence/align/localgapped.cp311-win_amd64.pyd,sha256=H0EHdNxRC6ax7TW8AKUOgL7Q5xWkt874PJOSmAQnhqo,996864
+biotite/sequence/align/localungapped.cp311-win_amd64.pyd,sha256=r7P7VnvpPkwNPsV_MHrLFT_8j8J_ACrh0lMSTPXAp1A,262144
+biotite/sequence/align/multiple.cp311-win_amd64.pyd,sha256=b9d0rp5wU6pTqbQ6l2XYG0F-dyP1SNtX8QdYBTclQh4,415744
+biotite/sequence/align/pairwise.cp311-win_amd64.pyd,sha256=VawKPXwPMoAxxkfDPxkYEmT42rUnHi9KaLKu02_Uf0U,542208
+biotite/sequence/align/permutation.cp311-win_amd64.pyd,sha256=1N4Ln9JePU6zjU5ReEpI2TPAvxwLHKoiUr0tAG6zdN0,186368
+biotite/sequence/align/selector.cp311-win_amd64.pyd,sha256=S60DvwtPkO-HzHzA4PkJZ7a9peGJ1oLpiW8FIEo9Cis,258048
+biotite/sequence/align/tracetable.cp311-win_amd64.pyd,sha256=DqBNBfeavDadFJOPhCEn7Cz9f1lz5FeFQs5qBSX1xRo,152064
+biotite/sequence/phylo/nj.cp311-win_amd64.pyd,sha256=6tn1hRP96jG-hCaZC9edW0r2vX1BeXJgZ6h21yPi67Q,172544
+biotite/sequence/phylo/tree.cp311-win_amd64.pyd,sha256=revuET-_BKApcz-cXH-nPNSSnGPUY15TwdvXHpLMYWw,210432
+biotite/sequence/phylo/upgma.cp311-win_amd64.pyd,sha256=x5s7-dTAzIm6o9IdFXPJOEmPGDaE04-TaTXCpgEIOf8,165376
+biotite/structure/io/pdb/hybrid36.cp311-win_amd64.pyd,sha256=E11zaTT9tGMxYHY9YWKSXwusIesUmpicKAZ-2FTxdLI,153088
+biotite/structure/io/pdbx/encoding.cp311-win_amd64.pyd,sha256=dlaT6o91WMbDaX10SaG0kg51YZib6MGkhB-Gfu15W6A,1005568
+biotite-1.0.1.dist-info/METADATA,sha256=lnwl1IjHDLJ5EVhHYSUQplx3-4Ql4gbbezrkspTCRK8,7159
+biotite-1.0.1.dist-info/WHEEL,sha256=tUtJ5bXThObXzu3Mmtrhn2LpWmyDlL72mq7DuHq3018,97
+biotite-1.0.1.dist-info/licenses/LICENSE.rst,sha256=wDDtR8LuBedgqNIor2N5YGv4nj9flZltCDSu2fhjGbo,1564
+biotite-1.0.1.dist-info/RECORD,,

biotite/structure/io/ctab.py

@@ -1,72 +0,0 @@
-# This source code is part of the Biotite package and is distributed
-# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
-# information.
-
-__name__ = "biotite.structure.io"
-__author__ = "Patrick Kunzmann"
-__all__ = ["read_structure_from_ctab", "write_structure_to_ctab"]
-
-import warnings
-from ..bonds import BondType
-
-
-def read_structure_from_ctab(ctab_lines):
-    """
-    Parse a *MDL* connection table (Ctab) to obtain an
-    :class:`AtomArray`. :footcite:`Dalby1992`.
-
-    DEPRECATED: Moved to :mod:`biotite.structure.io.mol.ctab`.
-
-    Parameters
-    ----------
-    ctab_lines : lines of str
-        The lines containing the *ctab*.
-        Must begin with the *counts* line and end with the `M END` line
-
-    Returns
-    -------
-    atoms : AtomArray
-        This :class:`AtomArray` contains the optional ``charge``
-        annotation and has an associated :class:`BondList`.
-
-    References
-    ----------
-
-    .. footbibliography::
-    """
-    warnings.warn("Moved to biotite.structure.io.mol.ctab", DeprecationWarning)
-    from biotite.structure.io.mol.ctab import read_structure_from_ctab
-    return read_structure_from_ctab(ctab_lines)
-
-
-def write_structure_to_ctab(atoms, default_bond_type=BondType.ANY):
-    """
-    Convert an :class:`AtomArray` into a
-    *MDL* connection table (Ctab). :footcite:`Dalby1992`
-
-    DEPRECATED: Moved to :mod:`biotite.structure.io.mol.ctab`.
-
-    Parameters
-    ----------
-    atoms : AtomArray
-        The array must have an associated :class:`BondList`.
-
-    Returns
-    -------
-    ctab_lines : lines of str
-        The lines containing the *ctab*.
-        The lines begin with the *counts* line and end with the `M END`
-        .line
-    default_bond_type : BondType
-        Bond type fallback in the *Bond block* if a bond has no bond_type
-        defined in *atoms* array. By default, each bond is treated as
-        :attr:`BondType.ANY`.
-
-    References
-    ----------
-
-    .. footbibliography::
-    """
-    warnings.warn("Moved to biotite.structure.io.mol.ctab", DeprecationWarning)
-    from biotite.structure.io.mol.ctab import write_structure_to_ctab
-    return write_structure_to_ctab(atoms, default_bond_type)

biotite/structure/io/mmtf/__init__.py

@@ -1,21 +0,0 @@
-# This source code is part of the Biotite package and is distributed
-# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
-# information.
-
-"""
-This subpackage is used for reading and writing an :class:`AtomArray` or
-:class:`AtomArrayStack` using the binary MMTF format. This format
-features a smaller file size and a highly increased I/O operation
-performance, than the text based file formats.
-
-DEPRECATED: Use :class:`biotite.structure.io.pdbx.BinaryCIFFile`
-instead.
-"""
-
-__name__ = "biotite.structure.io.mmtf"
-__author__ = "Patrick Kunzmann"
-
-from .assembly import *
-from .file import *
-from .convertfile import *
-from .convertarray import *