chainer / chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

MIT License

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Schnet add h #346

Closed mist714 closed 4 years ago

mist714 commented 5 years ago

Information of hydrogen atom is necessary to calculate three-dimensional distance accurately. Therefore, we added a code to calculate the distance by adding hydrogen once, and a code to remove it again if the number of hydrogen increases.

codecov-io commented 5 years ago

Codecov Report

Merging #346 into master will increase coverage by 0.01%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #346      +/-   ##
==========================================
+ Coverage   81.65%   81.66%   +0.01%     
==========================================
  Files         210      210              
  Lines        9647     9653       +6     
==========================================
+ Hits         7877     7883       +6     
  Misses       1770     1770

corochann commented 5 years ago

please add add_Hs option as kwargs for the method.

Can we check addHs is already called or not by checking mol's attrib?? If possible please call add_Hs only when mol 's addHs is not called yet.

Please remove assert check.

corochann commented 5 years ago

Can you update code @mist714 ?

mottodora commented 4 years ago

/test

pfn-ci-bot commented 4 years ago

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mottodora commented 4 years ago

fix by #390

corochann commented 4 years ago

done in #390