Add changes to achieve progress described #177
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The progress with Tutorial 4 is detailed in issue hjkgrp#176 hjkgrp#176
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## master #177 +/- ##
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- Coverage 25.69% 25.66% -0.03%
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Files 102 102
Lines 33825 33819 -6
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- Hits 8690 8681 -9
- Misses 25135 25138 +3
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| if dbfs and args.dbfs: | ||
| com = obab + ' ' + dbfs + ' ' + 'simres.smi -d -xf' + \ | ||
| finger + ' -s"' + smi + '" -al' + nmols | ||
| else: | ||
| mybash(obab + ' -isdf ' + dbsdf + ' -osdf -O tmp.sdf -d') | ||
| com = obab + ' tmp.sdf simres.smi -xf' + finger + ' -s"' + smi + '"' | ||
| com = obab + ' tmp.sdf -O simres.smi -xf' + finger + ' -s"' + smi + '"' # babel -> obabel |
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Hi @tlinjordet, thank you for going through the trouble of actually tracking these issues down. Openbabel3 support is relatively new to molSimplify and even though we recently had students go through all the tutorials, apparently none of them used OB3. Sorry that it took me so long to review and merge this PR! |
The progress and challenges from installation up through Tutorial 4 is detailed in issue #176.
In summary, the changes made from tag v1.7.3 are:
mybashwith subprocess because the previous version of the function failed/timed out.getsim,dissim, anddbsearchmainly to deal withobab = obabelgiven Open Babel v3.x.I am interested in understanding any misapprehensions on my own part to better understand molSimplify as a whole, beyond simply getting the package to work.
Note that as described in #176, at no point was I able to pass all the tests, even in the current master branch.