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I noticed while benchmarking that CHARMMStereochemistryRestraint takes a very long time to evaluate. After digging it seems that it's not creating dihedrals and angles (though bonds and impropers are …
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**[Original report](https://bitbucket.org/dan2097/opsin/issue/17) by Joe Polak (Bitbucket: [JoePolak](https://bitbucket.org/JoePolak), GitHub: [JoePolak](https://github.com/JoePolak)).**
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Work towards making CTS optional, by calling obabel locally.
Add "queryCTS=TRUE" to mbWorkflow, and do local calls otherwise.
Also edit the CTS timeout error message to hint that "queryCTS=FALSE" mig…
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When searching for a compound, for example in this case Erythrose, using the SMILES formula obtained from OpenPHACTS (http://ops.rsc.org/OPS1782071), it brings up the error message "Internal server er…
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There are a number of functions that probably don't need to be member functions. Perhaps only functions that add member variables (like add_component_pdb) or restructure them (like creating rigid bodi…
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_Issue by **[schymane](https://github.com/schymane)** from Monday Oct 28, 2013 at 13:07 GMT_
_Originally opened as https://github.com/sneumann/RMassBank/issues/29_
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Informative error when problem…
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How can I organize the python modules in pyext/src/ into subdirectories so that I can import them individually, or in a block? Is there anything particular I have to do so that the submodules are in t…
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``` python
In [2]: m = Chem.MolFromMolFile('bug_3dn.mol')
In [3]: Chem.AssignAtomChiralTagsFromStructure(m)
In [4]: Chem.MolToSmiles(m,True)
Out[4]: 'CN1CCC(O)(c2ccccc2)CC1'
In [5]: !cat bug_3dn.mo…
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Here's the thread:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03384.html
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Reported by Robert Feinstein in this thread: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02908.html
```
# Demo of RDKit reaction transform nuking stereocenters
from rdkit impor…