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I was speaking with Craig Williams at UQ yesterday about his [lovely cubane work](http://onlinelibrary.wiley.com/doi/10.1002/anie.201510675/abstract), which largely validates cubane as a bioisostere o…
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> Currently four database formats are offered for storing combustion experimental data. These are CloudFlame (Excel/CSV format), PrIMe (XML-based format), ReSpecTh (also XML-based format), and ChemKED…
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CDK version is 2.0
private final static SmilesGenerator smiGen = SmilesGenerator.absolute();
String smiles2 = smiGen.create(molecule); // IAtomContainer molecule
**Exception is :**
Caused by…
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Request for Gerhard Ecker gerhard.f.ecker@univie.ac.at
Emailed to bugs by Paul:
1) Export as SDF file
exporting the results as sdf file would be great; Tony of course knows best how to do that and wh…
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(Hi all - *lots* of issues here I'm late in dealing with (mainly the Competition), sorry, but a quick question just for today.
I need a recommendation for a logP calculator (from SMILES, InChI) tha…
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Hi,
I am using Open Babel 2.3.2 on Windows 7 x64, Windows XP x32, and Lubuntu 14 x64. In the three systems, there is something wrong with the interpretation of InChI's stereochemical layer. If I try …
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Hi,
I noticed that the output of obprop breaks in some cases. In addition, the output is not consistent.
For example, if obprop fails to create InChI for a molecule, the output looks like this…
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Converting the following inchi string does not work: InChI=1/C12H7BrN2OS/c13-9-6-15-12(16)8-5-10(17-11(8)9)7-1-3-14-4-2-7/h1-6H,(H,15,16)/f/h15H
$ echo "InChI=1/C12H7BrN2OS/c13-9-6-15-12(16)8-5-10(…
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Inchi output mode incorrectly considers chiral centers
with symmetric layouts to be undefined. Here are the
contents of a mol file containing a chiral center which
I believe is properly defined, a…
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I think there is a general problem in dealing with stereochemistry with SMILES strings, and that this bug is tied to [ 1742876 ] and [ 1792878 ], and possibly to a bunch of closed bugs. We are looking…