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When I use obchiral to determine the chirality of atoms in a molecule, obchiral gives the wrong chirality. The molecule attached, for example, has one R carbon atom and one S carbon atom. obchiral giv…
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if I convert from emory_2 to SMILES I get c1ccc2c(c1)nc([nH]2)S[C@@H](C(=O)Nc1ccccc1)C, but when I put c1ccc2c(c1)nc([nH]2)S[C@@H](C(=O)Nc1ccccc1)C in the 'Convert only molecules matching SMARTS:' box…
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When I compare L-Threonine and D-Threonine - C[C@H]([C@@H](C(=O)O)N)O and O=C(O)[C@H](N)[C@@H](O)C - with obgrep, it finds a match. Is that the intended behaviour?
Reported by: @ergo70
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Initially I thought it was just missing 3D coordinates:
I forgot about this problem when I recreated MiniDrugBank. SMIRKS string searching requires atom stereo and the 2D coordinates in DrugBank caus…
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This problem arose with OpenBabel 2.2.3 on Ubuntu 10.04. When presented with a chiral SMILES whose chiral center is bonded to more than four neighbors, src/formats/smilesformat.cpp may overrun memory…
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Written up here:
http://depth-first.com/articles/2007/06/25/interconvert-almost-any-smiles-and-inchi-with-ruby-open-babel
Reported by: @rapodaca
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While typing FreeSolv molecules with smirnoff99Frosst, I found 4 molecules that are potentially duplicated in the FreeSolv set. Below is the code snippet I used that found the duplicates:
```python…
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With the trunk code (under Windows), the molecules below cause the external InChI code to give a warning like:
Wrong 0D stereo descriptor(s): #3
S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O
c1…
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Hi,
I have noticed that on converting a Smiles string with chirality to sdf format, the resulting output file lacks any chiral information.
This is also evident on converting the sdf file back to …
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Converting this molecule to CML causes a crash in some stereo code in cmlformat.cpp
c12[C]3([C@H]4([N@@](CCc1c1ccccc1[nH]2)C[C@H](C=C4CC)C3))C(=O)OC
Reported by: @chrismorl