On Jan 7, 2011, at 3:22 AM, TJ O'Donnell wrote:
> [Cl-].CC(C)(C)c1[Te+]c(C(C)(C)C)cc(/C=C/C=C2C=C(C(C)(C)C)OC(C(C)(C)C)=C2)c1
> [18:13:52] Can't kekulize mol
Looks like it's the [Te] which should be written [te+].
>>> Chem.CanonSmiles("c1cc[te+]cc1")
'c1cc[Te+]cc1'
>>> Chem.MolFromSmiles(Chem.CanonSmiles("c1cc[te+]cc1"))
[03:49:42] Can't kekulize mol
Another problem is with
>>> Chem.CanonSmiles("c1cccc[se+]1")
'c1cc[Se+]cc1'
>>>
A scan of the code suggests the problem is in SmilesParse/SmilesWrite.cpp
The only branch for generating a lowercase atom symbol in the SMILES is
if(inOrganicSubset(num)){
// it's a member of the organic subset
if(!doKekule && atom->getIsAromatic() && symb[0] < 'a') symb[0] -=
('A'-'a');
but Te and Se aren't in the organic subset. A fix might be to change
*** rdkit/Code/GraphMol/SmilesParse/SmilesWrite.cpp 2010-12-04
18:30:00.000000000 +0100
--- rdkit/Code/GraphMol/SmilesParse/SmilesWrite.cpp.new 2011-01-07
03:57:17.000000000 +0100
***************
*** 102,107 ****
--- 102,108 ----
int iMass=static_cast<int>(atom->getMass()+.1);
res <<iMass;
}
+ if(!doKekule && atom->getIsAromatic() && symb[0] < 'a') symb[0] -=
('A'-'a');
res << symb;
bool chiralityIncluded=false;
but I haven't tested it out.
Andrew
da...@dalkescientific.com
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