The Pyrol is an old problem. Saturation doesn't work, the valences are wrong
and inchi fails because of this (lawfully, I would say). Can somebody else
comment on the current status of the saturation code? I am not up to date
about it.
On Tuesday 01 April 2008 18:13:50 Gianfranco wrote:
> Dear
Dear all
I'm using the following code for the generation of Inchi:
IAtomContainer atomContainer= sp.parseSmiles(SMILES);
CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
CDKHydrogenAdder hdx.addImplicitHydrogens(atomContainer);
AtomContainerManipulator.conve
On 01/04/2008, Egon Willighagen <[EMAIL PROTECTED]> wrote:
> On Tue, Apr 1, 2008 at 2:42 PM, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
> > > public String getPreferredNameExtension() ?
> >
> > Not specified in most cases. Where specified, not unique in many
> > cases. So not useful to me.
>
>
ok it works for me!
thanks a lot
> SmilesGenerator.setUseAromaticityFlag(boolean)
>
--
Gianfranco Frau
CRS4 - Bioinformatics
Phone +39 070 9250 438
Loc. Pixina Manna Edificio 1 Pula 09010 (CA), Italy
http://www.bioinformatica.crs4.org
msn contact: [EMAIL PROTECTED]
--
On Tue, Apr 1, 2008 at 3:47 PM, Nina Jeliazkova <[EMAIL PROTECTED]> wrote:
> Egon Willighagen написа:
> > On Tue, Apr 1, 2008 at 2:45 PM, Andreas Schüller <[EMAIL PROTECTED]> wrote:
> > > I suggest that the SmilesGenerator should produce lower case SMILES by
> > > default now with the SmilesPar
On Tue, Apr 1, 2008 at 3:31 PM, Gianfranco <[EMAIL PROTECTED]> wrote:
> but the problem seems to be at the level of the parser:
>
>
> IMolecule m = builder.newMolecule( sp.parseSmiles("c1c1"));
>
> AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(m);
> CDKHueck
Egon Willighagen написа:
On Tue, Apr 1, 2008 at 2:45 PM, Andreas Schüller
<[EMAIL PROTECTED]> wrote:
Hmmm, this looks like a SMILES round tripping problem to me.
Yes.
I suggest that the SmilesGenerator should produce lower case SMILES by
default now with the SmilesParser not d
but the problem seems to be at the level of the parser:
IMolecule m = builder.newMolecule( sp.parseSmiles("c1c1"));
AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(m);
CDKHueckelAromaticityDetector.detectAromaticity(m);
hdx.addImplicitHydrogens(m);
On Tue, Apr 1, 2008 at 2:45 PM, Andreas Schüller
<[EMAIL PROTECTED]> wrote:
> Hmmm, this looks like a SMILES round tripping problem to me.
Yes.
> I suggest that the SmilesGenerator should produce lower case SMILES by
> default now with the SmilesParser not deducing bond orders anymore but
> se
On Tue, Apr 1, 2008 at 3:14 PM, Gianfranco <[EMAIL PROTECTED]> wrote:
> I'm sorry but this code, with the code that you suggested, returns the
> same output (C1C1):
I filed a bug report.
Egon
--
http://chem-bla-ics.blogspot.com/
--
Dear Egon
I'm sorry but this code, with the code that you suggested, returns the
same output (C1C1):
>
>> try{
>>
>> //create molecule parsing the smile
>> SmilesParser sp = new
>> SmilesParser(DefaultChemObjectBuilder.getInstance());
>> IChemObjectBuilder builder = DefaultC
On Tue, Apr 1, 2008 at 2:42 PM, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
> > public String getPreferredNameExtension() ?
>
> Not specified in most cases. Where specified, not unique in many
> cases. So not useful to me.
Any suggestions, fixes most welcome.
Egon
--
http://chem-bla-ics.blo
On 01/04/2008, Egon Willighagen <[EMAIL PROTECTED]> wrote:
> Damn... I'm procrastinating... should be preparing for my defense... :(
>
>
> On Tue, Apr 1, 2008 at 2:25 PM, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
> > Is it possible to access the CDK API to get a list of file format readers?
?
> >
Hmmm, this looks like a SMILES round tripping problem to me.
I suggest that the SmilesGenerator should produce lower case SMILES by
default now with the SmilesParser not deducing bond orders anymore but
setting the aromaticity flags.
If I remember right the rationale for removing the bond deduc
Damn... I'm procrastinating... should be preparing for my defense... :(
On Tue, Apr 1, 2008 at 2:25 PM, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
> Is it possible to access the CDK API to get a list of file format readers?
>
> I have tried ReaderFactory().getFormats() but I am not sure what it's
>
Is it possible to access the CDK API to get a list of file format readers?
I have tried ReaderFactory().getFormats() but I am not sure what it's
doing (there's no JavaDoc), and it doesn't include the SmilesReader
for instance.
I note that access to these formats from scripting languages could
hav
On Tue, Apr 1, 2008 at 2:17 PM, Gianfranco Frau <[EMAIL PROTECTED]> wrote:
> please look out this code. It creates a IMolecule object from SMILES of
> benzene, uses the aromaticity detector and than generates again the SMILES
> from the molecule.
First of all, the SmilesGenerator will not use 'c'
dear all,
please look out this code. It creates a IMolecule object from SMILES of
benzene, uses the aromaticity detector and than generates again the
SMILES from the molecule.
The code print out the string: "C1C1", so a molecule without
aromaticity.
Is it correct? What's the matter?
tha
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