Dear Mark,
> Could you send the source code that runs for 15 minutes to the list? It
> should be relatively easy to debug it, to find out where things stall.
Thank you for lookng at this issue. here is the jython code I am using to
calculate partial charge for an atom.
sp = smilesParser()
smi =
"COC1=CC=C(c...@h]2n(C)C(=O)[...@h](C)NC(=O)[C@@H](C)NC(=O)[...@h]3cc4=cc=c(O)C(OC5=CC=C(C=C5)C(O)[...@h](N(C)C(=O)[...@h](C)NC2=O)C(=O)N3C)=C4)C=C1"
mol = sp.parseSimles(smi)
mol = reader.next()
desc = PartialTChargePEOEDescriptor ()
atoms = mol.atoms().iterator()
firstAtom = atoms.next()
pcharge = desc.calculate(firstAtom,
mol).getValue().doubleValue()
I also went through the code of of the one of the java object that is
instanced by PartialTChargePEOEDescriptor and one of its methods that is
called to calculate the partial charges, I found out some bizare code I paste
here:
public
class GasteigerMarsiliPartialCharges implements IChargeCalculator {
…
public IAtomContainer
assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge)
throws Exception {
….
double[] q_old = new double[ac.getAtomCount()];
for(int i = 0 ; i < q_old.length ; i++)
q_old[0] = 20.0; ////// STRANGE
….
the index should "i" not "0" if I understand this part of the code.
thanks ,
AYASRI
> From: cdk-user-requ...@lists.sourceforge.net
> Subject: Cdk-user Digest, Vol 42, Issue 13
> To: cdk-user@lists.sourceforge.net
> Date: Tue, 17 Nov 2009 15:55:13 +0000
>
> Send Cdk-user mailing list submissions to
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> Today's Topics:
>
> 1. Re: Strange SMILES produced by CDK (Charlie Zhu)
> 2. Re: Strange SMILES produced by CDK (Rajarshi Guha)
> 3. Re: Strange SMILES produced by CDK (Charlie Zhu)
> 4. Re: Cdk-user Digest, Vol 42, Issue 10 (Mark Rijnbeek)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 17 Nov 2009 22:51:20 +0800
> From: Charlie Zhu <zh.char...@gmail.com>
> Subject: Re: [Cdk-user] Strange SMILES produced by CDK
> To: rajarshi.g...@gmail.com
> Cc: cdk-user@lists.sourceforge.net
> Message-ID:
> <f6fd50230911170651m688045c4n2d9d43adbc27b...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I attached the original SDF file for those interested. The file was exported
> from Zinc.
>
> It will produce below SMILES when using IteratingMDLReader and
> SmilesGenerator
> [H]OC2=NN(C(=O)C=3C(=O)c1c([H])c([H])c(c([H])c1N([H])C2=3)Cl)C([H])([H])C#Cc4c([H])nc([H])c([H])c4([H])
>
> And below SMILES is outputed when using MDLReader and SmilesGenerator
> [H]NC2=CC(N(=C)O=3C(=C)C1=[H](C([H])=C(O)C([H])=C1([H]))O(N)C2=3)C([H])([H])C#CC=4C([H])=CN
>
> I am using CDK-1.2.3.jar on Windows 7 x64.
>
> Charlie
>
>
> On Tue, Nov 17, 2009 at 9:34 PM, Rajarshi Guha <rajarshi.g...@gmail.com>wrote:
>
> >
> >
> > On Tue, Nov 17, 2009 at 8:29 AM, Noel O'Boyle <baoille...@gmail.com>wrote:
> >
> >> BTW, the other more common use of bond symbols at ring closures is to
> >> designate cis/trans stereochemistry at a ring closure. See
> >>
> >> http://baoilleach.blogspot.com/2009/04/are-you-on-my-side-or-not-its-ez.html
> >>
> >
> > Gah! Of course.
> >
> >
> >
> > --
> > Rajarshi Guha
> > NIH Chemical Genomics Center
> >
> >
> > ------------------------------------------------------------------------------
> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> > trial. Simplify your report design, integration and deployment - and focus
> > on
> > what you do best, core application coding. Discover what's new with
> > Crystal Reports now. http://p.sf.net/sfu/bobj-july
> > _______________________________________________
> > Cdk-user mailing list
> > Cdk-user@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/cdk-user
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> -------------- next part --------------
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> Name: zinc_35.sdf
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 17 Nov 2009 09:56:35 -0500
> From: Rajarshi Guha <rajarshi.g...@gmail.com>
> Subject: Re: [Cdk-user] Strange SMILES produced by CDK
> To: Charlie Zhu <zh.char...@gmail.com>
> Cc: cdk-user@lists.sourceforge.net
> Message-ID:
> <773cea9e0911170656p9411beakfb14295969c83...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Do you see the problem with MDLV2000Reader (which is what the iterating
> version uses internally)?
>
> On Tue, Nov 17, 2009 at 9:51 AM, Charlie Zhu <zh.char...@gmail.com> wrote:
>
> > Hi,
> >
> > I attached the original SDF file for those interested. The file was
> > exported from Zinc.
> >
> > It will produce below SMILES when using IteratingMDLReader and
> > SmilesGenerator
> >
> >
> > [H]OC2=NN(C(=O)C=3C(=O)c1c([H])c([H])c(c([H])c1N([H])C2=3)Cl)C([H])([H])C#Cc4c([H])nc([H])c([H])c4([H])
> >
> > And below SMILES is outputed when using MDLReader and SmilesGenerator
> >
> > [H]NC2=CC(N(=C)O=3C(=C)C1=[H](C([H])=C(O)C([H])=C1([H]))O(N)C2=3)C([H])([H])C#CC=4C([H])=CN
> >
> > I am using CDK-1.2.3.jar on Windows 7 x64.
> >
> > Charlie
> >
> >
> > On Tue, Nov 17, 2009 at 9:34 PM, Rajarshi Guha
> > <rajarshi.g...@gmail.com>wrote:
> >
> >>
> >>
> >> On Tue, Nov 17, 2009 at 8:29 AM, Noel O'Boyle <baoille...@gmail.com>wrote:
> >>
> >>> BTW, the other more common use of bond symbols at ring closures is to
> >>> designate cis/trans stereochemistry at a ring closure. See
> >>>
> >>> http://baoilleach.blogspot.com/2009/04/are-you-on-my-side-or-not-its-ez.html
> >>>
> >>
> >> Gah! Of course.
> >>
> >>
> >>
> >> --
> >> Rajarshi Guha
> >> NIH Chemical Genomics Center
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> >> 30-Day
> >> trial. Simplify your report design, integration and deployment - and focus
> >> on
> >> what you do best, core application coding. Discover what's new with
> >> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> >> _______________________________________________
> >> Cdk-user mailing list
> >> Cdk-user@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/cdk-user
> >>
> >>
> >
>
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Tue, 17 Nov 2009 23:00:57 +0800
> From: Charlie Zhu <zh.char...@gmail.com>
> Subject: Re: [Cdk-user] Strange SMILES produced by CDK
> To: rajarshi.g...@gmail.com
> Cc: cdk-user@lists.sourceforge.net
> Message-ID:
> <f6fd50230911170700h5440ffc2w7bf209a3ea2ba...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yes, MDLV2000Reader gets the same result to IteratingMDLReader.
>
> Charlie
>
>
> On Tue, Nov 17, 2009 at 10:56 PM, Rajarshi Guha
> <rajarshi.g...@gmail.com>wrote:
>
> > Do you see the problem with MDLV2000Reader (which is what the iterating
> > version uses internally)?
> >
> >
> > On Tue, Nov 17, 2009 at 9:51 AM, Charlie Zhu <zh.char...@gmail.com> wrote:
> >
> >> Hi,
> >>
> >> I attached the original SDF file for those interested. The file was
> >> exported from Zinc.
> >>
> >> It will produce below SMILES when using IteratingMDLReader and
> >> SmilesGenerator
> >>
> >>
> >> [H]OC2=NN(C(=O)C=3C(=O)c1c([H])c([H])c(c([H])c1N([H])C2=3)Cl)C([H])([H])C#Cc4c([H])nc([H])c([H])c4([H])
> >>
> >> And below SMILES is outputed when using MDLReader and SmilesGenerator
> >>
> >> [H]NC2=CC(N(=C)O=3C(=C)C1=[H](C([H])=C(O)C([H])=C1([H]))O(N)C2=3)C([H])([H])C#CC=4C([H])=CN
> >>
> >> I am using CDK-1.2.3.jar on Windows 7 x64.
> >>
> >> Charlie
> >>
> >>
> >> On Tue, Nov 17, 2009 at 9:34 PM, Rajarshi Guha
> >> <rajarshi.g...@gmail.com>wrote:
> >>
> >>>
> >>>
> >>> On Tue, Nov 17, 2009 at 8:29 AM, Noel O'Boyle <baoille...@gmail.com>wrote:
> >>>
> >>>> BTW, the other more common use of bond symbols at ring closures is to
> >>>> designate cis/trans stereochemistry at a ring closure. See
> >>>>
> >>>> http://baoilleach.blogspot.com/2009/04/are-you-on-my-side-or-not-its-ez.html
> >>>>
> >>>
> >>> Gah! Of course.
> >>>
> >>>
> >>>
> >>> --
> >>> Rajarshi Guha
> >>> NIH Chemical Genomics Center
> >>>
> >>>
> >>> ------------------------------------------------------------------------------
> >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> >>> 30-Day
> >>> trial. Simplify your report design, integration and deployment - and
> >>> focus on
> >>> what you do best, core application coding. Discover what's new with
> >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> >>> _______________________________________________
> >>> Cdk-user mailing list
> >>> Cdk-user@lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/cdk-user
> >>>
> >>>
> >>
> >
> >
> > --
> > Rajarshi Guha
> > NIH Chemical Genomics Center
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 4
> Date: Tue, 17 Nov 2009 15:52:48 +0000
> From: Mark Rijnbeek <ma...@ebi.ac.uk>
> Subject: Re: [Cdk-user] Cdk-user Digest, Vol 42, Issue 10
> To: cdk-user@lists.sourceforge.net
> Message-ID: <4b02c6d0.2050...@ebi.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> > Dear Gwen,
> >
> > I am facing the same problem with the atomic descriptors in CDK. Partial
> > charge calculations take a longtime for some molecules before it returns
> > a value.
> > I tried your molecule (
> > COC1=CC=C(c...@h]2n(C)C(=O)[...@h](C)NC(=O)[C@@H](C)NC(=O)[...@h]3cc4=cc=c(O)C(OC5=CC=C(C=C5)C(O)[...@h](N(C)C(=O)[...@h](C)NC2=O)C(=O)N3C)=C4)C=C1
> >
> > ) for partial charge calculations and it took me more than 15 minutes to
> > return the partial charge values.
> >
> > I also noticed that polyaromatic molecules (fused aromatic rings) take
> > more than 10 minutes. This has something to do with the aromaticity
> > probably.
>
> Could you send the source code that runs for 15 minutes to the list? It
> should be relatively easy to debug it, to find out where things stall.
>
> Mark
>
>
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>
> ------------------------------
>
> _______________________________________________
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
> End of Cdk-user Digest, Vol 42, Issue 13
> ****************************************
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