Re: [Cdk-user] print MCS as aromatic smarts

2013-05-23 Thread John May
The 1.5.x branch is unstable. However there are features which are useful as they stand. In order to deliver there features in Knime new features which cause complications were removed. As far as I know the only thing which has currently been removed was SINGLE_OR_DOUBLE flag as this impacted s

Re: [Cdk-user] print MCS as aromatic smarts

2013-05-23 Thread Martin Guetlein
Hi John, So the cdk.jar that is part of the CDK-plugin ( i.e. this one: plugins/org.openscience.cdk.knime_1.4.2.201301221437/lib/cdk-1.5.1.jar), is not the actual cdk-1.5.1.jar that you can download at sourceforge? Why? Is there documentation about what has been removed? This could actually cause

Re: [Cdk-user] print MCS as aromatic smarts

2013-05-23 Thread John May
Just a note, The knime node isn't the 'official' jar. Some features which don't work (actually loosely relating to aromatic SMILES) have been removed. J On 23 May 2013, at 11:03, Martin Guetlein wrote: > Hi, > > This bug is still in the generator, I just checked in a fix here: > http://sour

Re: [Cdk-user] print MCS as aromatic smarts

2013-05-23 Thread Martin Guetlein
Hi, This bug is still in the generator, I just checked in a fix here: http://sourceforge.net/p/cdk/bugs/1177/ So far, I have fixed it locally and built my own cdk.jar, but now Im working on a Knime-Node that relys on the 'official' cdk.jar. I would be great if you could patch this? Thanks and kin

Re: [Cdk-user] print MCS as aromatic smarts

2011-10-05 Thread Egon Willighagen
On Wed, Oct 5, 2011 at 1:49 PM, Rajarshi Guha wrote: > Oh, there's a patch for this bug? Not for this bug in the generator... but I was wondering if it was related to the bug in the *parser*... for the latter I uploaded patches... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet

Re: [Cdk-user] print MCS as aromatic smarts

2011-10-05 Thread Rajarshi Guha
Oh, there's a patch for this bug? On Wed, Oct 5, 2011 at 12:05 AM, Egon Willighagen wrote: > On Wed, Oct 5, 2011 at 2:40 AM, Rajarshi Guha wrote: >> On a somewhat related note, why does the atom type set aromaticity. >> Shouldn't this be done via the perception class? > > Is this the same proble

Re: [Cdk-user] print MCS as aromatic smarts

2011-10-04 Thread Egon Willighagen
On Wed, Oct 5, 2011 at 2:40 AM, Rajarshi Guha wrote: > On a somewhat related note, why does the atom type set aromaticity. > Shouldn't this be done via the perception class? Is this the same problem with AtomTypeManipulator.configure() ? In the SMILES parser the new patches make sure to cache an

Re: [Cdk-user] print MCS as aromatic smarts

2011-10-04 Thread Rajarshi Guha
On a somewhat related note, why does the atom type set aromaticity. Shouldn't this be done via the perception class? On Tue, Oct 4, 2011 at 8:36 PM, Rajarshi Guha wrote: > It looks like the problem is in lines 404-405 in SmilesGenerator. > > It appears that even if useAromaticityFlag is set to TR

Re: [Cdk-user] print MCS as aromatic smarts

2011-10-04 Thread Rajarshi Guha
It looks like the problem is in lines 404-405 in SmilesGenerator. It appears that even if useAromaticityFlag is set to TRUE, the code performs atom typing as well as aromaticity perception. In fact, the atom typing step messes up the aromaticity flags on the atoms and as a result the resultant fra

Re: [Cdk-user] print MCS as aromatic smarts

2011-09-08 Thread Egon Willighagen
On Thu, Sep 8, 2011 at 9:33 AM, Martin Guetlein wrote: >> It might be solved by using SmilesGenerator.setUseAromaticityFlag(true)... > > setUseAromaticityFlag(true) is already part of the code, but has no effect > on this example. This was exactly why I had not replied yet... I had not had enough

Re: [Cdk-user] print MCS as aromatic smarts

2011-09-08 Thread Nina Jeliazkova
On 8 September 2011 10:33, Martin Guetlein wrote: > > > On Thu, Sep 8, 2011 at 9:26 AM, Egon Willighagen < > egon.willigha...@gmail.com> wrote: > >> Hi Martin, >> >> I have not had time to answer earlier; it was on my list, but since >> you seem stuck with it... >> >> On Fri, Sep 2, 2011 at 12:12

Re: [Cdk-user] print MCS as aromatic smarts

2011-09-08 Thread Martin Guetlein
On Thu, Sep 8, 2011 at 9:26 AM, Egon Willighagen wrote: > Hi Martin, > > I have not had time to answer earlier; it was on my list, but since > you seem stuck with it... > > On Fri, Sep 2, 2011 at 12:12 PM, Martin Guetlein > wrote: > > IMHO, the problem is that the smiles writer (is there a smart

Re: [Cdk-user] print MCS as aromatic smarts

2011-09-08 Thread Egon Willighagen
Hi Martin, I have not had time to answer earlier; it was on my list, but since you seem stuck with it... On Fri, Sep 2, 2011 at 12:12 PM, Martin Guetlein wrote: > IMHO, the problem is that the smiles writer (is there a smarts writer?) No. What is the data model you like to save as SMARTS? > ha

Re: [Cdk-user] print MCS as aromatic smarts

2011-09-07 Thread Martin Guetlein
Anyone? I could really need some help on this.. Thanks, Martin On Fri, Sep 2, 2011 at 12:12 PM, Martin Guetlein < martin.guetl...@googlemail.com> wrote: > Hi all, > > I would like to mine the MCS and print it as aromatic smarts. > Unfortunately, the aromaticity information gets lost, even thoug

[Cdk-user] print MCS as aromatic smarts

2011-09-02 Thread Martin Guetlein
Hi all, I would like to mine the MCS and print it as aromatic smarts. Unfortunately, the aromaticity information gets lost, even though the mcs-fragment has arom flags asigned (see code example below). IMHO, the problem is that the smiles writer (is there a smarts writer?) has its own armaticity d