joelib-help — JOELib-Help

[Joelib-help] Definition of a molecular graph and a new release

[Joerg K. W. <we...@in...>]

Hi Egon,
Hi all,

i've released a new JOELib version
http://sourceforge.net/projects/joelib/

with the following changes:

- Extended tutorial introducing formally molecular graphs.
   This is especially interesting for the Octet interface and
   the QSAR project.
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/JOELibPrimer.html

- E/Z SMARTS matching and adding improved autodetection for 2D/3D 
structures if not using SMILES as input.

- Extensive PMD, JavaNCSS offline statistics, so on long term runs there 
are some non-functioanlity things to do ... just for improving the 
design and becoming more user friendly :-)
http://www-ra.informatik.uni-tuebingen.de/software/joelib/statistics.html

Kind regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Joelib and Applet?

[Joerg K. W. <we...@in...>]

Hi Andreas,

> Ok, but I will have to modify Joelib for sure, right?
Right!

> Joelib itself has no builtin support for applets?
No.

> P.S.: Is there a way to match a SMARTS pattern if I don't use the static display routine in MoleculeViewer2D.java, but instead use the viewer.display (i.e. the dynamic) way? I resolved it setting the instantiation variable 'renderer' from protected to public...
O.k., that's better.

Kind regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Joelib and Applet?

[Andreas M. <ma...@in...>]

On Sat, Jul 17, 2004 at 10:48:42AM +0200, Joerg K. Wegner wrote:
> Hi Andreas,
> 
> should work, if you use only the drawing pane instead of a JFrame-wrapper.
> Some GUI-Builders support also a mixed class which is able to be an 
> applet and an application ... but i've since a long time not builded 
> real GUI's, so please have a look at your own.

Ok, but I will have to modify Joelib for sure, right?
Joelib itself has no builtin support for applets?

Thanks,
Andi

P.S.: Is there a way to match a SMARTS pattern if I don't use the static display routine in MoleculeViewer2D.java, but instead use the viewer.display (i.e. the dynamic) way? I resolved it setting the instantiation variable 'renderer' from protected to public...

Re: [Joelib-help] Joelib and Applet?

[Joerg K. W. <we...@in...>]

Hi Andreas,

should work, if you use only the drawing pane instead of a JFrame-wrapper.
Some GUI-Builders support also a mixed class which is able to be an 
applet and an application ... but i've since a long time not builded 
real GUI's, so please have a look at your own.

Kind regards, Joerg

P.S.: Greetings to Christoph.

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Joelib and Applet?

[Andreas M. <ma...@in...>]

Hi all,

I'm wondering whether I can turn my joelib-based molecule viewer from a
standalone application into an applet. Is Joelib Applet Compatible,
i.e. is there a possibility to draw in an applet? The
MoleculeViewer2D.display() method uses the ordinary awt...

Greetings
Andreas

[Joelib-help] Changed kernel ID + dummy atoms

[Joerg K. W. <we...@in...>]

Hi all,

I've added dummy atom support for MDL-SDF import to CVS.

The hashed kernel ID has changed from
'715333816'
to
'-2141483117'

So please: 'Don't panic'
This will not change your descriptor calculation results, because the 
changes affects only the 'dummy' atoms.

    - joelib/src/joelib/io/MDLSD.java
      Added dummy atom support for 'Du' entries.

    - joelib/src/joelib/data/plain/types.txt
      Internal representation of dummy atoms changed from 'X' to 'Xx'.
      Now we are conform with joelib/src/joelib/data/plain/element.txt

See also:
joelib/kernel.txt for details and detailed ID changes.

FINALLY, you can treat all desriptor calculations with the kernel ID's
'715333816' and '-2141483117'
as equivalent, because nothing relevant has changed in the chemical 
representation.

Kind regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Import/export performance + up/down auto-detection (part II)

[Joerg K. W. <we...@in...>]

Hi,

CVS version has changed again !

Some time ago the performance was discussed:
http://sourceforge.net/mailarchive/forum.php?thread_id=4857368&forum_id=26962

I've found another reason for a slower loading process.

All molecules uses (since that release) a unique SMILES hash code, which 
enables uniqueness checkings.
This must be calculated at least once, so this requires also runtime.
1. for creating unique renumbering (Morgan), runtime ~O(N^3), because 
it's a modified breadth first search (BFS).
2. hashing

And because the actual up/down auto-detection contained a bug, all hash 
codes have changed. So, this is an offical warning for users using this 
code as part of an ID or something else.

This should not in general used as primary key in a database, but for 
uniqueness checking this is a fast possibility, if you store this value.

I think i will add a flag, use simple hashing or something else to be 
available with the next release in JOEMol, which then will avoid the 
'unique' hashing method.

But then also all auto-assign methods for cis/trans and up/down should 
use joelib.util.IsomerismDetection which is not the case at the moment 
(e.g. JOEMol2Smi has it's own method).
So i've replaced the actual auto-detection method in the SMILES 
generator by the auto-detection method in
// if the autoAssignFlag is true also up/down flags are assigned
IsomerismDetection.isCisTransBond(bond, autoAssignFlag);

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] stereochemistry in TestSmarts

[Joerg K. W. <we...@in...>]

Hi all,

o.k. bug and missing feature. Here are the details:

111. BUG (serious ! Please check the new functionality in CVS !)
joelib.smiles.JOEMol2Smi
https://sourceforge.net/tracker/?func=detail&atid=425969&aid=983990&group_id=39708

Was caused because the first atom was always detected as
recognized.
Fixed !
Furthermore i've found interchanged UP/DOWN assignments at
the end of this method. So i've changed ALL assignment types.
All users should check all kind of import/export methods
affecting SMILES and SMARTS matching methods with up/down
and cis/trans support heavily.
PLEASE !

222. Up/Down searching functionality in SMARTS was simply not activated
Fixed !
I've added the test cases to
joelib/src/resources/smartsEvaluation/evaluation.txt

Please remember, that the internal auto-detection assign ALWAYS 'up' as 
preferred case. So cis cases will be always stored as up/up. In 
trans-cases the match is inverted.

I will wait at least two weeks for a new release !!!
If anyone of you has time, please check the modified recognition, which 
affects the SMILES export.

###############################
## cis/trans detection
###############################
C\C=C/C                        a_carbon_in_abcd_with_trans 
        trans-butene#1
C/C=C\C                        a_carbon_in_abcd_with_trans 
        trans-butene#4
C/C=C/C                        a_carbon_in_abcd_with_trans 
        trans-butene
C\C=C\C                        a_carbon_in_abcd_with_trans 
        trans-butene
C\C=C\C                        a_carbon_in_abcd_with_cis 
        cis-butene#1#4
# this can not be found for MDL SDF import, because JOELib's auto-assign 
method assign C\C=C\C !!!
C/C=C/C                        a_carbon_in_abcd_with_cis 
        cis-butene
#
C/C=C\C                        a_carbon_in_abcd_with_cis 
        cis-butene
C\C=C/C                        a_carbon_in_abcd_with_cis 
        cis-butene

Kind regards, Joerg

> Thanks for your quick respose.  However, this doesn't seem to change the
> results I get for TestSmarts.
> 
> * Joerg K. Wegner <we...@in...> [2004-06-30 10:18 +0200]:
> 
>>Hi all,
>>
>>As already submitted be Gerd this is a bug in the SMARTS parser. So i 
>>opened a bug tracking task and will close it today and check in to CVS.
>>
>>
>>>Bugs item #982570, was opened at 2004-06-30 08:09
>>>You can respond by visiting:
>>>
>>
>>https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
>>
>>>Initial Comment:
>>>The SMARTS encoder writes Stereo-Up as '\' and
>>>Stereo-Down as '/' but the specs says it vise versa.
>>>----------------------------------------------------------------------
>>>You can respond by visiting:
>>>
>>
>>https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
>>
>>If you want a quick fix change line
>>-2467- case ('/'):
>>with
>>-2479- case ('\\'):
>>
>>Kind regards, Joerg
>>
>>
>>>Hi everyone, I'm new to Joelib and need a little help.
>>>
>>>I'm having trouble getting the TestSmarts[1] program to recognize
>>>stereochemistry.  For example, the SMARTS "C\C=C/C" won't match a
>>>molecule made with that same SMILES string.  I've tried several releases,
>>>including the 2004-06-21, on Solaris.  SMARTSEvaluationDefault.sh runs
>>>with no mismatches.
>>>
>>>I run: 
>>>
>>>
>>>>java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C
>>>
>>>where butene.trans.sdf is:
>>> 4  3  0  0  1  0            999 V2000
>>>   0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>  -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>  -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>>> 1  2  1  0  0  0  0
>>> 2  3  2  0  0  0  0
>>> 3  4  1  0  0  0  0
>>>M  END
>>>$$$$
>>>
>>>Any suggestions on what I may be doing wrong or what the problem is?
>>>
>>> 1. 
>>> http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html
>>
>>
>>-- 
>>Dipl. Chem. Joerg K. Wegner
>>Center of Bioinformatics Tuebingen (ZBIT)
>>Department of Computer Architecture
>>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
>>Phone: (+49/0) 7071 29 78970
>>Fax: (+49/0) 7071 29 5091
>>E-Mail: mailto:we...@in...
>>WWW:    http://www-ra.informatik.uni-tuebingen.de
>>--
>>Never mistake motion for action.
>>                                    (E. Hemingway)
>>
>>Never mistake action for meaningful action.
>>                               (Hugo Kubinyi,2004)
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email sponsored by Black Hat Briefings & Training.
>>Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
>>digital self defense, top technical experts, no vendor pitches, 
>>unmatched networking opportunities. Visit www.blackhat.com
>>_______________________________________________
>>Joelib-help mailing list
>>Joe...@li...
>>https://lists.sourceforge.net/lists/listinfo/joelib-help
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] stereochemistry in TestSmarts

[Dave R. <dr...@re...>]

Thanks for your quick respose.  However, this doesn't seem to change the
results I get for TestSmarts.

* Joerg K. Wegner <we...@in...> [2004-06-30 10:18 +0200]:
> Hi all,
> 
> As already submitted be Gerd this is a bug in the SMARTS parser. So i 
> opened a bug tracking task and will close it today and check in to CVS.
> 
> > Bugs item #982570, was opened at 2004-06-30 08:09
> > You can respond by visiting:
> > 
> https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
> > Initial Comment:
> > The SMARTS encoder writes Stereo-Up as '\' and
> > Stereo-Down as '/' but the specs says it vise versa.
> > ----------------------------------------------------------------------
> > You can respond by visiting:
> > 
> https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
> 
> If you want a quick fix change line
> -2467- case ('/'):
> with
> -2479- case ('\\'):
> 
> Kind regards, Joerg
> 
> >Hi everyone, I'm new to Joelib and need a little help.
> >
> >I'm having trouble getting the TestSmarts[1] program to recognize
> >stereochemistry.  For example, the SMARTS "C\C=C/C" won't match a
> >molecule made with that same SMILES string.  I've tried several releases,
> >including the 2004-06-21, on Solaris.  SMARTSEvaluationDefault.sh runs
> >with no mismatches.
> >
> >I run: 
> >
> >>java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C
> >
> >where butene.trans.sdf is:
> >  4  3  0  0  1  0            999 V2000
> >    0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >    0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >   -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >   -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >  1  2  1  0  0  0  0
> >  2  3  2  0  0  0  0
> >  3  4  1  0  0  0  0
> >M  END
> >$$$$
> >
> >Any suggestions on what I may be doing wrong or what the problem is?
> >
> >  1. 
> >  http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html
> 
> 
> -- 
> Dipl. Chem. Joerg K. Wegner
> Center of Bioinformatics Tuebingen (ZBIT)
> Department of Computer Architecture
> Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
> Phone: (+49/0) 7071 29 78970
> Fax: (+49/0) 7071 29 5091
> E-Mail: mailto:we...@in...
> WWW:    http://www-ra.informatik.uni-tuebingen.de
> --
> Never mistake motion for action.
>                                     (E. Hemingway)
> 
> Never mistake action for meaningful action.
>                                (Hugo Kubinyi,2004)
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
> digital self defense, top technical experts, no vendor pitches, 
> unmatched networking opportunities. Visit www.blackhat.com
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help

-- 
Dave Roe		dr...@re...

[Joelib-help] Re: [Joelib-devel] Descriptors and silent mode

[Joerg K. W. <we...@in...>]

Hi Nicolas,

> -> first, is there a silent mode, to avoid the printing of the descriptors
> loading ?
All debug, info, error messages can be switched off in the
joelib/src/log4j.properties
file.
So switch all DEBUG and INFO to ERROR and nothing will be printed.

> -> second, what is the meaning of the order of the values when for example
> you ask for "Atom_in_donor" descriptor and you have as output the following
> line: 5<0,0,1,0,0> ?
> Is this mean that the atom label 2 is donor ?
No, atom starts with 1,2,3, ..., N
So atom 3 is a Donor.
You can also use the general
joelib.molecule.types.AtomProperties
interface

> -> third, I have asked for Gasteiger-Marsili calculation: a first one is
> done without adding Hydrogens, and the second one with adding H in my
> molecules. But, at the end the results are different. What does it means ? I
> thought that this calculation take always the Hydrogens influence ?
Oh, this is a critical question and has no general answer.

 From the computer science standpoint of view you these are two cases 
and some descriptors are sensitive to hydrogens, others are not.
Why are some descriptors hydrogen independent ?
1. Some use only heavy weight atoms to calculate the descriptors.
2. Some simply remove the hydrogens, before they are calculated.

Of course, this is a serious problem, when having the case that one 
whants all sigma partial charges and on the other side you are 
interested in one special descriptor using only heavy weight atoms BUT 
here with the sigma partial charge atom property.
So this is and indexing conflict and of course can not be the same.

So, if calculating and accessing atom properties you can/should check 
the hydrogen atom state of the molecule, which is not big deal.
I've at least checked these things for the standard descriptor 
calculation class.

The easiest solution is to remove hydrogens, because they are still 
implicitely available via the JOELib expert system, but on the other 
hand the user might be interested in protonated molecules assigned by 
another program, e.g. Corina which is also really good to assign hydrogens.

> -> and fourth, how  could you explain that, for the same molecule:
> "Atom_in_donor" is 5<0,0,1,0,0>
> "Atom_in_acceptor" is 5<0,0,0,1,0>
> "Atom_in_donor_or_acceptor" is 5<0,0,0,0,0> ?
It's only one kind of possible and really huge discrete assignment/label 
space.
So, if you have a look at the used SMARTS pattern in and all literature 
references given there:
joelib.desc.types.AtomInDonAcc
joelib.desc.types.AtomInDonor
joelib.desc.types.AtomInAcceptor
see also
joelib.desc.types.HBA1
joelib.desc.types.HBA2
joelib.desc.types.HBD1
joelib.desc.types.HBD2
you can see that they use all different descriptions. And additionally 
then remind that SMARTS matching is based on the chemical expert systems 
used, so even if you use the same SMARTS, you will with a high 
probability get a nice number of mismatches.
E.g. i got once a time a complained from a NCI which compared the NCI 
and JOELib results. YES, that's a problem and i complain every time and 
in all publications, that we need here an 'chemical expert' system 
standard which we can test against.
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomtyper.html

If you do not like them, create your own descriptor. If you want it more 
dynamic use SMARTS from a text file, but then i recommend to inroduce 
also an ID as done for the JOELib expert systems. This guarantees you 
that you will notice if another user changes on single SMARTS entry, 
which can definitely occur, because we are talking about expert systems. 
  Which are a really evolving type of label assignment (or more general 
model/hypothesis).

See here interfaces:
joelib.data.SoftCodedKernel
joelib.data.HardCodedKernel

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Needing developers

[Joerg K. W. <we...@in...>]

Dear developers,
dear community,

as already mentioned i've less time at the moment and i can only 
guarantee to maintain JOELib as it should be maintained.
I will also submit new functionalities, like maximum common substructure 
search in 2-3 months, then we have an extensively tested release.

Now my help request to all developers and all people which can advertise 
our projects. Please bear in mind that i've plannded to end my PhD 
thesis until the middle of 2005, so we need also other people which are 
able to maintain JOELib, because my spare-time is restricted.
But i've no time for refactor-maintenance, which recommended for long 
term time slides.

I'm really interested in a QSAR data mining tool based on Java.
http://joelib.sf.net
http://qsar.sf.net
http://octet.sourceforge.net/
http://cdk.sf.net

And as you know JOELib has already some
- descriptors and
- data mining tools (Weka interface and class structure containing 
molecules)
- basic algorithms, like sub-optimal distance matrix with O(N^3)
- Labeling functions for molecular graphs as atom labels (atom properties)
- Labeling functions for molecular graphs as bond labels (bond properties)

I'm not sure if Rich and Egon have the same opinion, but from my 
standpoint of view it is crucial important that this community helps us 
to implement things.
We, the project administrators can assign tasks and help you understand 
the actual packages, but we can not implement all things we need on our 
own, as at the moment.

So, especially the JOELib project needs more developers and anybody 
which is willingly to implement the basic Octet-JOELib interface as 
starting point.
Example was already given at:
http://www-ra.informatik.uni-tuebingen.de/mitarb/wegner/tmp/octet/
The changes are found in CDKTools 0.2.1, which can be downloaded at:
http://sourceforge.net/project/showfiles.php?group_id=96108
Javadoc is at:
http://octet.sourceforge.net/api.html

What i like to see in the interface is an analogue structure as shown 
here, especially with respect to the chemical expert systems (chemical 
kernel) in JOELib:
The following ASAP articles were posted to the ACS Web Edition of 
Journal of Chemical Information and Computer Sciences on June 17, 2004.
Title:   Some Basic Data Structures and Algorithms for Chemical Generic 
Programming
Authors:   Wei Zhang, Tingjun Hou, Xuebin Qiao, and Xiaojie Xu
Link:     http://dx.doi.org/10.1021/ci049938s

Kind regards, Joerg Kurt Wegner

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] stereochemistry in TestSmarts

[Joerg K. W. <we...@in...>]

Hi all,

As already submitted be Gerd this is a bug in the SMARTS parser. So i 
opened a bug tracking task and will close it today and check in to CVS.

 > Bugs item #982570, was opened at 2004-06-30 08:09
 > You can respond by visiting:
 > 
https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708
 > Initial Comment:
 > The SMARTS encoder writes Stereo-Up as '\' and
 > Stereo-Down as '/' but the specs says it vise versa.
 > ----------------------------------------------------------------------
 > You can respond by visiting:
 > 
https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708

If you want a quick fix change line
-2467- case ('/'):
with
-2479- case ('\\'):

Kind regards, Joerg

> Hi everyone, I'm new to Joelib and need a little help.
> 
> I'm having trouble getting the TestSmarts[1] program to recognize
> stereochemistry.  For example, the SMARTS "C\C=C/C" won't match a
> molecule made with that same SMILES string.  I've tried several releases,
> including the 2004-06-21, on Solaris.  SMARTSEvaluationDefault.sh runs
> with no mismatches.
> 
> I run: 
> 
>>java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C
> 
> where butene.trans.sdf is:
>   4  3  0  0  1  0            999 V2000
>     0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  0  0  0  0
>   2  3  2  0  0  0  0
>   3  4  1  0  0  0  0
> M  END
> $$$$
> 
> Any suggestions on what I may be doing wrong or what the problem is?
> 
>   1. http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] stereochemistry in TestSmarts

[Dave R. <dr...@re...>]

Hi everyone, I'm new to Joelib and need a little help.

I'm having trouble getting the TestSmarts[1] program to recognize
stereochemistry.  For example, the SMARTS "C\C=C/C" won't match a
molecule made with that same SMILES string.  I've tried several releases,
including the 2004-06-21, on Solaris.  SMARTSEvaluationDefault.sh runs
with no mismatches.

I run: 
> java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C
where butene.trans.sdf is:
  4  3  0  0  1  0            999 V2000
    0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
M  END
$$$$

Any suggestions on what I may be doing wrong or what the problem is?

  1. http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html
-- 
Dave Roe		dr...@re...

Re: [Joelib-help] Set properties of a Renderer2DModel

[Joerg K. W. <we...@in...>]

Hi Andreas,

> boolean myKekuleFlag=true;
> boolean myDrawNumbersFlag=true;
> model.setKekuleStructure(myKekuleFlag);
> model.setDrawNumbers(myDrawNumbersFlag);
o.k.

> viewer.molecule=mol;
> viewer.display();
NO, storing object and render objects are not the same !

try:
RenderingAtoms ratoms=viewer.getAtomContainer();
ratoms.add(mol);
viewer.display();

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Set properties of a Renderer2DModel

[Andreas M. <ma...@in...>]

On Mon, Jun 21, 2004 at 04:22:58PM +0200, Joerg K. Wegner wrote:
> Hi Andreas,
> 
> it will work for more parameters if you do not work with a static 
> environment.
> 
> So use:
> MoleculeViewer2D viewer = new MoleculeViewer2D();
> Renderer2DModel model = viewer.getRenderer2DModel();
> 
> then try:
> boolean myKekuleFlag=true;
> model.setKekuleStructure(myKekuleFlag);


boolean myKekuleFlag=true;
boolean myDrawNumbersFlag=true;
model.setKekuleStructure(myKekuleFlag);
model.setDrawNumbers(myDrawNumbersFlag);
viewer.molecule=mol;
viewer.display();

I use this, but it opens just a blank window. What should I do to display it?
Thanks,

Andi

[Joelib-help] New release

[Joerg K. W. <we...@in...>]

Minor feature enhancement release:
https://sourceforge.net/forum/forum.php?forum_id=385130
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Set properties of a Renderer2DModel

[Joerg K. W. <we...@in...>]

Hi Andreas,

it will work for more parameters if you do not work with a static 
environment.

So use:
MoleculeViewer2D viewer = new MoleculeViewer2D();
Renderer2DModel model = viewer.getRenderer2DModel();

then try:
boolean myKekuleFlag=true;
model.setKekuleStructure(myKekuleFlag);

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Set properties of a Renderer2DModel

[Andreas M. <ma...@in...>]

Hi all,

there is a possibility to set default values in joelib.gui.render.Renderer2DModel.java, but changes lead to no effect.
However, if I change settings in joelib.gui.render.MoleculeViewer2D.java in the 

public static void display(JOEMol molecule, String _title,
        JOESmartsPattern smarts, String eTransfer, String retroSynth,
        String conjRing, String labels)

routine via for example

r2dm.setDrawNumbers(true);

it works, at least for some properties (unfortunately not for .useKekuleStructure, which I'd like to use).
Sincerely,

Andi

Re: [Joelib-help] Darstellung / Fehler in SMARTS-Matching (?)]

[Joerg K. W. <we...@in...>]

Hi Andreas,

> having discussed this with my collegue it occurs to us as a misunderstanding:
> We didn't want to argue if this were two aromatic rings or not, but merely if the
> two marked *edges* are falsely marked, i.e. if it is incorrect to mark edges as 
> match just because the neighbouring atoms match.
Oh yes, you're right.
Problem occurs in joelib.gui.render.Render2D: line 305

So, only atom are added to the rendering engine and it draws then bonds 
to all neighbour atoms.
So, we need to add also the bonds obtained from the SMARTS matching or 
more exact the bonds between all atoms ONLY in the SMARTS matching and 
its correct order !

So this is a bug, not a feature.

As said, i've less time, but i will add a bug report to the tracking 
system (here is the tracking ID):
https://sourceforge.net/tracker/?func=detail&atid=425969&aid=973996&group_id=39708

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Darstellung / Fehler in SMARTS-Matching (?)]

[Andreas M. <ma...@in...>]

Hi all,

----- Forwarded message from "Joerg K. Wegner" <we...@in...> -----
1. SMARTS matching
>http://www.informatik.uni-freiburg.de/~maunza/screenshot.jpeg 
>SMILES ist "OC1C(O)C(CO)OC1N2C=CC(=N)NC2=O"
>SMARTS ist "O=O=c:n:c:c:c:n-C-O-C-C-C-O"
You can at least formulate an aromatic tautomeric form, so i'm not sure, 
too. But it looks o.k. for me, other opinions from users ?
JOELib counts also electrons for SMARTS matching, see aromaticity typer 
and text definition aromatic.txt

having discussed this with my collegue it occurs to us as a misunderstanding:
We didn't want to argue if this were two aromatic rings or not, but merely if the
two marked *edges* are falsely marked, i.e. if it is incorrect to mark edges as 
match just because the neighbouring atoms match.

Greets,

Andi

[Joelib-help] Re: [Joelib-devel] smarts

[Joerg K. W. <we...@in...>]

Hi JOElib members,

this is a cross-post from the developer mailing list, because i think 
some of you might be also interested in a SMARTS pattern discussion.
For previous mails, see developer mailing list.

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] SMARTS testing and examples added to CVS

[Joerg K. W. <we...@in...>]

Hi all,

1. SMARTS matching test class to check cross-dependencies for the atom 
typer or simple testing purpose. So, this is the first step to be able 
to formulate a classification problem for the atom type assignment 
process. So let me know if you are interested to discuss the details for 
this idea. I think this can be published, also.

2. I'm preparing a new updated CVS version and i've added the SMARTS 
testing class
joelib/src/joelib/smarts/test/SMARTSEvaluation.java

and the examples defined in
joelib/src/resource/smartsEvaluation/evaluation.txt

and all the corresponding molecule files
joelib/src/resource/smartsEvaluation/*.mol

to the CVS of JOELib.
Please remember that the CVS checkout process has changed:
http://sourceforge.net/cvs/?group_id=39708

The included default batch testing can be started with:
SMARTSEvaluationDefault.sh

The result is stored in:
evaluationResult.txt

and should look like the following lines, if no error occured. If 
mismatches occured they will be printed first !
======================================================

Checking 73 SMARTS patterns.
----------------------------------------------
Correct matches: 315
Mismatches:      0
----------------------------------------------
Parsed SMARTS patterns:

[#8][#1] hydroxy_group_explicit_h
LEAF(ELEM,8) vb: 0
OR(SINGLE,AROM) with grow: true src: 0 dst: 1
LEAF(ELEM,1) vb: 0


----------------------------------------------
[#8;H1] hydroxy_group
ANDLO(LEAF(ELEM,8),LEAF(HCOUNT,1)) vb: 0


----------------------------------------------
[*;!#6;r3] heteroatoms_in_3-ring
ANDLO(ANDLO(LEAF(CONST,1),NOT(LEAF(ELEM,6))),LEAF(SIZE,3)) vb: 0

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: Re: [Joelib-help] Darstellung / Fehler in SMARTS-Matching (?)]

[Andreas M. <ma...@in...>]

Hi all,

> in english please !!!

I'm sorry! Just forgot, mailing in different languages all day leads to errors.
Excuse me please, will pay attention in the future.

Greets
Andi

Re: [Joelib-help] Darstellung / Fehler in SMARTS-Matching (?)

[Joerg K. W. <we...@in...>]

Hi Andi,

in english please !!!

1. SMARTS matching
> http://www.informatik.uni-freiburg.de/~maunza/screenshot.jpeg 
> SMILES ist "OC1C(O)C(CO)OC1N2C=CC(=N)NC2=O"
> SMARTS ist "O=O=c:n:c:c:c:n-C-O-C-C-C-O"
You can at least formulate an aromatic tautomeric form, so i'm not sure, 
too. But it looks o.k. for me, other opinions from users ?
JOELib counts also electrons for SMARTS matching, see aromaticity typer 
and text definition aromatic.txt

2. Can i switch of implicite hydrogens in 2D rendering ?
No, not at the moment.
You can add a support request to the JOELib tracking system for that.
This requires an additional property in the RenderingModel, something like:
joelib.gui.render.Renderer2DModel.showImpliciteHydrogens=false
analogue to the other properties in joelib.properties.

Not a big deal, but i've less time at the moment and it seems not to get 
better the next weeks. So any developers are really welcome.

3. Show aromatic rings as ring.
Yes, switch
joelib.gui.render.Renderer2DModel.useKekuleStructure=true
to
joelib.gui.render.Renderer2DModel.useKekuleStructure=false

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Darstellung / Fehler in SMARTS-Matching (?)

[Andreas M. <ma...@in...>]

Hallo Joerg,

1) unter 

http://www.informatik.uni-freiburg.de/~maunza/screenshot.jpeg 

gibt es eine Darstellung eines Molekuels mit gematchtem SMARTS mithilfe von JOELib.

SMILES ist "OC1C(O)C(CO)OC1N2C=CC(=N)NC2=O"
SMARTS ist "O=O=c:n:c:c:c:n-C-O-C-C-C-O"

Nach Meinung meines Kollegen C. Helma duerften die mit Pfeilen markierten Kanten
*nicht* rot eingefaerbt werden. Trifft das zu (bin selber kein Chemiker)?

2) zwei weitere Fragen zur gewuenschten chemischen Darstellung:

Kann man die Darstellung der Kohlenstoffe ("C") und der mit
ihnen verbundenen Wasserstoffe ("H") ausschalten - sie sollten
sich implizit aus den Ecken ergeben?

Kann man aromatische Ringe nicht als alternierende Einfach- und
Doppelbindungen (Kekule-Schreibweise, derzeitige Darstellung)
sondern durch einen Kreis in ihrer Mitte darstellen?

Viele Gruesse,

Andi