joelib-help — JOELib-Help

[Joelib-help] Re: joelib.test.DescriptorSelection

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

Dear Dr. Ambrogio,

> first of all thanks for making available JOELib.
thanks ...
... i'm crossposting this message also to the JOELib-help mailing list.
You can join if you want ...
http://sourceforge.net/mail/?group_id=39708


> I successfully used the Convert application for adding descriptors to SD files. However I do not need all the descriptors. Then I tried to use DescriptorSelection to "select" the descripors I need.
That's exactly the same way i use it, especially when calculating 
autocorrelation or other more extended descriptors (not public).

> The problem is that it's not clear to me the syntax, in particular the format of the descriptors list and what the "delimiter" is.
Let's try to resolve that...

> I tried: 
> C:\FreeSoft\JOELib>java -cp %CLASSPATH% joelib.test.Convert -iSDF -oSDF +d c:\temp\sample.sdf c:\tem
> p\sample_wd.sdf
All fine !

> Then:
> C:\FreeSoft\JOELib>java.exe -cp %CLASSPATH% joelib.test.DescriptorSelection -iSDF c:\temp\sample_wd.
> sdf -oSDF c:\temp\sample_wd2.sdf c:\temp\Sample_desc.txt normal ;
> 13:34:44 [INFO ] joelib.data.JOEElementTable              - Using element table: joelib/data/plain/e
> lement.txt
> 13:34:44 [INFO ] joelib.io.IOTypeHolder                   - 12 input/output types loaded.
> 13:34:44 [INFO ] joelib.process.filter.FilterFactory      - 5 filter informations loaded.
> Exception in thread "main" java.lang.NullPointerException
>         at joelib.test.DescriptorSelection.parseCommandLine(DescriptorSelection.java:167)
>         at joelib.test.DescriptorSelection.main(DescriptorSelection.java:301)
> 
> where c:\temp\Sample_desc.txt is:
> 
> Number_of_bonds;LogP;Topological_radius
No, this should be simply:

Number_of_bonds
LogP
Topological_radius

so you can simply use the JOELib statistic-file and import it under 
Excel and extract the descriptor names you want !;-)

> Can you help me in getting DescriptorSelection work?
> Thanks in advance.
Was me a pleasure.

> By the way I've also have a couple of "bug reports":
> - In the Tutorial I've noticed that "bor", "chlor", "brom", "iod", "fluor" and "phosphor" are used instead of "boron", "chlorine", "bromine", "iodine", "fluorine" and "phosphorus".
> 
> - In the .bat files, there are extra semicolons at the end of the "set CLASSPSTH" instructions.
Thanks, i will fix it.

> Thanks again.
> 
> Ambrogio

Regards, Joerg

P.S.: BTW there exists also a descriptor normalization under
joelib.process.types.DescVarianceNorm if you plan to normalize your data 
with mean=0, sdtdev=1, which requires a little bit of programming. E.g. 
you can add this process simply to the selection process pipe in
joelib.test.DescriptorSelection

P.P.S.: All descriptors in
joelib\data\plain\desc2ignore.txt
defined in the joelib.properties file as:
joelib.process.types.DescVarianceNorm.descriptors2ignore=joelib/data/plain/desc2ignore.txt
will be ignored for normalization. This is extremely usefull if you have 
  an nominal classification problem or the sdf-file contains also some 
id's, ...

-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de

[Joelib-help] JOELib: 3D viewer + Ghemical MM

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

Hello,

> how can use 3D viewer in JOELib?
> regards
two ways:
1. call simple application
joelib-dir> sh viewer.sh yourMoleculeFile.extension

JOElib will load the given yourMoleculeFile and detects the file format 
from the given extension.
To get an overview over the implementation have a look at:
joelib.gui.molviewer.java3d.ViewerFrame

2. create your own application (embed 3D viewer in your JFrame)
the relevant class is:
joelib.gui.molviewer.java3d.graphics3D.JPanel3D
and
joelib.gui.molviewer.java3d.util.MolViewerEventAdapter
when you want to catch clicked atoms and bonds.

private JPanel3D molPanel; //a private global variable
private CentralLookup lookup; //a private global variable
...
lookup = CentralLookup.getLookup();
molPanel = new JPanel3D();
CentralDisplayAdapter c = new CentralDisplayAdapter(molPanel);
lookup.addObject("CentralDisplay", c);
molPanel.addMolViewerEventListener(new MolViewerEventAdapter());
// now you can add the molPanel to your frame, e.g.
// this.add(molPanel, BorderLayout.CENTER);
...
// how to change molecules and options ???
molPanel.setRenderStyle(RenderStyle.BALL_AND_STICK);
molPanel.setRenderStyle(RenderStyle.STICK);
molPanel.setRenderStyle(RenderStyle.WIRE);
// when changing atoms or delete bonds or something you should use
molPanel.clear();
molPanel.addMolecule(changedMolecule);
...
// for more examples have a look at
//joelib.gui.molviewer.java3d.ViewerFrame
// e.g. adding H's, delete H's, change atomPropertyColoring, ....

the event adapter class catches the events and prints them to the 
standard output.
If you want your own methods you can simply create your class
cp MolViewerEventAdapter MyMolViewerEventAdapter
with a replaced functionality in the methods:
atomPicked and bondPicked !
and use instead
molPanel.addMolViewerEventListener(new MyMolViewerEventAdapter());

> M.Karthikeyan

Regards, Joerg

P.S.: I've found a bug in stripSalts and more serious in deleteBond in 
the JOEMol class, because i've changed some time ago the return value of 
getContigousFragments(), so be aware that i've fixed it, but it's not 
checked in until now.

P.P.S.: I've activated the JNI interface to Ghemical to calculate 
Tripos5.2 MM and minimize molecule energy (rotatable bonds). 
Unfortunately this works only under Windows/Cygwin and Linux/IBM-SDK, 
because SUN's JDK causes some internal JNI exceptions (JDK BUG!!!).
Let's see if this will be stable enough to make it available with JOELib.

-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de

Re: [Joelib-help] Multiple molecules input to Convert

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

Re: [Joelib-help] Multiple molecules input to Convert

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

Re: [Joelib-help] Multiple molecules input to Convert

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

[Joelib-help] Multiple molecules input to Convert

[Peter Murray-R. <pm...@ca...>]

Greetings,

I'm interested in exploring JOELIB for querying medium numbers of CML files 
in a repository.  I have issued convert.bat with appropriate parameters for 
a file with several CML molecules in a <list> element. I include a small 
example at the bottom with just two.

D:\sourceforge\joelib\JOELib-20030519>convert  -icml test.cml -osdf junk1.sdf
C:\j2sdk1.4.1/bin/java.exe -cp 
.;C:\xml\saxon\saxon7.jar;C:\sourceforge\markup\l
ib\wh2fo.jar;C:\sourceforge\jumbo\lib\jakarta-regexp-1.2.jar;C:\Xindice\java\lib
\Xindice.jar;D:\sourceforge\joelib\JOELib-20030519\build;C:\j2sdk1.4.1\lib\tools
.jar;D:\sourceforge\joelib\JOELib-20030519\build;.;lib\ant.jar;;lib\crimson.jar;
;lib\jaxp.jar;;lib\junit-3.2.jar;;lib\log4j.jar;;lib\xerces.jar;;C:\j2sdk1.4.1\l
ib\tools.jar;D:\sourceforge\joelib\JOELib-20030519\build;.;lib\ant.jar;;lib\crim
son.jar;;lib\jaxp.jar;;lib\junit-3.2.jar;;lib\log4j.jar;;lib\xerces.jar; 
joelib.
test.Convert -icml test.cml -osdf junk1.sdf
23:03:40 [INFO ] joelib.data.JOEElementTable              - Using element 
table:
  joelib/data/plain/element.txt
23:03:40 [INFO ] joelib.io.IOTypeHolder                   - 12 input/output 
type
s loaded.
23:03:41 [INFO ] joelib.io.types.ChemicalMarkupLanguage   - Using Xerces 
XML par
ser.
23:03:41 [INFO ] joelib.io.types.ChemicalMarkupLanguage   - Deactivated 
validati
on
23:03:41 [INFO ] joelib.test.Convert                      - Start file 
conversio
n ...
23:03:42 [INFO ] joelib.data.JOEAromaticTyper             - Using 
aromaticity mo
del: joelib/data/plain/aromatic.txt
23:03:42 [INFO ] joelib.data.JOEAtomTyper                 - Using atom type 
mode
l: joelib/data/plain/atomtype.txt
23:03:42 [INFO ] joelib.test.Convert                      - ... 1 molecules 
succ
essful converted in 861 ms.
D:\sourceforge\joelib\JOELib-20030519>dir junk1.sdf
  Volume in drive D is data
  Volume Serial Number is 7C28-B533

  Directory of D:\sourceforge\joelib\JOELib-20030519

16/06/2003  23:03                4,194 junk1.sdf
                1 File(s)          4,194 bytes
                0 Dir(s)   1,918,160,896 bytes free

The junk1.sdf consists of the two molecules merged together rather than two 
separate MOL files in an SDF file.  The input was:

<list><molecule title="NSC 1"><atomArray><atom id="a1" elementType="O" 
x3="0.0021" y3="-0.0041" z3="0.0020"></atom>
<atom id="a2" elementType="O" x3="-0.0691" y3="5.2414" z3="0.0323"></atom>
<atom id="a3" elementType="C" x3="-0.0144" y3="1.2102" z3="0.0087"></atom>
<atom id="a4" elementType="C" x3="-1.3034" y3="1.9312" z3="0.031"></atom>
<atom id="a5" elementType="C" x3="1.2546" y3="1.9661" z3="6.0E-4"></atom>
<atom id="a6" elementType="C" x3="-1.3215" y3="3.2712" z3="0.0389"></atom>
<atom id="a7" elementType="C" x3="1.2365" y3="3.3061" z3="0.0085"></atom>
<atom id="a8" elementType="C" x3="-0.0526" y3="4.0271" z3="0.0252"></atom>
<atom id="a9" elementType="C" x3="-2.598" y3="1.16" z3="0.0445"></atom>
<atom id="a10" elementType="H" x3="2.1971" y3="1.4389" z3="-0.0112"></atom>
<atom id="a11" elementType="H" x3="-2.2641" y3="3.7984" z3="0.0511"></atom>
<atom id="a12" elementType="H" x3="2.1643" y3="3.8588" z3="-0.0015"></atom>
<atom id="a13" elementType="H" x3="-2.3843" y3="0.0912" z3="0.0355"></atom>
<atom id="a14" elementType="H" x3="-3.1608" y3="1.4105" z3="0.9438"></atom>
<atom id="a15" elementType="H" x3="-3.1853" y3="1.4206" z3="-0.836"></atom>
</atomArray>
<bondArray><bond atomRefs2="a1 a3" id="b1" order="2"></bond>
<bond atomRefs2="a2 a8" id="b2" order="2"></bond>
<bond atomRefs2="a3 a5" id="b3" order="1"></bond>
<bond atomRefs2="a3 a4" id="b4" order="1"></bond>
<bond atomRefs2="a4 a6" id="b5" order="2"></bond>
<bond atomRefs2="a4 a9" id="b6" order="1"></bond>
<bond atomRefs2="a5 a7" id="b7" order="2"></bond>
<bond atomRefs2="a5 a10" id="b8" order="1"></bond>
<bond atomRefs2="a6 a8" id="b9" order="1"></bond>
<bond atomRefs2="a6 a11" id="b10" order="1"></bond>
<bond atomRefs2="a7 a8" id="b11" order="1"></bond>
<bond atomRefs2="a7 a12" id="b12" order="1"></bond>
<bond atomRefs2="a9 a13" id="b13" order="1"></bond>
<bond atomRefs2="a9 a14" id="b14" order="1"></bond>
<bond atomRefs2="a9 a15" id="b15" order="1"></bond>
</bondArray>
</molecule>
<molecule title="NSC 2"><atomArray><atom id="a1" elementType="C" 
x3="-0.0165" y3="1.3666" z3="0.0096"></atom>
<atom id="a2" elementType="C" x3="8.2041" y3="6.9305" z3="2.5032"></atom>
<atom id="a3" elementType="C" x3="0.0021" y3="-0.0041" z3="0.0020"></atom>
<atom id="a4" elementType="C" x3="1.1892" y3="2.1056" z3="0.0020"></atom>
<atom id="a5" elementType="C" x3="2.5286" y3="4.0208" z3="-0.0013"></atom>
<atom id="a6" elementType="C" x3="4.7319" y3="5.7338" z3="2.3165"></atom>
<atom id="a7" elementType="C" x3="7.0224" y3="6.1538" z3="2.5156"></atom>
<atom id="a8" elementType="C" x3="9.4205" y3="6.3592" z3="2.7733"></atom>
<atom id="a9" elementType="C" x3="1.1946" y3="-0.7124" z3="-0.0132"></atom>
<atom id="a10" elementType="C" x3="2.384" y3="1.3506" z3="-0.0135"></atom>
<atom id="a11" elementType="C" x3="7.1801" y3="4.7823" z3="2.8185"></atom>
<atom id="a12" elementType="C" x3="9.5376" y3="5.0085" z3="3.0668"></atom>
<atom id="a13" elementType="C" x3="2.393" y3="-0.0213" z3="-0.021"></atom>
<atom id="a14" elementType="C" x3="8.4019" y3="4.2188" z3="3.0869"></atom>
<atom id="a15" elementType="N" x3="5.7567" y3="6.5587" z3="2.2741"></atom>
<atom id="a16" elementType="S" x3="5.5106" y3="4.1804" z3="2.7344"></atom>
<atom id="a17" elementType="S" x3="3.0264" y3="6.0746" z3="2.0342"></atom>
<atom id="a18" elementType="S" x3="2.9255" y3="5.7375" z3="0.0045"></atom>
<atom id="a19" elementType="S" x3="3.6321" y3="2.6151" z3="-0.0192"></atom>
<atom id="a20" elementType="N" x3="1.3439" y3="3.4473" z3="0.0074"></atom>
<atom id="a21" elementType="H" x3="-0.9624" y3="1.8878" z3="0.0169"></atom>
<atom id="a22" elementType="H" x3="8.1482" y3="7.9844" z3="2.274"></atom>
<atom id="a23" elementType="H" x3="-0.9329" y3="-0.5446" z3="0.0084"></atom>
<atom id="a24" elementType="H" x3="10.3079" y3="6.9745" z3="2.757"></atom>
<atom id="a25" elementType="H" x3="1.1876" y3="-1.7924" z3="-0.0186"></atom>
<atom id="a26" elementType="H" x3="10.5055" y3="4.5777" z3="3.2764"></atom>
<atom id="a27" elementType="H" x3="3.3299" y3="-0.5584" z3="-0.0325"></atom>
<atom id="a28" elementType="H" x3="8.4764" y3="3.1655" z3="3.3136"></atom>
</atomArray>
<bondArray><bond atomRefs2="a1 a3" id="b1" order="2"></bond>
<bond atomRefs2="a1 a4" id="b2" order="1"></bond>
<bond atomRefs2="a1 a21" id="b3" order="1"></bond>
<bond atomRefs2="a2 a8" id="b4" order="2"></bond>
<bond atomRefs2="a2 a7" id="b5" order="1"></bond>
<bond atomRefs2="a2 a22" id="b6" order="1"></bond>
<bond atomRefs2="a3 a9" id="b7" order="1"></bond>
<bond atomRefs2="a3 a23" id="b8" order="1"></bond>
<bond atomRefs2="a4 a10" id="b9" order="2"></bond>
<bond atomRefs2="a4 a20" id="b10" order="1"></bond>
<bond atomRefs2="a5 a18" id="b11" order="1"></bond>
<bond atomRefs2="a5 a20" id="b12" order="2"></bond>
<bond atomRefs2="a5 a19" id="b13" order="1"></bond>
<bond atomRefs2="a6 a17" id="b14" order="1"></bond>
<bond atomRefs2="a6 a15" id="b15" order="2"></bond>
<bond atomRefs2="a6 a16" id="b16" order="1"></bond>
<bond atomRefs2="a7 a15" id="b17" order="1"></bond>
<bond atomRefs2="a7 a11" id="b18" order="2"></bond>
<bond atomRefs2="a8 a12" id="b19" order="1"></bond>
<bond atomRefs2="a8 a24" id="b20" order="1"></bond>
<bond atomRefs2="a9 a13" id="b21" order="2"></bond>
<bond atomRefs2="a9 a25" id="b22" order="1"></bond>
<bond atomRefs2="a10 a19" id="b23" order="1"></bond>
<bond atomRefs2="a10 a13" id="b24" order="1"></bond>
<bond atomRefs2="a11 a16" id="b25" order="1"></bond>
<bond atomRefs2="a11 a14" id="b26" order="1"></bond>
<bond atomRefs2="a12 a14" id="b27" order="2"></bond>
<bond atomRefs2="a12 a26" id="b28" order="1"></bond>
<bond atomRefs2="a13 a27" id="b29" order="1"></bond>
<bond atomRefs2="a14 a28" id="b30" order="1"></bond>
<bond atomRefs2="a17 a18" id="b31" order="1"></bond>
</bondArray>
</molecule>
</list>

Hope this makes sense...

P.

[Joelib-help] Simple Web Start application available

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

Hi all,

now there is a simple (!!!) Web Start application for JOELib available.
http://www-ra.informatik.uni-tuebingen.de/software/joelib/download.html

So, please don't complain the basic functionalities of the GUI version, 
the extended GUI version will be available in a few months !;-)

Regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de

Re: [Joelib-help] molecular volume?

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

Hello Richard,

> Great package, first of all!  I finally got started working with it.  As 
> for my question, is there a class that contains a method to calculate 
> molecular volume?  I noticed atom VDW volume, but was interested in the 
> whole volume. thank you for your consideration.
thank's, it contains a lot of work and is still in development progress.

No, but it contains MolarRefractivity (MR) by using a GroupContribution 
algorithm developed by Stephen Jelfs.
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/descriptors/descriptors.html

for more informations see e.g.:
http://www.ualberta.ca/~csps/JPPS5(3)/R.Carrasco/molecular.htm
"...the molar refractivity represents the real volume of the molecules. 
Molar refractivity..."

> Richard Kho
Regards, Joerg


-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de

[Joelib-help] molecular volume?

[Richard K. <rk...@Tr...>]

Dear JOELIB users,

=20

Great package, first of all!  I finally got started working with it.  As
for my question, is there a class that contains a method to calculate
molecular volume?  I noticed atom VDW volume, but was interested in the
whole volume. thank you for your consideration.

=20

Richard Kho

=20

Re: [Joelib-help] Matlab interface

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

Hello,

using JDK1.4 under Matlab is a little bit tricky:
By the way i'm very interested at the work of other matlab users,
something we should discuss more in detail (if interested). Was ist sb für
eine Abkürzung für das MPI, gibt es evtl. eine Schnittstelle für eine
wissenschaftliche Zusammenarbeit ?

INSTALLATION:
1. use JVM 1.4 or higher version
1.1. Set the system environment variable MATLAB_JAVA, e.g. using Cygwin
under Windows
setenv MATLAB_JAVA 1.4.1_01
or use the Menu (under W2K)
Properties/System Properties/extended/EnvironmentVariables/New

1.2. Then copy your java jre directory to the matlab directory
cp -R yourJavaDirectory/jre yourMatlabPath/sys/java/jre/win32/jre1.4.1_01

When using another java version use
setenv MATLAB_JAVA 1.4.2
cp -R yourJavaDirectory/jre yourMatlabPath/sys/java/jre/win32/jre1.4.2

and so on ...

2. using external java libraries
2.1. For using joelib under Matlab you must add
joelib.jar AND log4j.jar to
yourMatlabPath/toolbox/local/classpath.txt

2.2. and copy the joelib.jar file and the log4.jar file to
yourMatlabPath/java/jarext

E.g.:
$matlabroot/java/jarext/joelib.jar
$matlabroot/java/jarext/log4j.jar

Log4J can be downloaded from the Jakarta log4j web site or
you can simply use the included library in joelib/lib/log4j.jar

---------------------------------------------------------------
EXAMPLES:
1. Visualize molecules
cd c:/workingAt/joelib/matlab/
showmolecules('multiple.mol', 'SDF');

2. Load all native descriptors from a molecule
cd c:/workingAt/joelib/matlab/
descriptors=loaddescriptors('test_moe_desc.mol', 'SDF');

Regards, Joerg

On Wed, 9 Apr 2003, Christian Merkwirth wrote:

> Dear JOELib Users and Developers,
> 
> I have two problems using JOELIB with Matlab :
> 
> - Only one of the Matlab examples work, the other one gives an error:
> 
> >> loaddescriptors('test_moe_desc.mol', 'SDF');
> ??? Java exception occurred:
> java.lang.NoClassDefFoundError: java/lang/CharSequence
>       at
> joelib.molecule.GenericDataHolder.getData(GenericDataHolder.java:449)
>       at joelib.molecule.JOEMol.getData(JOEMol.java:3252)
>       at
> joelib.util.iterator.NativeValueIterator.hasNext(NativeValueIterator.java:136)
> .
> 
> Error in ==> C:\Documents and Settings\Administrator\My
> Documents\Projekte\Matlab\Toolboxes\joelibToolbox\loaddescriptors.m
> On line 42  ==> hasNext=native.hasNext;
> 
> >> version
> 
> ans =
> 
> 6.5.0.180913a (R13)
> 
> >> version -java
> 
> ans =
> 
> Java 1.3.1_01 with Sun Microsystems Inc. Java HotSpot(TM) Client VM
>     (mixed mode)
> 
> I'm using Matlab 6.5 under Windows 2000 on a Thinkpad.
> 
> 
> - I would like to write a simple Matlab script that reads all the molecules
> from an SDF file, add hydrogens where necessary and corrects aromatic
> bonds.
>  The corrected structures I would like to convert to Matlab data types,
> just a list of element types for each atom and a connectivity matrix. Since
> I'm absolute
> beginner in Java, I don't know where to start here. Could you give me some
> hints ?
> 
> 
> Best regards,
> Christian Merkwirth
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------
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> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
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> 

Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de

[Joelib-help] Matlab interface

[Christian M. <cm...@mp...>]

Dear JOELib Users and Developers,

I have two problems using JOELIB with Matlab :

- Only one of the Matlab examples work, the other one gives an error:

>> loaddescriptors('test_moe_desc.mol', 'SDF');
??? Java exception occurred:
java.lang.NoClassDefFoundError: java/lang/CharSequence
      at
joelib.molecule.GenericDataHolder.getData(GenericDataHolder.java:449)
      at joelib.molecule.JOEMol.getData(JOEMol.java:3252)
      at
joelib.util.iterator.NativeValueIterator.hasNext(NativeValueIterator.java:136)
.

Error in ==> C:\Documents and Settings\Administrator\My
Documents\Projekte\Matlab\Toolboxes\joelibToolbox\loaddescriptors.m
On line 42  ==> hasNext=native.hasNext;

>> version

ans =

6.5.0.180913a (R13)

>> version -java

ans =

Java 1.3.1_01 with Sun Microsystems Inc. Java HotSpot(TM) Client VM
    (mixed mode)

I'm using Matlab 6.5 under Windows 2000 on a Thinkpad.


- I would like to write a simple Matlab script that reads all the molecules
from an SDF file, add hydrogens where necessary and corrects aromatic
bonds.
 The corrected structures I would like to convert to Matlab data types,
just a list of element types for each atom and a connectivity matrix. Since
I'm absolute
beginner in Java, I don't know where to start here. Could you give me some
hints ?


Best regards,
Christian Merkwirth

Re: [Joelib-help] installation help?

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

Hello Richard,

> I feel dumb for asking, but help would be much appreciated!
I feel dumb for saying, this was my fault.
I've had a bug in the ant script to build the source code distribution.

1. I've updated the distribution files !
Use the source code distribution to compile JOELib on your own (i 
recommend this before using the binary release !!! It's more developer 
like !;-)

2. use CVS release, this should be always up to date (latest bug fixes)
cvs -d:pserver:ano...@cv...:/cvsroot/joelib co joelib

By the way, if you are behind a firewall, the CVS access is a little bit 
tricky !;-)

Regards, Joerg

> 
>  
> 
> I am trying to get started with JOELib and am having difficulty 
> installing on Win2000. I have j2sdk1.4.1_01 and apache-ant-1.5.2 running 
> fine. When I go to the JOELib\ant\ directory and run “ant compile”, I get
> 
>  
> 
> BUILD FAILED
> 
> file:D:/JOELib-20030134/ant/build.xml:392: srcdir 
> "D:\JOELib-20030131\src" does not exist!
> 
>  
> 
> I then tried downloading the source packages and tried the same 
> procedure and got a little further, but had the following problem:
> 
>  
> 
> BUILD FAILED
> 
> file:D:/JOELib-20030304/ant/build.xml:454: 
> D:\JOELib-20030304\src\joelib\io\types\cml\data not found.
> 
>  
> 
> I’ve tried several of the binary and source packages and get the same 
> errors. Am I missing something here?
> 
>  
> 
> Thank you.
> 
>  
> 
> richard
> 
>  
> 
>  
> 


-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de

[Joelib-help] installation help?

[Richard K. <rk...@Tr...>]

Dear JOELib users,

=20

I feel dumb for asking, but help would be much appreciated!

=20

I am trying to get started with JOELib and am having difficulty
installing on Win2000. I have j2sdk1.4.1_01 and apache-ant-1.5.2 running
fine. When I go to the JOELib\ant\ directory and run "ant compile", I
get=20

=20

BUILD FAILED

file:D:/JOELib-20030134/ant/build.xml:392: srcdir
"D:\JOELib-20030131\src" does not exist!

=20

I then tried downloading the source packages and tried the same
procedure and got a little further, but had the following problem:

=20

BUILD FAILED

file:D:/JOELib-20030304/ant/build.xml:454:
D:\JOELib-20030304\src\joelib\io\types\cml\data not found.

=20

I've tried several of the binary and source packages and get the same
errors. Am I missing something here?

=20

Thank you.

=20

richard

=20

=20

Re: [Joelib-help] Simple ChemTransformation Question

[<we...@in...>]

Hello,

i have answered in the developer thread, because this is implicitely
also library design question.

Regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de

[Joelib-help] Simple ChemTransformation Question

[Daniel C. M. <Dan...@uc...>]

Hello, I'm currently an OpenBabel user, but am interested in
"converting"

I'm mostly interested in SMILES/SMARTS transformations capabilities.

In particular, Can I represent the following transformation:

CC=O => CC(O)=O

I tried this (in OpenBabel)

[C:1]=[O:2]>>[C:1](O)=[O:2]

But it didn't work.

I'd actually hoped it could be as simple as C=O>>C(O)=O, but this was
not to be, so I'm looking around for other options.

Can JOElib do this sort of thing?

Of course, t is quite likely this is due to my lack of SMARTS knowledge
rather than the software ;)

-- 
Daniel Charles McShan <Dan...@uc...>
University of Colorado Health Science Center