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From: phanirao p. <pha...@ya...> - 2007-01-02 10:50:49
|
Hi, I am Phani. Thanks for your previous response. Now I want to execute one programme with TotalHAtomCount class. So what should I do? If you have some examles of that then please forward to me. I am waiting eagrly for your response. Thanks & Regards Phani Kumar Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php |
From: Egon W. <e.w...@sc...> - 2006-12-27 15:29:35
|
Dear CDK community members, Please find on SourceForge, the third issue of volume three of CDK News, aka CDK News 3.3, with these articles: M. Rojas Cherto, Discovering Partial Atomic Charges in Pi-Systems R. Guha, Updates to the R-CDK Interface R. Guha, Implementation of the Kier & Hall chi Descriptors C. Steinbeck, Clashes and Conflicts This issue (and older issues) can be downloaded from: http://sourceforge.net/project/showfiles.php?group_id=20024&package_id=124796 while individual articles can be downloaded from: http://www.cdknews.org/ Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: <nik...@no...> - 2006-12-27 11:37:54
|
I will be out of the office starting 22.12.2006 and will not return until 02.01.2007. |
From: Egon W. <e.w...@sc...> - 2006-12-27 10:45:24
|
Hi Jani, (please continue on the cdk-user mailing list) On Wednesday 27 December 2006 11:27, jani basha wrote: > I am Jani. I am concentrating on CDK. I installed > jdk1.5 update version & I am working on that. I want > to execute below program, please give suggestions to > me to do that. > > For that purpose any paths I have to set. If so > please send me those detailes. See below. > package org.openscience.cdk.applications.swing.editor; <snip> > public class AtomContainerEditor extends > ChemObjectEditor { <snip> > } You cannot execute this code directly, as it is not a 'Java application', i.e. it does not have a main() method. Instead, this class is used within JChemPaint, so that would be the way to run it. Look up how to compile and run JChemPaint; Compiling can be done with: $ ant -f build-jchempaint.xml and then you can 'run' the created jchempaint.jar with something like: $ java -jar dist/jar/jchempaint.jar though you need to change it to the correct name of the jar. Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Egon W. <e.w...@sc...> - 2006-12-26 10:19:16
|
On Tuesday 26 December 2006 11:07, phanirao palivela wrote: > Tx for giving previous response.....based on that i successfully > compiled a cdk related program named EventCMLDemo.java > the output is as follows....... > > F:\cdk-source\build>java EventCMLDemo cu.cml > Processing cu.cml.... .succeeded! Normally, this should have stated something like this too: " 50 atoms processed" That is, if you have many molecules, or one rather large one; specifically, this is outputed after each one molecule if 50 or more atoms new atoms are found... Each processed molecule is indicated by a '.'... therefore, I can see that your cu.cml has one molecule. > Actually we dont know wt is the output of this program....but we > successfully executed the program...i wnt to know the exact output of this > program.... and its use... Check the source code: 1. the frameRead() method in the inner IReaderListener class does the atom counting and printing the '.' for each molecule 2. the process(String ifilename) takes each command line option as file name and tries to read it with the CMLMolReadListener. This CMLMolReadListener is the CML equivalent of the IteratingMDLReader, and will pass around IAtomContainer's one by one, much like the IteratingMDLReader. This allows you to process CML files with millions of molecules, without necessarily running into OutOfMemory problems. I hope this helps, Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: phanirao p. <pha...@ya...> - 2006-12-26 10:08:04
|
Hi.... Tx for giving previous response.....based on that i successfully compiled a cdk related program named EventCMLDemo.java the output is as follows....... F:\cdk-source\build>java EventCMLDemo cu.cml Processing cu.cml.... .succeeded! Actually we dont know wt is the output of this program....but we successfully executed the program...i wnt to know the exact output of this program.... and its use... would u plz suggest me regarding this problem ASAPL Thanks Phani Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php |
From: Egon W. <ewi...@un...> - 2006-12-21 11:58:24
|
On Thursday 21 December 2006 10:22, phanirao palivela wrote: > Thx alot for gr8 response ..... > i downloaded java 1.5 and i excuted...... > still i am getting the same errors... > i wnt to know is there is any class path required for cdk...... > plz suggest me.... Indeed, you need to set the JAVA_HOME environment variable. How to do that, depends on the operating system you are using, but googling will help here. You can verify by running 'ant info' that Ant is picking up the correct installed JDK. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ewi...@un...> - 2006-12-20 09:19:59
|
Hi Phani, CML requires Java 1.5, and the CDK build system should detect wether it is available or that Java 1.4 is installed. Depending on that, it should compile the CML depending stuff. Clearly, this build system is broken, as it tries to compile Java 1.5 depending code, with your Java 1.4 compiler. A simple work around is to install the Java JDK 1.5 or 1.6. Please consider that. Regards, Egon On Wednesday 20 December 2006 08:38, phanirao palivela wrote: > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 16 Dec 2006 11:20:12 +0100 > From: Egon Willighagen > Subject: Re: [Cdk-user] New to Cdk > To: cdk...@li... > Message-ID: <200...@un...> > Content-Type: text/plain; charset="iso-8859-15" > > On Friday 15 December 2006 11:35, phanirao palivela wrote: > > this is phani... iam student of Biochemistry and i wnt to work this > > cdk .. and also i have the knowledge of java..could u suggest me in what > > way i am able to work with this cdk.. > > Hi Phani, > > the first step would be to download the latest released distribution at > [1], install ant from [2] and compile it. Then browse the documentation > [3], and possibly look at the JUnit test in the org.openscience.cdk.test.* > packages which contains *a lot of* example code. If you are looking for > specific code, then our keyword list is rather informative [4]. > > Just email of you have more questions, > > Looking forward to hearing from you, > > Egon Willighagen > > 1.http://sourceforge.net/project/showfiles.php?group_id=20024 > 2.http://ant.apache.org/ > 3.http://cdk.sourceforge.net/api/ > 4.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/keywords >.html > > > ........................................................................... >........................................................... > ........................................................................... >....................................................... Hi.. > Thanx for sending those links...i downloaded everything from that > links and i downloaded (cdk-source-20060718) ....everything is working > perfectly when iam excuted by using ant..... but iam getting following > errors...... > i dont know what is the problem ... > could any one suggest me for redusing those problems,,,, > follwing are the erros... > > [javadoc] Loading source files for package > org.openscience.cdk.test.config.ato mtypes... > [javadoc] Loading source files for package > org.openscience.cdk.test.config.iso topes... > [javadoc] Loading source files for package > org.openscience.cdk.test.controller ... > [javadoc] Loading source files for package > org.openscience.cdk.test.database.. . > [javadoc] Loading source files for package > org.openscience.cdk.test.debug... [javadoc] Loading source files for > package org.openscience.cdk.test.dict... [javadoc] Loading source files for > package org.openscience.cdk.test.event... [javadoc] Loading source files > for package org.openscience.cdk.test.exception. .. > [javadoc] Loading source files for package > org.openscience.cdk.test.fingerprin t... > [javadoc] Loading source files for package > org.openscience.cdk.test.geometry.. . > [javadoc] Loading source files for package > org.openscience.cdk.test.geometry.a lignment... > [javadoc] Loading source files for package > org.openscience.cdk.test.graph... [javadoc] Loading source files for > package org.openscience.cdk.test.graph.inva riant... > [javadoc] Loading source files for package > org.openscience.cdk.test.graph.rebo nd... > [javadoc] Loading source files for package > org.openscience.cdk.test.gui.smiles ... > [javadoc] Loading source files for package > org.openscience.cdk.test.index... [javadoc] Loading source files for > package org.openscience.cdk.test.internet.. . > [javadoc] Loading source files for package org.openscience.cdk.test.io... > [javadoc] Loading source files for package > org.openscience.cdk.test.io.cml... [javadoc] Loading source files for > package org.openscience.cdk.test.io.iterato r... > [javadoc] Loading source files for package > org.openscience.cdk.test.isomorphis m... > [javadoc] Loading source files for package > org.openscience.cdk.test.isomorphis m.matchers... > [javadoc] Loading source files for package > org.openscience.cdk.test.iupac... [javadoc] Loading source files for > package org.openscience.cdk.test.layout... [javadoc] Loading source files > for package org.openscience.cdk.test.libio.joel ib... > [javadoc] Loading source files for package > org.openscience.cdk.test.libio.open babel... > [javadoc] Loading source files for package > org.openscience.cdk.test.libio.weka ... > [javadoc] Loading source files for package > org.openscience.cdk.test.limitation s... > [javadoc] Loading source files for package > org.openscience.cdk.test.limitation s.tools... > [javadoc] Loading source files for package > org.openscience.cdk.test.math... [javadoc] Loading source files for package > org.openscience.cdk.test.math.qm... [javadoc] Loading source files for > package org.openscience.cdk.test.modeling.b uilder3d... > [javadoc] Loading source files for package > org.openscience.cdk.test.modeling.f orcefield... > [javadoc] Loading source files for package > org.openscience.cdk.test.nonotify.. . > [javadoc] Loading source files for package > org.openscience.cdk.test.qsar... [javadoc] Loading source files for package > org.openscience.cdk.test.qsar.descr iptors.atomic... > [javadoc] Loading source files for package > org.openscience.cdk.test.qsar.descr iptors.bond... > [javadoc] Loading source files for package > org.openscience.cdk.test.qsar.descr iptors.molecular... > [javadoc] Loading source files for package > org.openscience.cdk.test.qsar.model .R... > [javadoc] Loading source files for package > org.openscience.cdk.test.qsar.model .R2... > [javadoc] Loading source files for package > org.openscience.cdk.test.qsar.model .weka... > [javadoc] Loading source files for package > org.openscience.cdk.test.reaction.t ype... > [javadoc] Loading source files for package > org.openscience.cdk.test.renderer.. . > [javadoc] Loading source files for package > org.openscience.cdk.test.ringsearch ... > [javadoc] Loading source files for package > org.openscience.cdk.test.ringsearch .cyclebasis... > [javadoc] Loading source files for package > org.openscience.cdk.test.similarity ... > [javadoc] Loading source files for package > org.openscience.cdk.test.smiles... [javadoc] Loading source files for > package org.openscience.cdk.test.smiles.sma rts... > [javadoc] Loading source files for package > org.openscience.cdk.test.structgen. .. > [javadoc] Loading source files for package > org.openscience.cdk.test.structgen. deterministic... > [javadoc] Loading source files for package > org.openscience.cdk.test.templates. .. > [javadoc] Loading source files for package > org.openscience.cdk.test.tools... [javadoc] Loading source files for > package org.openscience.cdk.test.tools.mani pulator... > [javadoc] Loading source files for package > org.openscience.cdk.test.validate.. . > [javadoc] Loading source files for package org.openscience.cdk.tools... > [javadoc] Loading source files for package > org.openscience.cdk.tools.features. .. > [javadoc] Loading source files for package > org.openscience.cdk.tools.manipulat or... > [javadoc] Loading source files for package > org.openscience.cdk.validate... [javadoc] Constructing Javadoc > information... > [javadoc] > E:\cdk-source-20060718\src\org\openscience\cdk\applications\Descript > orCalculator.java:65: cannot access org.xmlcml.cml.element.CMLMolecule > [javadoc] bad class file: > E:\cdk-source-20060718\jar\jumbo52.jar(org/xmlcml/cm > l/element/CMLMolecule.class) > [javadoc] class file has wrong version 49.0, should be 48.0 > [javadoc] Please remove or make sure it appears in the correct > subdirectory of the classpath. > [javadoc] import org.xmlcml.cml.element.CMLMolecule; > [javadoc] ^ > [javadoc] 1 error > [javadoc] Generating Javadoc > [javadoc] Javadoc execution > [javadoc] javadoc: Cannot find doclet class > net.sf.cdk.tools.MakeCDKSetFilesDo clet > [javadoc] 1 error > checkDocletResults: > failIfNoDocletResults: > compile-init: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > checkPlatforms: > check: > dist.init: > compile-needed-test: > compile-module: > [echo] Compiling classes for CDK's libio-cml module. > [echo] Datafiles defined: true > [echo] Extra files defined: ${module.extrafiles.present} > [echo] CDK dependencies defined: true > [echo] Library dependencies defined: true > [echo] Developer Library dependencies defined: > ${module.devellibdepends.pre sent} > [delete] Deleting directory E:\cdk-source-20060718\build > [mkdir] Created dir: E:\cdk-source-20060718\build > [mkdir] Created dir: E:\cdk-source-20060718\build\src > [copy] Copying 1 file to E:\cdk-source-20060718\build\src > [javac] Compiling 1 source file to E:\cdk-source-20060718\build > [javac] > E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja va:43: > cannot resolve symbol > [javac] symbol : class Convertor > [javac] location: package cml > [javac] import org.openscience.cdk.libio.cml.Convertor; > [javac] ^ > [javac] > E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja > va:121: cannot resolve symbol > [javac] symbol : variable Convertor > [javac] location: class org.openscience.cdk.io.RssWriter > [javac] > rdfElement.addNamespaceDeclaration("cml",Convertor.N S_CML); > [javac] ^ > [javac] > E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja > va:190: cannot resolve symbol > [javac] symbol : class Convertor > [javac] location: class org.openscience.cdk.io.RssWriter > [javac] Convertor convertor=new Convertor(true,null); > [javac] ^ > [javac] > E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja > va:190: cannot resolve symbol > [javac] symbol : class Convertor > [javac] location: class org.openscience.cdk.io.RssWriter > [javac] Convertor convertor=new Convertor(true,null); > [javac] ^ > [javac] 4 errors > BUILD FAILED > E:\cdk-source-20060718\build.xml:570: The following error occurred while > executi ng this line: > E:\cdk-source-20060718\build.xml:446: Compile failed; see the compiler > error out put for details. > Total time: 1 minute 15 seconds > > > > Thanks Phani > > Send free SMS to your Friends on Mobile from your Yahoo! Messenger. > Download Now! http://messenger.yahoo.com/download.php -- http://chem-bla-ics.blogspot.com/ |
From: phanirao p. <pha...@ya...> - 2006-12-20 07:39:11
|
---------------------------------------------------------------------- Message: 1 Date: Sat, 16 Dec 2006 11:20:12 +0100 From: Egon Willighagen Subject: Re: [Cdk-user] New to Cdk To: cdk...@li... Message-ID: <200...@un...> Content-Type: text/plain; charset="iso-8859-15" On Friday 15 December 2006 11:35, phanirao palivela wrote: > this is phani... iam student of Biochemistry and i wnt to work this > cdk .. and also i have the knowledge of java..could u suggest me in what > way i am able to work with this cdk.. Hi Phani, the first step would be to download the latest released distribution at [1], install ant from [2] and compile it. Then browse the documentation [3], and possibly look at the JUnit test in the org.openscience.cdk.test.* packages which contains *a lot of* example code. If you are looking for specific code, then our keyword list is rather informative [4]. Just email of you have more questions, Looking forward to hearing from you, Egon Willighagen 1.http://sourceforge.net/project/showfiles.php?group_id=20024 2.http://ant.apache.org/ 3.http://cdk.sourceforge.net/api/ 4.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/keywords.html ...................................................................................................................................... .................................................................................................................................. Hi.. Thanx for sending those links...i downloaded everything from that links and i downloaded (cdk-source-20060718) ....everything is working perfectly when iam excuted by using ant..... but iam getting following errors...... i dont know what is the problem ... could any one suggest me for redusing those problems,,,, follwing are the erros... [javadoc] Loading source files for package org.openscience.cdk.test.config.ato mtypes... [javadoc] Loading source files for package org.openscience.cdk.test.config.iso topes... [javadoc] Loading source files for package org.openscience.cdk.test.controller ... [javadoc] Loading source files for package org.openscience.cdk.test.database.. . [javadoc] Loading source files for package org.openscience.cdk.test.debug... [javadoc] Loading source files for package org.openscience.cdk.test.dict... [javadoc] Loading source files for package org.openscience.cdk.test.event... [javadoc] Loading source files for package org.openscience.cdk.test.exception. .. [javadoc] Loading source files for package org.openscience.cdk.test.fingerprin t... [javadoc] Loading source files for package org.openscience.cdk.test.geometry.. . [javadoc] Loading source files for package org.openscience.cdk.test.geometry.a lignment... [javadoc] Loading source files for package org.openscience.cdk.test.graph... [javadoc] Loading source files for package org.openscience.cdk.test.graph.inva riant... [javadoc] Loading source files for package org.openscience.cdk.test.graph.rebo nd... [javadoc] Loading source files for package org.openscience.cdk.test.gui.smiles ... [javadoc] Loading source files for package org.openscience.cdk.test.index... [javadoc] Loading source files for package org.openscience.cdk.test.internet.. . [javadoc] Loading source files for package org.openscience.cdk.test.io... [javadoc] Loading source files for package org.openscience.cdk.test.io.cml... [javadoc] Loading source files for package org.openscience.cdk.test.io.iterato r... [javadoc] Loading source files for package org.openscience.cdk.test.isomorphis m... [javadoc] Loading source files for package org.openscience.cdk.test.isomorphis m.matchers... [javadoc] Loading source files for package org.openscience.cdk.test.iupac... [javadoc] Loading source files for package org.openscience.cdk.test.layout... [javadoc] Loading source files for package org.openscience.cdk.test.libio.joel ib... [javadoc] Loading source files for package org.openscience.cdk.test.libio.open babel... [javadoc] Loading source files for package org.openscience.cdk.test.libio.weka ... [javadoc] Loading source files for package org.openscience.cdk.test.limitation s... [javadoc] Loading source files for package org.openscience.cdk.test.limitation s.tools... [javadoc] Loading source files for package org.openscience.cdk.test.math... [javadoc] Loading source files for package org.openscience.cdk.test.math.qm... [javadoc] Loading source files for package org.openscience.cdk.test.modeling.b uilder3d... [javadoc] Loading source files for package org.openscience.cdk.test.modeling.f orcefield... [javadoc] Loading source files for package org.openscience.cdk.test.nonotify.. . [javadoc] Loading source files for package org.openscience.cdk.test.qsar... [javadoc] Loading source files for package org.openscience.cdk.test.qsar.descr iptors.atomic... [javadoc] Loading source files for package org.openscience.cdk.test.qsar.descr iptors.bond... [javadoc] Loading source files for package org.openscience.cdk.test.qsar.descr iptors.molecular... [javadoc] Loading source files for package org.openscience.cdk.test.qsar.model .R... [javadoc] Loading source files for package org.openscience.cdk.test.qsar.model .R2... [javadoc] Loading source files for package org.openscience.cdk.test.qsar.model .weka... [javadoc] Loading source files for package org.openscience.cdk.test.reaction.t ype... [javadoc] Loading source files for package org.openscience.cdk.test.renderer.. . [javadoc] Loading source files for package org.openscience.cdk.test.ringsearch ... [javadoc] Loading source files for package org.openscience.cdk.test.ringsearch .cyclebasis... [javadoc] Loading source files for package org.openscience.cdk.test.similarity ... [javadoc] Loading source files for package org.openscience.cdk.test.smiles... [javadoc] Loading source files for package org.openscience.cdk.test.smiles.sma rts... [javadoc] Loading source files for package org.openscience.cdk.test.structgen. .. [javadoc] Loading source files for package org.openscience.cdk.test.structgen. deterministic... [javadoc] Loading source files for package org.openscience.cdk.test.templates. .. [javadoc] Loading source files for package org.openscience.cdk.test.tools... [javadoc] Loading source files for package org.openscience.cdk.test.tools.mani pulator... [javadoc] Loading source files for package org.openscience.cdk.test.validate.. . [javadoc] Loading source files for package org.openscience.cdk.tools... [javadoc] Loading source files for package org.openscience.cdk.tools.features. .. [javadoc] Loading source files for package org.openscience.cdk.tools.manipulat or... [javadoc] Loading source files for package org.openscience.cdk.validate... [javadoc] Constructing Javadoc information... [javadoc] E:\cdk-source-20060718\src\org\openscience\cdk\applications\Descript orCalculator.java:65: cannot access org.xmlcml.cml.element.CMLMolecule [javadoc] bad class file: E:\cdk-source-20060718\jar\jumbo52.jar(org/xmlcml/cm l/element/CMLMolecule.class) [javadoc] class file has wrong version 49.0, should be 48.0 [javadoc] Please remove or make sure it appears in the correct subdirectory of the classpath. [javadoc] import org.xmlcml.cml.element.CMLMolecule; [javadoc] ^ [javadoc] 1 error [javadoc] Generating Javadoc [javadoc] Javadoc execution [javadoc] javadoc: Cannot find doclet class net.sf.cdk.tools.MakeCDKSetFilesDo clet [javadoc] 1 error checkDocletResults: failIfNoDocletResults: compile-init: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's libio-cml module. [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.pre sent} [delete] Deleting directory E:\cdk-source-20060718\build [mkdir] Created dir: E:\cdk-source-20060718\build [mkdir] Created dir: E:\cdk-source-20060718\build\src [copy] Copying 1 file to E:\cdk-source-20060718\build\src [javac] Compiling 1 source file to E:\cdk-source-20060718\build [javac] E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja va:43: cannot resolve symbol [javac] symbol : class Convertor [javac] location: package cml [javac] import org.openscience.cdk.libio.cml.Convertor; [javac] ^ [javac] E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja va:121: cannot resolve symbol [javac] symbol : variable Convertor [javac] location: class org.openscience.cdk.io.RssWriter [javac] rdfElement.addNamespaceDeclaration("cml",Convertor.N S_CML); [javac] ^ [javac] E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja va:190: cannot resolve symbol [javac] symbol : class Convertor [javac] location: class org.openscience.cdk.io.RssWriter [javac] Convertor convertor=new Convertor(true,null); [javac] ^ [javac] E:\cdk-source-20060718\build\src\org\openscience\cdk\io\RssWriter.ja va:190: cannot resolve symbol [javac] symbol : class Convertor [javac] location: class org.openscience.cdk.io.RssWriter [javac] Convertor convertor=new Convertor(true,null); [javac] ^ [javac] 4 errors BUILD FAILED E:\cdk-source-20060718\build.xml:570: The following error occurred while executi ng this line: E:\cdk-source-20060718\build.xml:446: Compile failed; see the compiler error out put for details. Total time: 1 minute 15 seconds Thanks Phani Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php |
From: Egon W. <ewi...@un...> - 2006-12-18 11:38:00
|
On Monday 18 December 2006 12:15, Andreas Sch=FCller wrote: > sounds like an interesting option. Is there a list of unstable modules > or a list of known bugs? Yes, most modules are actually stable, or *very* close to that. Others need many= =20 more JUnit tests, but are likely working quite well. Consider that, overall, only <1.5% of the JUnit tests fails. An overview can be found at Nightly [1], where failing JUnit tests are=20 reported, and other quality assurance testing, like tests for unused code,= =20 JavaDoc quality metrics, and PMD tests. All open bugs can be found at [2]. Typical areas of concern right now, is the unknown state of atom typing and= =20 the SMILES parsing (of strings with lower case element symbols and missing explicit bond orders). Most of the rest is really related to yet missing=20 functionality. We have passed the 2750 JUnit tests, of various complexity. There is no specific list of functionality that is super stable yet, but th= is=20 at least includes: =2D the functionality of the data storage classes =2D isomorphism checking, substructure matching, and MCSS =2D finger printing (see multiple usages in other projects) =2D many QSAR descriptors (see QA articles in CDK News) Things that work quite well, but not perfect, include: =2D CML, MDL mol reading =2D structure diagram generation =2D the editor Things that work generally well, unless for certain specific situations: =2D SMILES parsing (see above) =2D 3D structure generation (limited ring system template database) This is what I can think of right now. About other important functionality = I=20 am unaware of the quality, as I do not use it myself. Would be good to make= a=20 quality list in the wiki... Egon 1.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ 2.http://sourceforge.net/tracker/?atid=3D120024&group_id=3D20024&func=3Dbro= wse =2D-=20 CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ewi...@un...> - 2006-12-16 10:14:01
|
On Friday 15 December 2006 11:35, phanirao palivela wrote: > this is phani... iam student of Biochemistry and i wnt to work this > cdk .. and also i have the knowledge of java..could u suggest me in what > way i am able to work with this cdk.. Hi Phani, the first step would be to download the latest released distribution at [1], install ant from [2] and compile it. Then browse the documentation [3], and possibly look at the JUnit test in the org.openscience.cdk.test.* packages which contains *a lot of* example code. If you are looking for specific code, then our keyword list is rather informative [4]. Just email of you have more questions, Looking forward to hearing from you, Egon Willighagen 1.http://sourceforge.net/project/showfiles.php?group_id=20024 2.http://ant.apache.org/ 3.http://cdk.sourceforge.net/api/ 4.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/keywords.html -- CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Stefan K. <ste...@un...> - 2006-12-15 17:25:06
|
> 2) Both WeightDescriptor and getCanonicalMass gave sometimes one or mor= e H > atom less molecular weight. > For example, getCanonicalMass of "CN(CC2=3DCC=3DCO2)C1=3DCC=3DCC=3DC1" = gives 186.23, > It should be 187.23 (C12H13NO). > Since analyseAtomContainer at the same class of getCanonicalMass gives = the > correct formula, > > 397: mass +=3D ac.getAtom(f).getHydrogenCount() * > getCanonicalMass(h); > > could not count exact Hydrogen number. > > How about calculation of getCanonicalMass using the same algorithms wit= h > analyseAtomContainer? I changed the code to use the same algorithm; MFAnalyser now gives correc= t=20 formula and canonical mass for your smiles. Stefan > > getMass() and getNaturalMass() are also including the same problems. > > Thanks in advance. > > > Takayuki KOTANI > > > > > -----------------------------------------------------------------------= -- > Using Tomcat but need to do more? Need to support web services, securit= y? > Get stuff done quickly with pre-integrated technology to make your job > easier Download IBM WebSphere Application Server v.1.0.1 based on Apach= e > Geronimo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat= =3D121642 > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user --=20 Stefan Kuhn B. Sc. M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 My public PGP key is available at http://pgp.mit.edu |
From: phanirao p. <pha...@ya...> - 2006-12-15 10:35:53
|
Hi this is phani... iam student of Biochemistry and i wnt to work this cdk .. and also i have the knowledge of java..could u suggest me in what way i am able to work with this cdk.. Thanking u Phani Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php |
From: Egon W. <ewi...@un...> - 2006-12-13 19:30:54
|
Hi all, since quite some time now, CDK has the concept of stable and unstable modules, but in light of the upcoming CDK 1.0 release (january?), it might be interesting to add an option to the build system to exclude on compile time code with known bugs. Would an option to now compile code with known bugs be appreciated? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Egon W. <e.w...@sc...> - 2006-12-09 11:35:16
|
Hi all, CDK News is moving towards the use of the Open Journal System [1], and has a new website at: http://cdknews.org/ The new system changes a lot of editorial activities, but seems to be a serious improvement, over the already relatively high quality of our newsletter. One notable new feature, is that we now have a as-soon-as-publishable (ASAP) section, which contains all articles ready for publication, but not yet published in a released issue. The ASAP section currently contains two articles, and is available from: http://wiki.cubic.uni-koeln.de/cdknews/index.php/CDKNews/issue/view/10 of which an RSS feed is available: http://wiki.cubic.uni-koeln.de/cdknews/index.php/CDKNews/feed/atom Regards, Egon Willighagen -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Sneha <sne...@gm...> - 2006-12-08 12:28:28
|
Hi Cdk-user! Your friend Sneha from , just invited you to her online photo albums and journals at Zorpia.com. So what is Zorpia? It is an online community that allows you to upload unlimited amount of photos, write journals and make friends. We also have a variety of skins in store for you so that you can customize your homepage freely. Join now for free! Please click the following link to join Zorpia: http://signup.zorpia.com/signup?invitation_key=825386b66ee52c40af9e14b70c7243f4&referral=snehaun This message was delivered with the Sneha's initiation. If you wish to discontinue receiving invitations from us, please click the following link: http://signup.zorpia.com/email/optout/Cdk...@li... |
From: Sulev S. <su...@ch...> - 2006-11-28 09:32:03
|
On Nov 27, richard apodaca wrote: > I have a group of molecules, some of which contain a > common substructure. I want to display the molecules > with common substructures using the same orientation > for each. How can I do this in CDK? > > I had a look at Kabsch Alignment: > > http://cdk.sourceforge.net/api/org/openscience/cdk/geometry/alignment/KabschAlignment.html > > but I'm not sure it's what I'm looking for. If not, > does CDK have the capability I described? > You are on the right path. See sample 2 in the KabschAlignment's javadoc. I've not done it myself, but I would do it as follows: 1. use UniversalIsomorphismTester to find the maximal common substructure between two molecules 2. for both molecules identify atoms that belong to the common substructure (i.e. set up atom arrays a1 and a2 in the sample 2). Again, the UniversalIsomorphismTester can be used here. 3. use KabschAlignment for the alignement 4. use some 3D visualization tool for the display. Jmol perhaps? Best wishes, Sulev |
From: <ten...@gm...> - 2006-11-28 07:54:46
|
Hi, currently molecules cannot be aligned properly from scratch. When you have a known common substructure, do substructure search and use the Kabsch Alignment with the given substructure match. This alignment only works for very similar molecules, but should be enough to align at least the substructures and with them the rest of the molecules. But no guaranty for success, best regards Christian -------- Original-Nachricht -------- Datum: Mon, 27 Nov 2006 22:16:44 -0800 (PST) Von: richard apodaca <ric...@ya...> An: cdk...@li... Betreff: [Cdk-user] Kabsch Alignment > I have a group of molecules, some of which contain a > common substructure. I want to display the molecules > with common substructures using the same orientation > for each. How can I do this in CDK? > > I had a look at Kabsch Alignment: > > http://cdk.sourceforge.net/api/org/openscience/cdk/geometry/alignment/KabschAlignment.html > > but I'm not sure it's what I'm looking for. If not, > does CDK have the capability I described? > > thanks, > Rich > > ____________________________ > Richard Apodaca > Blog: http://depth-first.com > > > > ____________________________________________________________________________________ > Yahoo! Music Unlimited > Access over 1 million songs. > http://music.yahoo.com/unlimited > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer |
From: richard a. <ric...@ya...> - 2006-11-28 06:16:52
|
I have a group of molecules, some of which contain a common substructure. I want to display the molecules with common substructures using the same orientation for each. How can I do this in CDK? I had a look at Kabsch Alignment: http://cdk.sourceforge.net/api/org/openscience/cdk/geometry/alignment/KabschAlignment.html but I'm not sure it's what I'm looking for. If not, does CDK have the capability I described? thanks, Rich ____________________________ Richard Apodaca Blog: http://depth-first.com ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited |
From: Rajarshi G. <rg...@in...> - 2006-11-27 21:13:15
|
On Mon, 2006-11-27 at 19:29 +0100, M.Schumann wrote: > Hi, > > is there a documentation of the algorithm, which the NumericalSurface in > org.openscience.cdk.geometry.surface uses? > It looks like it only uses the vdw-radii of the atoms of a molecule. The > JavaDoc says, that NumericalSurface is based on the "DCLM method by > Peter McCluskey". Is there a free paper about it? The DCLM method is actually by Eisenhaber et al. (J. Comp. Chem., 1995, 16(3), 273-284) The version in the CDK is based on the (slightly simplified) implementation of the DCLM method by McCluskey used in MMTK. ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All syllogisms have three parts, therefore this is not a syllogism. |
From: M.Schumann <mai...@st...> - 2006-11-27 18:29:56
|
Hi, is there a documentation of the algorithm, which the NumericalSurface in org.openscience.cdk.geometry.surface uses? It looks like it only uses the vdw-radii of the atoms of a molecule. The JavaDoc says, that NumericalSurface is based on the "DCLM method by Peter McCluskey". Is there a free paper about it? bye Martin |
From: Rajarshi G. <rg...@in...> - 2006-11-27 16:20:47
|
On Fri, 2006-10-20 at 09:18 +0100, Robert Stones wrote: > Hi > > I was wondering being new to CDK. Is there a way to generate a library > of fragments of a molecule where want particular bond is not allowed to > be broken. > > so C=O not to be broken so from C-C-C=O > > C-C-C=O > > C=O > > C-C=O I just saw this thread so my comment might be redundant. In my generalized fragmenter code (http://cheminfo.informatics.indiana.edu/~rguha/code/java/index.html#frags) it would be relatively simple to pass a set of fragments (which should not be broken). I had planned to do something like this at one point (since breaking a carbonyl double bond is probably not useful). Also, on a related note, I've noticed the inclusion of *Reaction classes. What are they for? From this thread it looks like they can be used for fragmentation - but is there a broader focus for these classes? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- I'm related to people I don't relate to." -Calvin |
From: Miguel R. C. <Mig...@un...> - 2006-11-27 15:46:25
|
Hi Robert, > Miguel getting close but for my molecule I am getting only 12 Reactions > so I guess only 24 fragments generated ? > > IReactionSet has 12 reactions. I would like to generate all fragments > with the bond 15-16 present (see my jpeg attached which I can state > which bond to keep in all the fragments generated) which should give me > 59 fragments with aromatic bonds not to be broken. as you wanted I create a class (make a look at CleavageBondMultiReactionTes= t)=20 to obtain a multifragmentation. So from your Molecule object =3D=20 CCc1cccc(CC)c1N(COC)C(=3DO)CCl I get more fragments. But nevertheless I don= 't=20 obtain 59 but 62 fragments. But I hope that this time will help you. Cheers, Miquel =2D-- Miguel Rojas Cherto Cologne University BioInformatics Center Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49(0)221-470-7786 ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com |
From: Egon W. <ewi...@un...> - 2006-11-26 15:36:36
|
Hi all, I know that some of you are using trunk/, which has seen a bumpy development the last couple of weeks. But I am happy to announce that the bug count is back down to 39 failing JUnit tests. That's about 1.43%. That is not bad at all, and good compared with just before the bug squash party (BSP), as several of the currently failing tests are written *after* that BSP. See [1] for details about all 2723 tests! Conclusion: if you are running trunk/, today would be an excellent day to get back into sync. "So, how is CDK 1.0 getting along, then?", you might wonder... well, with this good step forward, I think we are getting there. This remains to be done: - complete the API transition [2] - fix remaining failing JUnit tests and reported bugs (or at least as many as possible of them) Help is always welcome, in any kind of form. See [3] for details. Egon 1.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/junitsummary.html 2.http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=refactoringkernelclasses 3.http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=howtohelpdevelopment -- http://chem-bla-ics.blogspot.com/ |
From: Egon W. <e.w...@sc...> - 2006-11-24 07:10:53
|
On Thursday 23 November 2006 15:34, mon...@ti... wrote: > i would Know where i can find the RTool class because I didn't find > anything about it. Try the JavaDoc: http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/ > I must do a structural match of two direct graphs > but not referring to chemical applications. There should be no problem in wrapping anything as an atom. Use the getOverlaps() method in [1]. > My work is about ontology mapping.Please help me !!!!!!!!!! I hope this helps. Egon ps. please use the user list for this thread. 1.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |