----------------------------------------------------------------------
Message: 1
Date: Sat, 16 Dec 2006 11:20:12 +0100
From: Egon Willighagen
Subject: Re: [Cdk-user] New to Cdk
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
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
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