Monday, November 23, 2009

Blog moved

In November 2009 I decided to close down my old blog »Chemistry-To-Informatics«
and from then run it as a more personal website.
I found the old blog articles on Blogger, blogging and web design
outdated and not relevant anymore, so they have been removed for good.
If you want to read something else, you are welcome to explore my
current websites: http://blog.chemdom.com/

Sunday, November 16, 2008

Compiling specific modules in CDK

When I try to test some specific module in cdk I am using the -Dmodule functionality with the Ant build.xml build system. Since the update in src the compile module have a continue procedure, here you have a good example.
Thus, if I want to test only the module formula, I am doing the following:


$ rm dist/jar/cdk-formula.jar
$ rm dist/jar/cdk-test-formula.jar
$ rm reports/result-formula.txt
$ ant -Dmodule=formula -Dsource=src/main compile-module
$ ant -Dmodule=test-formula -Dsource=src/test compile-module
$ ant -Dmodule=formula test-module
$ cat reports/results-formula.txt

The three first line remove all code related to formula. Afterwards the module, the test is compiled. Finally the tests are tested.

One of the inconvenient which I come across is that I had to write each time the same thing and when I changed of module rewrite again. In short I would like to write only the module to test. That is the origin I wrote a small script which may be it can interest somebody.


#!/bin/bash
#====================================================#

# Script to compile specific module of the Chemistry Development kit with the #

# the Ant build.xml system. #

#====================================================#


ANT="ant"
BUILD="build.xml"


if [ ! -f $BUILD ]

then

echo "Build file [$BUILD] not found - Aborting"

exit

fi


if [ $# -ne 1 ]

then

echo "Error in $0 - Invalid Argument Count"

echo "Syntax: $0 module_name"

exit

else

modJ="dist/jar/cdk-"$1".jar"

if [ -f $modJ ]

then

echo "removing "$modJ

fi


mod_testJ="dist/jar/cdk-test-"$1".jar"

if [ -f $mod_testJ ]

then

echo "removing "$mod_testJ

fi


mod_report="reports/result-"$1".txt"

if [ -f $mod_report ]

then

echo "removing "$mod_report

fi


script1=$ANT" -f "$BUILD" -Dmodule="$1" -Dsource=src/main compile-module"

echo "building: "$script1

$script1


script2=$ANT" -f "$BUILD" -Dmodule=test-"$1" -Dsource=src/test compile-module"

echo "building: "$script2

$script2


script3=$ANT" -f "$BUILD" -Dmodule="$1" test-module"

echo "building: "$script3

$script3


cat $mod_report

fi

Saturday, October 4, 2008

My Machine

Did you ever imagine...

Did you ever imagine that you would spend the majority of your life interacting with a lifeless machine.

Thinking for a Living™


Me neither.

Saturday, September 20, 2008

Actual overview of chemoinformatic toolkits

There is a great poster from Andrew Dalke from Sweden which shows the timeline of several chemoinformatics toolkits, avalaible on the at his blog. Tools are necessary for computational life science. It makes possible the "art" of interpreteting the chemical information some times out of reach of humans.


It is nice to see that CDK it is one of the strongest in JAVA tools.

Wednesday, September 10, 2008

Metabolomics Platform in Tarragona

New news for those who are interested in metabolomics and tarragona. In Tarragona city known as acronym TRG a new platform, the Metabolomics Platform , has been created. It is funded by URV university and CIBERDEM.
The research group, leaded by Prof. Xavier Correig Blanchar, has initiated to inspecte some issues in the filed of metabolomics applications. I am very happy to see that progress from a city which I love.

Sunday, June 8, 2008

Editor for RDFiles in Bioclipse

Chemical reactions are a very important processes explaining our metabolism. More complex is its visual representation take account the mechanism. The Chemistry Development Kit (CDK) is a Java library for structural bio- and chemoinformatics which supports reactions between others.

So, I hacked up in Bioclipse code to provide this functionality with a new RDFEditor plugin. It is following the same structure than the SDFEditor plugin.

Apart from reading and rendering the reaction, it also reads and displays properties in a table. Important feature to find similarities and dissimilarities between reactions.

Motivation

I don't know