Wednesday, February 16, 2011

Descriptors generated from a SDF file to Excel

Just came across the power mv output of descriptor calculation in an excel format,we have seen how to calculate the descriptor using the chemistry development kit,the same output can be generated on a excel sheet using jxl.jar, a Java API. Java Excel API is a mature, open source java API enabling developers to read, write, and modifiy Excel spreadsheets dynamically. The program works with cdk-1.3.4.jar and cdk-jchempaint-8.jar. Hope everyone is hacking their way across cdk ,please follow the blog and subscribe to the post, untill next time .wq:

Screenshot of the Descriptors in Excel

Saturday, February 12, 2011

Moleular Structure Generation Using cdk-1.3.8.jar and jchempaint-16.jar

Dear All,

    Hope all are having a great time working with Chemistry Devolelopment Kit. We had seen how to render the chemical structure from SMILES using cdk-1.3.4.jar and cdk-jchempaint-8.jar. It also works fine with cdk-1.3.8 and cdk-jchempaint-16.jar . A screenshot of it in action is given below.

Screenshot of the program

Wednesday, February 2, 2011

cdk Rendering Image from SMILES

The code below takes SMILES string as input and renders the structure diagram of the molecule. The program works with cdk-1.3.4.jar and cdk-jchempaint-8.jar

Screen shot of above program in action

Tuesday, February 1, 2011

Introduction to Chemistry Development Kit for OSDD Community

Dear all,
thought of giving an intro into the Chemistry development kit,please execuse the untimely one,should have posted the introduction prima ,think of it as a quentin tarantino movie:) lets start with a nice excerpt from the Chemistry Development kit Readme file, The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in the programming language Java(tm).This is a library of useful data structures and algorithms to manipulate them from the area of structural chemo- and bioinformatics. As such, it is intended for the use by programmers, who wish to save some effort by reusing code. It is not intended for the enduser. If you consider yourself to be more like user, you might not find what you wanted.

So thats the important part,a little bit of programming and lot of help from the various IDE's(eclipse,netbeans,komodo) present we can work on this. CDK is a really useful tool, with lots of classes and libraries to help us out.. unlike paid softwares u dont have to confine ur self to the bunch of functions they provide u with.. theres been a lot of instances where i have lamented on the money spent on s/w :`-( .... so as with the true jest of what OSDD stands for,we have to scale the potentiality of the Chemsitry development kit a open source software and believe me with guys like egon and company at the helm of things we wouldnt be stranded at any line of a programe ,coz there is help from around the globe..

hoping this humble intro to set things in motion for us to play our part in the projection of this open source software, i wish u happy coding:)

Friday, January 14, 2011

GUI for Descriptor Calculation from USER INPUT SMILES

This Program takes a Smiles string as input and generates corresponding Descriptor Specification and Descriptor Value. It uses cdk1.3.7.jar and cdk-jchempaint-8.jar.

Screeen Shot of the above program

Monday, January 3, 2011

cdk varying out puts

started using cdk for descriptor calculations ,here is the code

While i run this as a standalone program or thro netbeans in a linux machine i get the o/p for bcut descriptor.when on windows thro netbeans 6.8 the complete o/p is generated ..any suggestions???