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How to compute the principal moments of inertia for a set of molecules

Asked by , Edited by Alfons Nonell-Canals

I have different sets of molecules and I would like to compute the principal moment o inertia for the molecules of each set. I am looking for a way to do it easy and fast.

Usually, to manage molecules and compute different descriptors I program my own scripts with python and pybel but now, I have no idea how to do it.

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1 answer

1

matteo floris [ Editor ]

Hi, there is a CDK implementation of principal moment of inertia descriptor:


org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor


This is a piece of code (any 3D input file):


MomentOfInertiaDescriptor descriptor = new MomentOfInertiaDescriptor();

IMolecule m = null;

IteratingMDLReader reader = new IteratingMDLReader(

new FileReader(new File( "MMsInc_STRUCTURES.sdf)), 

NoNotificationChemObjectBuilder.getInstance() );


while (reader.hasNext()) {

m = (IMolecule) reader.next();

DoubleArrayResult retval = (DoubleArrayResult) descriptor.calculate(m).getValue();

System.out.println( m.getProperty("cdk:Title") + " " + retval);    

}



NN comments
chem-bla-ics
-

Matteo, a short code example would have been nice…

matteo floris
-
-bla-ics Ok Egon, but I din’t find how to put html tags (pre or blockquote)….

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