printJPlogP.nf

#!/usr/bin/env nextflow


@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='0.0.9')
@Grab(group='org.openscience.cdk', module='cdk-qsarmolecular', version='2.3')

import net.bioclipse.managers.CDKManager
import org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
import org.openscience.cdk.interfaces.IAtomContainer


Channel
    .fromPath("./query_result.tsv")                            
    .splitCsv(header: ['wikidata', 'smiles' , 'isoSmiles'], sep:'\t') 
    .map{ row -> tuple(row.wikidata, row.smiles, row.isoSmiles) } 
    .set { molecules_ch }                               
  


process printJPlogP {                                   
    input:
    set wikidata, smiles, isoSmiles from molecules_ch     
    
    /* maxForks 1 */  
  
    exec:
	println "Running.."  
	if (smiles != null){
	cdk = new CDKManager(".");
	try {
	  molecule = cdk.fromSMILES(smiles)
	  descriptor = new JPlogPDescriptor()
          jplogp = descriptor.calculate(molecule.getAtomContainer()).value.toString()
	  println "$molecule has JPLogP : " + jplogp
	} catch (Exception exc) {
	  println "Error in parsing this SMILE $smiles"
	}
	}else {
	cdk = new CDKManager(".");
	try {
	  molecule = cdk.fromSMILES(isoSmiles)
	  descriptor = new JPlogPDescriptor()
          jplogp = descriptor.calculate(molecule.getAtomContainer()).value.toString()
	  println "$molecule has JPLogP : " + jplogp
	} catch (Exception exc) {
	  println "Error in parsing this isoSMILE $isoSmiles"
	}	 
	}
}