jonalv

package net.bioclipse.managers.tests;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;

import java.io.ByteArrayInputStream;
import java.lang.reflect.AccessibleObject;
import java.lang.reflect.Method;

import net.bioclipse.core.domain.BioList;

jonalv

mol = cdk.fromSMILES("C(C1C(C(C(C(O1)O)O)O)O)O");
mol = cdk.addExplicitHydrogens(mol);
cdk.generate3dCoordinates(mol);
fileName = "/Virtual/" + cdk.molecularFormula(mol) + ".cml";
cdk.saveMolecule(mol, fileName, true);
ui.open(fileName);
jmol.minimize();
jmol.run("move 0 360 90 -20 0 0 0 0 5");

jonalv

var file = "/Sample Data/SDF/borken.sdf";
iterator = cdk.createMoleculeIterator(file);
var i = 0;
js.print("\n");
var numberOff = cdk.numberOfEntriesInSDF(file);
var molecules = cdk.createMoleculeList();

while ( iterator.hasNext() ) {
	m = iterator.next();
	i++;

jonalv

var dbName = "exampleScriptDB";
 
if ( structuredb.allDatabaseNames().contains(dbName) ) {
  structuredb.deleteDatabase(dbName);
}

structuredb.createDatabase(dbName);

smiles = new Array("Cc1ccccc1", "CCO", "O=O");
names = new Array("toluene", "beer", "air");

jonalv

var dbName = "exampleScriptDB";
 
if ( structuredb.allDatabaseNames().contains(dbName) ) {
  structuredb.deleteDatabase(dbName);
}

structuredb.createDatabase(dbName);

smiles = new Array("Cc1ccccc1", "CCO", "O=O");
names = new Array("toluene", "beer", "air");

jonalv

var dbName = "exampleScriptDB";

if ( structuredb.allDatabaseNames().contains(dbName) ) {
	structuredb.deleteDatabase(dbName);
}

toluene = cdk.fromSMILES("Cc1ccccc1");
ethanol = cdk.fromSMILES("CCO");
oxygen  = cdk.fromSMILES("O=O");