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olas/buildmol

Created April 16, 2009 17:07
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Build a mol in JCP via script
Raw
buildmol
/*******************************************************************************
* Bioclipse-script to iteratively build a molecule in JChemPaint
* Author: Ola Spjuth
******************************************************************************/
//Start with a carbon and open in JCP
mol=cdk.fromSMILES("C")
mol2=cdk.generate2dCoordinates(mol)
ui.open(mol2)
//Add some atoms and bonds and wait 1 sec in between
atom=jcp.getModel().getAtomContainer().getAtom(0);
jcp.addAtom("C", atom)
js.delay(1)
atom=jcp.getModel().getAtomContainer().getAtom(1);
jcp.addAtom("C", atom)
js.delay(1)
atom=jcp.getModel().getAtomContainer().getAtom(2);
jcp.addAtom("C", atom)
js.delay(1)
atom=jcp.getModel().getAtomContainer().getAtom(3);
jcp.addAtom("C", atom)
js.delay(1)
atom=jcp.getModel().getAtomContainer().getAtom(4);
jcp.addPhenyl(atom)
js.delay(1)
atom=jcp.getModel().getAtomContainer().getAtom(jcp.getModel().getAtomContainer().getAtomCount()-1);
jcp.addAtom("C", atom)
js.delay(1)
atom=jcp.getModel().getAtomContainer().getAtom(jcp.getModel().getAtomContainer().getAtomCount()-1);
jcp.addAtom("C", atom)
js.delay(1)
atom=jcp.getModel().getAtomContainer().getAtom(jcp.getModel().getAtomContainer().getAtomCount()-1);
jcp.addRing(atom,5)
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