Created
April 16, 2009 17:07
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Build a mol in JCP via script
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| /******************************************************************************* | |
| * 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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