Examples of atoms()

Examples of org.openscience.cdk.interfaces.IRing.atoms()

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                try {
                    IAtom toleave = chemModelRelay.getRenderer().getRenderer2DModel().getMerge().keySet().iterator().next();
                    IAtom toshift = (IAtom)chemModelRelay.getRenderer().getRenderer2DModel().getMerge().get(chemModelRelay.getRenderer().getRenderer2DModel().getMerge().keySet().iterator().next()).clone();
                    toleave.getPoint2d().sub(toshift.getPoint2d());
                    Point2d pointSub = new Point2d(toleave.getPoint2d().x, toleave.getPoint2d().y);
                    for(IAtom atom: newRing.atoms()){
                        atom.getPoint2d().sub(pointSub);
                    }
                } catch (CloneNotSupportedException e) {
                    //should not happen
                }
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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            }
            double bondLength = ((ControllerHub)this.chemModelRelay).calculateAverageBondLength(this.chemModelRelay.getIChemModel().getMoleculeSet());
           
            ringPlacer.placeRing(ring, worldCoord, bondLength, RingPlacer.jcpAngles);
           
            for(IAtom atom : ring.atoms())
                this.chemModelRelay.addPhantomAtom(atom);
            for(IBond atom : ring.bonds())
                this.chemModelRelay.addPhantomBond(atom);
            //and look if it would merge somewhere
            chemModelRelay.getRenderer().getRenderer2DModel().getMerge().clear();
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Examples of org.openscience.cdk.interfaces.IRing.atoms()

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                this.chemModelRelay.addPhantomAtom(atom);
            for(IBond atom : ring.bonds())
                this.chemModelRelay.addPhantomBond(atom);
            //and look if it would merge somewhere
            chemModelRelay.getRenderer().getRenderer2DModel().getMerge().clear();
            for(IAtom atom : ring.atoms()){
                IAtom closestAtomInRing = this.chemModelRelay.getClosestAtom(atom);
                if( closestAtomInRing != null) {
                        chemModelRelay.getRenderer().getRenderer2DModel().getMerge().put(closestAtomInRing, atom);
                }
            }
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