Can you comment on what you try to achieve? The method that you are referring to is a quite specialised method for structure diagram layout. Are you trying to create 2D drawings of some molecule or fragment, or maybe something else?
Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 18. Nov 2019, at 11:32, 努力努力 <843982...@qq.com> wrote: > > Dear all, > i want to understand how to add rings in the atom.In the function > "Addring",I find the code "ringPlacer.PlaceSpiroRing" and then jump to the > function "placeSpiroRing".And I have some problems about this function.Why do > we have special treatment when degree==4 and numplace==2? In my > understanding, "degree" is the number of bonds connected to sharedAtoms, and > numPlaced is the number of other Atoms ring except sharedAtoms. > Looking forward to your reply. Thank you! > > The source code from CDK is here： > public void placeSpiroRing(IRing ring, IAtomContainer sharedAtoms, Point2d > sharedAtomsCenter, Vector2d ringCenterVector, double bondLength) { > > IAtom startAtom = sharedAtoms.getAtom(0); > List<IBond> mBonds = > molecule.getConnectedBondsList(sharedAtoms.getAtom(0)); > final int degree = mBonds.size(); > logger.debug("placeSpiroRing: D=", degree); > > // recalculate the ringCentreVector > if (degree != 4) { > > int numPlaced = 0; > for (IBond bond : mBonds) { > IAtom nbr = bond.getOther(sharedAtoms.getAtom(0)); > if (!nbr.getFlag(CDKConstants.ISPLACED)) > continue; > numPlaced++; > } > > if (numPlaced == 2) { > // nudge the shared atom such that bond lengths will be > // equal > startAtom.getPoint2d().add(ringCenterVector); > sharedAtomsCenter.add(ringCenterVector); > } > > double theta = Math.PI-(2 * Math.PI / (degree / 2)); > rotate(ringCenterVector, theta); > } > > double radius = getNativeRingRadius(ring, bondLength); > Point2d ringCenter = new Point2d(sharedAtomsCenter); > if (degree == 4) { > ringCenterVector.normalize(); > ringCenterVector.scale(radius); > } else { > // spread things out a little for multiple spiro centres > ringCenterVector.normalize(); > ringCenterVector.scale(2*radius); > } > ringCenter.add(ringCenterVector); > double addAngle = 2 * Math.PI / ring.getRingSize(); > > IAtom currentAtom = startAtom; > double startAngle = GeometryUtil.getAngle(startAtom.getPoint2d().x - > ringCenter.x, > startAtom.getPoint2d().y - > ringCenter.y); > > /* > * Get one bond connected to the spiro bridge atom. It doesn't matter > in > * which direction we draw. > */ > List rBonds = ring.getConnectedBondsList(startAtom); > > IBond currentBond = (IBond) rBonds.get(0); > > Vector atomsToDraw = new Vector(); > /* > * Store all atoms to draw in consequtive order relative to the chosen > * bond. > */ > for (int i = 0; i < ring.getBondCount(); i++) { > currentBond = ring.getNextBond(currentBond, currentAtom); > currentAtom = currentBond.getOther(currentAtom); > if (!currentAtom.equals(startAtom)) > atomsToDraw.addElement(currentAtom); > } > logger.debug("currentAtom " + currentAtom); > logger.debug("startAtom " + startAtom); > > atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, > startAngle, addAngle, radius); > > }
RingPlacer.java
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