This is very old code and it seem that others changed it (to the better :)) since I wrote it long time ago. If I understand you correctly, there is actually no bug, just an apparent inconsistency that you are reporting. The simplest thing would be for you to remove the case distinction and see what happens. Maybe that reveals the reason for the distinction.
I’d love to dig into this but I lack the time for such fun these days Very sad. :D All the best, 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 16:24, 努力努力 <843982...@qq.com> wrote: > > Thanks for your reply. > I want to implement a JChemPaint in C#. In fact, I used a CDK port, named > NCDK which is C# impementation implementation of the Chemistry Development > Kit. https://github.com/kazuyaujihara/NCDK. > But I have got some bugs. I want to read the source code of CDK and fix it. > The bug is like this: > When we addRing, we need to calculate the position of the virtual ring. From > the code , I understand that the position of the new ring need to be > calculated by some variables, include the new ring center, startAngle, > addAngle, radius. > The code in function "placeSpiroRing" is > atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, > addAngle, radius); > The variable ringCenter is dependent on the variable ringCenterVector which > is a vector pointing the the center of the new ring. > > For example, when I want to add a triangle to a shared atom, It satisfies > numplace==2.It seems that the sharedAtom' s position will be changed. > The code in function "placeSpiroRing" is > if (numPlaced == 2) { > // nudge the shared atom such that bond lengths will be > // equal > startAtom.getPoint2d().add(ringCenterVector); > sharedAtomsCenter.add(ringCenterVector); > } > And when degree == 4 and degree != 4, ringCenterVector is differently > recalculate. Why? > The code in function "placeSpiroRing" is > if (degree == 4) { > ringCenterVector.normalize(); > ringCenterVector.scale(radius); > } else { > // spread things out a little for multiple spiro centres > ringCenterVector.normalize(); > ringCenterVector.scale(2*radius); > } > I'm confused. Or I understand it wrong. > > Thank you for taking your time to read this letter again. > > ------------------ 原始邮件 ------------------ > 发件人: "Christoph Steinbeck"<christoph.steinb...@uni-jena.de>; > 发送时间: 2019年11月18日(星期一) 晚上6:55 > 收件人: "努力努力"<843982...@qq.com>; > 抄送: "cdk-user"<cdk-user@lists.sourceforge.net>; > 主题: Re: [Cdk-user] Questions about the function "Addring" > > 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); > > > > } > > > _______________________________________________ > > Cdk-user mailing list > > Cdk-user@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
