It's calculated differently because without it the rings get laid out on top of each other. Example case, you can reverse this commit:
https://github.com/cdk/cdk/commit/6533533a95b5e9ca0d55d0d37ab5f048a25e88f7#diff-da65f1759b150e9510a643e017112b3f And see how it lays out the following. C1CO[Fe]234(O1)OCCO2.C(CO3)O4 [image: image.png] The old code would generate this: [image: image.png] because the bond vector was pointing towards the centre of the ring. John On Wed, 20 Nov 2019 at 16:36, Christoph Steinbeck < christoph.steinb...@uni-jena.de> wrote: > 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 >
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