[Cdk-user] ?????? Questions about the function "Addring"

???????? Tue, 26 Nov 2019 00:12:21 -0800

Thank you for your reply.
I'm sorry for being busy with the project lately and not responding to this 
letter in time.



If I understand correctly, this change is to solve the problem that the new 
ring cannot be added when the degree of sharedAtoms == 4 (already symmetrical 
layout).
Perhaps the difference between the usage of C # code and Java caused the wrong 
result when NCDK ported from the CDK code.&nbsp;
And I will be continue to look for syntax errors.


All the best.




------------------&nbsp;????????&nbsp;------------------
??????:&nbsp;"John Mayfield"<john.wilkinson...@gmail.com&gt;;
????????:&nbsp;2019??11??21??(??????) ????1:03
??????:&nbsp;"Christoph Steinbeck"<christoph.steinb...@uni-jena.de&gt;;
????:&nbsp;"????????"<843982...@qq.com&gt;;"cdk-user"<Cdk-user@lists.sourceforge.net&gt;;
????:&nbsp;Re: [Cdk-user] Questions about the function "Addring"



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









The old code would generate this:







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&gt; 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..
 
 &gt; On 18. Nov 2019, at 16:24, ???????? <843982...@qq.com&gt; wrote:
 &gt; 
 &gt; Thanks for your reply.
 &gt; 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.&nbsp; https://github.com/kazuyaujihara/NCDK.
 &gt; But I have got some bugs. I want to read the source code of CDK and fix 
it.
 &gt; The bug is like this:
 &gt; 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.
 &gt; The code in function "placeSpiroRing" is
 &gt; atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, 
addAngle, radius);
 &gt; The variable ringCenter is dependent on the variable ringCenterVector 
which is a vector pointing the the center of the new ring.
 &gt; 
 &gt; 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.
 &gt; The code in function "placeSpiroRing" is
 &gt; if (numPlaced == 2) {
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;// nudge the 
shared atom such that bond lengths will be
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;// equal
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;startAtom.getPoint2d().add(ringCenterVector);
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;sharedAtomsCenter.add(ringCenterVector);
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;}
 &gt; And when degree == 4 and degree != 4, ringCenterVector is differently 
recalculate. Why?
 &gt; The code in function "placeSpiroRing" is
 &gt; if (degree == 4) {
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.normalize();
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.scale(radius);
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;} else {
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;// spread things out a 
little for multiple spiro centres
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.normalize();
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.scale(2*radius);
 &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;}
 &gt; I'm confused. Or I understand it wrong.
 &gt; 
 &gt; Thank you for taking your time to read this letter again.
 &gt; 
 &gt; ------------------ ???????? ------------------
 &gt; ??????: "Christoph Steinbeck"<christoph.steinb...@uni-jena.de&gt;;
 &gt; ????????: 2019??11??18??(??????) ????6:55
 &gt; ??????: "????????"<843982...@qq.com&gt;;
 &gt; ????: "cdk-user"<cdk-user@lists.sourceforge.net&gt;;
 &gt; ????: Re: [Cdk-user] Questions about the function "Addring"
 &gt; 
 &gt; Can you comment on what you try to achieve?
 &gt; The method that you are referring to is a quite specialised method for 
structure diagram layout. 
 &gt; Are you trying to create 2D drawings of some molecule or fragment, or 
maybe something else?
 &gt; 
 &gt; Kind regards,&nbsp; &nbsp;Chris
 &gt; 
 &gt; ?? 
 &gt; Prof. Dr. Christoph Steinbeck
 &gt; Analytical Chemistry - Cheminformatics and Chemometrics
 &gt; Friedrich-Schiller-University Jena, Germany
 &gt; Phone Secretariat: +49-3641-948171
 &gt; http://cheminf.uni-jena.de
 &gt; http://orcid.org/0000-0001-6966-0814
 &gt; 
 &gt; What is man but that lofty spirit - that sense of enterprise.
 &gt; ... Kirk, "I, Mudd," stardate 4513.3..
 &gt; 
 &gt; &gt; On 18. Nov 2019, at 11:32, ???????? <843982...@qq.com&gt; wrote:
 &gt; &gt; 
 &gt; &gt; Dear all,
 &gt; &gt;&nbsp; &nbsp; &nbsp;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.
 &gt; &gt;&nbsp; &nbsp; &nbsp;Looking forward to your reply. Thank you!
 &gt; &gt; 
 &gt; &gt; The source code from CDK is here??
 &gt; &gt; public void placeSpiroRing(IRing ring, IAtomContainer sharedAtoms, 
Point2d sharedAtomsCenter, Vector2d ringCenterVector, double bondLength) {
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;IAtom startAtom = 
sharedAtoms.getAtom(0);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;List<IBond&gt; mBonds = 
molecule.getConnectedBondsList(sharedAtoms.getAtom(0));
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;final int degree = mBonds.size();
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;logger.debug("placeSpiroRing: D=", 
degree);
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;// recalculate the ringCentreVector
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;if (degree != 4) {
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;int numPlaced = 0;
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;for (IBond bond : 
mBonds) {
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;IAtom 
nbr = bond.getOther(sharedAtoms.getAtom(0));
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;if 
(!nbr.getFlag(CDKConstants.ISPLACED))
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;continue;
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;numPlaced++;
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;}
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;if (numPlaced == 2) {
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;// 
nudge the shared atom such that bond lengths will be
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;// equal
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;startAtom.getPoint2d().add(ringCenterVector);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;sharedAtomsCenter.add(ringCenterVector);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;}
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;double theta = 
Math.PI-(2 * Math.PI / (degree / 2));
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;rotate(ringCenterVector, theta);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;}
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;double radius = 
getNativeRingRadius(ring, bondLength);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Point2d ringCenter = new 
Point2d(sharedAtomsCenter);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;if (degree == 4) {
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.normalize();
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.scale(radius);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;} else {
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;// spread things out 
a little for multiple spiro centres
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.normalize();
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;ringCenterVector.scale(2*radius);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;}
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;ringCenter.add(ringCenterVector);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;double addAngle = 2 * Math.PI / 
ring.getRingSize();
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;IAtom currentAtom = startAtom;
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;double startAngle = 
GeometryUtil.getAngle(startAtom.getPoint2d().x - ringCenter.x,
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;startAtom.getPoint2d().y - ringCenter.y);
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;/*
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; * Get one bond connected to the 
spiro bridge atom. It doesn't matter in
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; * which direction we draw.
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; */
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;List rBonds = 
ring.getConnectedBondsList(startAtom);
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;IBond currentBond = (IBond) 
rBonds.get(0);
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Vector atomsToDraw = new Vector();
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;/*
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; * Store all atoms to draw in 
consequtive order relative to the chosen
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; * bond.
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; */
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;for (int i = 0; i < 
ring.getBondCount(); i++) {
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;currentBond = 
ring.getNextBond(currentBond, currentAtom);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;currentAtom = 
currentBond.getOther(currentAtom);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;if 
(!currentAtom.equals(startAtom))
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;atomsToDraw.addElement(currentAtom);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;}
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;logger.debug("currentAtom&nbsp; " + 
currentAtom);
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;logger.debug("startAtom&nbsp; " + 
startAtom);
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp;atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, 
addAngle, radius);
 &gt; &gt; 
 &gt; &gt;&nbsp; &nbsp; &nbsp;}
 &gt; 
 &gt; &gt; _______________________________________________
 &gt; &gt; Cdk-user mailing list
 &gt; &gt; Cdk-user@lists.sourceforge.net
 &gt; &gt; https://lists.sourceforge.net/lists/listinfo/cdk-user
 &gt; 
 &gt; 
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 &gt; Cdk-user@lists.sourceforge.net
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[Cdk-user] ?????? Questions about the function "Addring"

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