On 19 November 2011 09:19, Egon Willighagen <[email protected]>wrote:
> Hi all,
>
> I like to hear comments on this email from Sergey.
>
> Interesting... I have never used the compare() methods...
the current
> implementation says a bond is the same if it contains the same IAtom
> *objects*.
>
> interesting indeed.
> But I do not know why this implementation is like this... ideas?
>
> In addition to the uses which return false below, I think this will return
> true:
>
> IAtom atom1 = new Atom("C");
> IAtom atom2 = new Atom("C");
> IBond bond1 = new Bond(atom1, atom2, IBond.Order.SINGLE);
> IBond bond2 = new Bond(atom1, atom2, IBond.Order.SINGLE);
> System.out.println(bond1.compare(bond2));
>
> If not mistaken, that will return true...
>
Sounds like two different semantics of compare method; obviously both have
reasons to exist.
The authors know better, but the current implementation seems to have in
mind e.g. graph algorithms, where atoms are distinct graph nodes.
The other interpretation, comparing atoms themselves is useful, but a bit
trickier - should it include equality of atom symbols only, or atom types,
aromaticity flags, bond flags, 3D coordinates of atoms, etc? IMHO matcher
classes are better suited for this purpose.
Best regards,
Nina
>
> Comments please...
>
> Egon
>
> ---------- Forwarded message ----------
> From: Сергей Соснин <[email protected]>
> Date: 2011/10/4
> Subject: [cdk-bugs] Bonds comparison trouble
> To: [email protected]
>
>
> Hi,
> I have faced that bonds comparison works some unexpected.
>
> For example this code:
>
> IBond bond1 = new Bond(new Atom("C"), new Atom("C"),
> IBond.Order.SINGLE);
> IBond bond2 = new Bond(new Atom("C"), new Atom("C"),
> IBond.Order.SINGLE);
> System.out.println(bond1.compare(bond2));
>
> returns false
>
> moreover
>
> IBond bond1 = new Bond(new Atom("C"), new Atom("C"),
> IBond.Order.SINGLE);
> IBond bond2 = (IBond)bond1.clone();
> System.out.println(bond1.compare(bond2));
>
> also returns false
>
> well, it's not that one expect
>
> Method “compare” is ok but it uses “contains” one, so i think that root
> of this trouble is here (code from Bond.java)
>
> public boolean contains(IAtom atom) {
> if (atoms == null) return false;
> for (IAtom localAtom : atoms) {
> if (localAtom == atom) return true; // !!!
> }
> return false;
> }
> This method will return true only if atom and localAtom are the same
> only, not equal.
> I think true way is to use atom.compare(localAtom);
> Is it a bug?
> CDK version is 1.4.4
>
> --
> Serg
>
>
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>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Institutet för miljömedicin
> Karolinska Institutet (http://ki.se/imm)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
> ------------------------------------------------------------------------------
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> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
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contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
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