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*.
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...
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)
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All the data continuously generated in your IT infrastructure
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.
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