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chemfilter improvised Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>
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Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
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@asad @rajarshi
asad authored and rajarshi committed Jun 26, 2010
1 parent 8f3c70a commit 2a7ee54
Showing 1 changed file with 25 additions and 19 deletions.
44 changes: 25 additions & 19 deletions src/main/org/openscience/cdk/smsd/filters/ChemicalFilters.java
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Expand Up @@ -640,25 +640,31 @@ private double getBondScore(double score, Map<IBond, IBond> bondMaps) {

private double getBondFormalChargeMatches(IBond RBond, IBond PBond) {

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@egonw

egonw Jun 26, 2010

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JavaDoc on private methods is very much recommended. It is not entirely clear to me what this method is doing.
double score = 0.0;
if (RBond.getAtom(0).getID().equals(PBond.getAtom(0).getID())
&& RBond.getAtom(1).getID().equals(PBond.getAtom(1).getID())) {
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(0).getFormalCharge() != PBond.getAtom(0).getFormalCharge()) {
score += Math.abs(RBond.getAtom(0).getFormalCharge() - PBond.getAtom(0).getFormalCharge());
}
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(1).getFormalCharge() != PBond.getAtom(1).getFormalCharge()) {
score += Math.abs(RBond.getAtom(1).getFormalCharge() - PBond.getAtom(1).getFormalCharge());
}
} else if (RBond.getAtom(1).getID().equals(PBond.getAtom(0).getID())
&& RBond.getAtom(0).getID().equals(PBond.getAtom(1).getID())) {
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(1).getFormalCharge() != PBond.getAtom(0).getFormalCharge()) {
score += Math.abs(RBond.getAtom(1).getFormalCharge() - PBond.getAtom(0).getFormalCharge());
}
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(0).getFormalCharge() != PBond.getAtom(1).getFormalCharge()) {
score += Math.abs(RBond.getAtom(0).getFormalCharge() - PBond.getAtom(1).getFormalCharge());
if (RBond != null
&& PBond != null
&& RBond.getAtom(0).getID() != null && PBond.getAtom(0).getID() != null
&& RBond.getAtom(1).getID() != null && PBond.getAtom(1).getID() != null) {

if (RBond.getAtom(0).getID().equals(PBond.getAtom(0).getID())
&& RBond.getAtom(1).getID().equals(PBond.getAtom(1).getID())) {
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(0).getFormalCharge() != PBond.getAtom(0).getFormalCharge()) {
score += Math.abs(RBond.getAtom(0).getFormalCharge() - PBond.getAtom(0).getFormalCharge());
}
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(1).getFormalCharge() != PBond.getAtom(1).getFormalCharge()) {
score += Math.abs(RBond.getAtom(1).getFormalCharge() - PBond.getAtom(1).getFormalCharge());
}
} else if (RBond.getAtom(1).getID().equals(PBond.getAtom(0).getID())
&& RBond.getAtom(0).getID().equals(PBond.getAtom(1).getID())) {
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(1).getFormalCharge() != PBond.getAtom(0).getFormalCharge()) {
score += Math.abs(RBond.getAtom(1).getFormalCharge() - PBond.getAtom(0).getFormalCharge());
}
if (!RBond.getOrder().equals(PBond.getOrder())
&& RBond.getAtom(0).getFormalCharge() != PBond.getAtom(1).getFormalCharge()) {
score += Math.abs(RBond.getAtom(0).getFormalCharge() - PBond.getAtom(1).getFormalCharge());
}

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@egonw

egonw Jun 26, 2010

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So, what had changed here? Is the 'improvised' a typo of 'improved'? If not, what did you improvise; if it is, what did you improve? Was there a bug? Well, you get the idea now of good commit messages...

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@asad

asad Jun 26, 2010

Author Contributor

Line 643 to 646 is new.

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@asad

asad Jun 26, 2010

Author Contributor

it will skip the test if atom IDs are not set.

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@egonw

egonw Jun 26, 2010

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Very good. I expected something like that, but as said... you have to guide the reader... add comments in the source code like:

// deal with situations where atom IDs are not set

(Or something like that)
}
}
return score;
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2 comments on commit 2a7ee54

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@asad asad commented on 2a7ee54 Jun 26, 2010

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The idea behind this class is to differentiate between charged atoms and non changed atoms. eg: the score will rank c=o > c-o± > c-o.

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@egonw egonw commented on 2a7ee54 Jun 26, 2010

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Good. Such information would be useful to have as JavaDoc or comments in the source code. You know, but readers of your code do not. The whole point of Open Source is the many eyes, but just like with a journal publication, you must guide the reader through the test... JavaDoc, code comments, and good coding style are only for this purpose... not to make it more difficult to get your code accepted :)

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