[Cdk-devel] [ cdk-Patches-2942196 ] Uniform behavour of mdl(V2000)reader

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Patches item #2942196, was opened at 2010-01-29 07:29
Message generated for change (Settings changed) made by rajarshi
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Category: None
Group: Needs Review
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Stefan Kuhn (shk3)
Assigned to: Rajarshi Guha (rajarshi)
Summary: Uniform behavour of mdl(V2000)reader

Initial Comment:
The MDLReader l. 488 and the MDLV2000Reader l. 545 have different behaviour for the same situation. I think this is due to code duplication between these classes, they should share the reading of atoms and bonds.

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>Comment By: Rajarshi Guha (rajarshi)
Date: 2010-02-25 20:14

Message:
Looks good. Applied to cdk-1.2.x and pushed

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Comment By: Egon Willighagen (egonw)
Date: 2010-02-24 15:24

Message:
Rajarshi, can you please review the patch?

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Comment By: Egon Willighagen (egonw)
Date: 2010-02-24 15:22

Message:
Adding patch to synchronize behavior.

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Comment By: Stefan Kuhn (shk3)
Date: 2010-01-29 10:47

Message:
Please have a look at the code. The MDLV2000Reader removes 3d coordinates
if all are 0,0,0, the MDLReader doesn't. It looks like the f (totalX == 0.0
&& totalY == 0.0 && totalZ == 0.0) was added later, but forgotten in
MDLReader. If nothing else is possible, we can make a static helper method
handleCoordinates or so.

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Comment By: Egon Willighagen (egonw)
Date: 2010-01-29 09:52

Message:
Please describe the expected behavior which you like to see for both.

(Code duplication is generally bad, indeed. Not so easy to fix here, as
the format for the atom and bond block as actually different (line
lengths), so sharing the same method is at least not possible...)

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