[Cdk-devel] [ cdk-Patches-2805271 ] MDLWriter IO option to force writing 2D coordinates

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Patches item #2805271, was opened at 2009-06-12 09:34
Message generated for change (Tracker Item Submitted) made by egonw
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Category: None
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Egon Willighagen (egonw)
Assigned to: Nobody/Anonymous (nobody)
Summary: MDLWriter IO option to force writing 2D coordinates

Initial Comment:
Right now, the MDLWriter in 1.2.x writes 3D coordinates if 2D and 3D is available in the CDK model (which I am perfectly happy with, and makes sense because it contains more information than the 2D coordinates). However, JChemPaint/Bioclipse may read a 3D file, create 2D coordinates on the fly, and result in a model with 2D and 3D. If people then choose to save MDL molfile, they expect 2D to be written (CML could contain both, but MDL molfile not) as saving from a 2D editor.

This patch, therefore, introduces an IO option for the MDLWriter to force writing of 2D coordinates if 2D and 3D is available, allowing overwriting the default behavior. The patch adds unit tests for the default behavior (0001), the new IO option (0002), and a unit test for the new IO option (0003).

While the patch is new functionality, it is a minor extension and needed for Bioclipse 2.0, and therefore aimed at cdk-1.2.x; it needs two reviewers.

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