jchempaint

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however see this code in JCPAApplet.java ``` // the newly opened file should nicely fit the screen theJcpp.getRenderPanel().setFitToScreen(true); theJcpp.getRenderPanel().update(theJcpp.getRenderPanel().getGraphics()); // ..enable zooming by removing constraint again theJcpp.getRenderPanel().setFitToScreen(false); ```

rwst

that is according to our molecule definition

rwst

Depending on the SMILES encoding, rendrering of some polycycles may be wrong. 1. Try molecule O1CC2C(C(CC23)C=C3)COS1 : rendering not ok; 2. If you try another encoding of the same molecule,...

rwst

do we need a separate package?

rwst

1. place ethane (no explicit Hs) 2. click H button 3. click one of ethane's Cs (must be wrong, cannot confirm)

rwst

CDKException with manual input of SMILES of a salt

1

https://sourceforge.net/apps/trac/jchempaint/ticket/113 However, the same [NH4+].CP(=O)(O)CCC(N)C(=O)[O-] in a MOL file is displayed as usual. This is NOT considered a CDK problem and should be fixed in JCP.

rwst

see Nucleosides/Adenosine

rwst

error message and clean state after SMILES C1C1 instead of NullPtr

1

Both input of C1C1 from text field and file gives (different) exceptions. It should give an error message box, rejecting the input. The cause is primarily a CDK issue, see...

rwst

my guess is this can only be solved using templates either in the renderer, or by the user. But who knows?

rwst

depends on https://sourceforge.net/p/cdk/bugs/1269/ java.lang.NullPointerException at javax.vecmath.Tuple2d.(Tuple2d.java:82) at javax.vecmath.Vector2d.(Vector2d.java:86) at org.openscience.cdk.layout.AtomPlacer.distributePartners(AtomPlacer.java:163) at org.openscience.cdk.layout.HydrogenPlacer.placeHydrogens2D(HydrogenPlacer.java:112) at org.openscience.cdk.layout.HydrogenPlacer.placeHydrogens2D(HydrogenPlacer.java:68) at org.openscience.cdk.layout.StructureDiagramGenerator.generateExperimentalCoordinates(StructureDiagramGenerator.java:280) at org.openscience.cdk.layout.StructureDiagramGenerator.generateExperimentalCoordinates(StructureDiagramGenerator.java:248) at org.openscience.jchempaint.controller.ControllerHub.generateNewCoordinates(ControllerHub.java:1266) at org.openscience.jchempaint.controller.ControllerHub.cleanup(ControllerHub.java:1227) at org.openscience.jchempaint.action.CleanupAction.actionPerformed(CleanupAction.java:61)

rwst