Override Target file with N mapping

[asad]

Presently its overwriting the target mol in NMCS option. Needs fixing....

[gilleain]

Can't reproduce this bug. If I give the command :

./SMSD -T SDF -t Data/arom.sdf -N -O MOL -o tmp.mol

then I get the subgraph in tmp.mol and Data/arom.sdf is still there.

[asad]

Try these files
a) query git clone git://gist.github.com/934995.git gist-934995 (1.mol)
b) target git clone git://gist.github.com/934989.git gist-934989 (connected.sdf)

java -Xms500M -Xmx500M -cp SMSD20110421.jar cmd.SMSDcmd -Q MOL -q 1.mol -T SDF -t connected.sdf -N -r -g

The reported error is

Exception in thread "main" java.lang.NullPointerException
at org.openscience.reactionblast.graphics.direct.LabelManager.setUsedPosition(LabelManager.java:126)
at org.openscience.reactionblast.graphics.direct.DirectAtomDrawer.drawAtomID(DirectAtomDrawer.java:292)
at org.openscience.reactionblast.graphics.direct.DirectAtomDrawer.drawAtom(DirectAtomDrawer.java:131)
at org.openscience.reactionblast.graphics.direct.DirectAtomDrawer.drawAtoms(DirectAtomDrawer.java:92)
at org.openscience.reactionblast.graphics.direct.DirectMoleculeDrawer.drawMolecule(DirectMoleculeDrawer.java:116)
at org.openscience.reactionblast.graphics.direct.layout.ZoomToFitGridLayout.layout(ZoomToFitGridLayout.java:50)
at cmd.ImageGenerator.createImage(Unknown Source)
at cmd.ImageGenerator.createImage(Unknown Source)
at cmd.OutputHandler.writeImage(Unknown Source)
at cmd.SMSDcmd.runSingleQueryMultipleTarget(Unknown Source)
at cmd.SMSDcmd.run(Unknown Source)
at cmd.SMSDcmd.main(Unknown Source)

This is also followed by overwriting of the Target.mol.

[gilleain]

Ok, so there are several separate issues here:

1. The -Q/q options are not currently designed to be used with -N.
2. The NPE in the graphics was already fixed, but had not been added.
3. Overwriting the Target mol.

The second of these is now fixed in 75f8744 - in the sense that it no longer throws errors, but the underlying problem (label crowding) is more difficult.

The first problem is less clear : if this combination of arguments is valid, the N-MCS method in SMSDcmd will have to be re-written. If they are not meant to be used together, then perhaps SMSD should throw an error?

I'm not sure about the third problem. If the command was -Q MOL ... -T SDF, then each target in the sdf file is written out to a separate file. Also, a large number of images are created. Perhaps there should be separate issues for these?

[asad]

Thanks Gilleain,
Yes we need to think about label crowding and rewriting the options, but presently SMSD should throw some kind of error in handling unsupported options.