displaying 2D SMILES on network map

[cov...@mail.nih.gov]

Has anyone successfully displayed SMILES or 2D images as a property of a node? I have constructed a network

of parent and child scaffolds. Each node has an ID as its label. I would like to add either the SMILES for that scaffold,

or a structural image. Each image can be constructed externally using CDK, JChem, ChemOffice, etc. However I do

not find an example in the Tutorials for Ctypscape 3.2.1 that indicates how this might be done.

 

As an aside, does anyone have a step by step procedure for building the galFiltered.cys example on page 98 of the manual?

This example might have some ideas on how to do this.

 

Thanks

 

[Scooter Morris]

Hi,
    Take a look at the chemViz2 app.  I think it does exactly what you're looking for (and a lot more).  It's available in the app store and you can read about here: http://www.cgl.ucsf.edu/cytoscape/chemViz2/index.shtml  I'll be happy to answer any questions about it.

-- scooter

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[cov...@mail.nih.gov]

Scooter,

Thanks for the information. Write-up makes it look like what I need. As always, getting through the first door is the problem. How do I connect the node 'name' to its 'smiles'? I have a large network imported as 4 columns (node1 node2 interaction activity; as in 6019 6608 pp 68.0). A spring weighted (by activity) network is created and as a test case, a subnet component with 20 nodes is extracted. I have a text file with each node's identifier (numbers from 1-6000) and its cannonical smiles. I do not seem to be able to make the connection between the 20 sub-network nodes and the smiles attribute for each node. Can you provide the way to do this? I have tried Import > table and load > file, but with no success.  Under the apps' settings I do not see the menu as shown on the second page of the article, where node.Smiles is highlighted.

You help is much appreciated.
David