Lhasa Limited has just committed some new nodes into their community contribution. These nodes process structures through SmartCyp (site of metabolism for Cyp P450 enzymes) and WhichCyp (isophorm binding prediction).
These applications are release under the Lesser GPL licence and more information can be found here: http://www.farma.ku.dk/smartcyp/ and http://www.farma.ku.dk/whichcyp/ .
The underlying code was updated to CDK 1.5.12 (in line with the release in KNIME). A small dataset of 13 compounds has been processed and the ranking returned are the same, there is some deviation in calculated values for score and other values. An example workflow should shortly be available showing these differences.
More details can be found here: https://tech.knime.org/book/lhasa-community-contribution-metabolism
The nodes should be available from the nightly build (hopefully tonight): http://update.knime.org/community-contributions/trunk
thanks for brining SmartCyp and WhichCyp to KNIME.
The nodes works fine on my Ubuntu system with the latest KNIME (3.1.1) and nightly CDK/Lhasa plug-ins.
However, the same setup (installation, plugins) does not work on a Windows 7 64-bit machine. The SmartCyp node runs without error and produces a correctly sized output table but all image and value columns are empty (missing). The second output port is empty.
The workflow itself couldn't be any simpler: table creator -> smartcyp.
Any idea what's going on here?
I spotted an issue with image generation yesterday when 3D coordinates a present (a null pointer is thrown by the CDK Image rendering, this also seems to happen for the CDK Value renderring of the CDK cell but it is caught and managed).
I've updated the node to regenerate 2D coordinates prior to theimage render and this appears to have fixed this bug. This has been commited to the trunk and I've added a new test to cover 3D structures, jenkins is building now.
Do you know if your structures have 3D coordinates?
I've added in some additional logging to help a user identify an issue. If you can share an example structure(s) that you are having this issue on I'm happy to see if I can recreate the issue and then provide a fix?
EDIT: the 3D coordinate bug is now available for update from the trunk, please let me know if this isn't the issue you were having.
I installed the nodes today (Feb 6) and face similar problem on a Win7 64-bits system with the SMARTCyp node. It finishes immediately with the following error, and fails to produce images of the results:
ERROR SMARTCyp 2.4.2 2:1 Failed to process row: Row0 appending missing values
The WhichCyp node on the other hand works fine. I draw structures with the MarvinSketch node as input, so these are 2D.
I will install a fresh version of KNIME and see whether I can recreate the issue. It's running fine on my machine which is Win7 64 bit.
-- Update: I downloaded KNIME 3.1.1, installed on a Windows 7 64 bit machine and ran SMARTCyp without issue.
-- Update 2: I ran SMARTCyp on another machine and found the issue. There was a piece of debug code that hadn't been removed that was pointing to a specific location. It is building now and should be available in the trunk soon.
All good now, thanks for fixing this so swiftly!
I had another look at the plugin today and I can confirm that it now works beautifully.