On Thu, 2006-02-09 at 09:24 +0100, [EMAIL PROTECTED] wrote: > 2. When calculating the numerical surface with NumericalSurface.java > on a read in PDB file I get a CDK exception : > org.openscience.cdk.exception.NoSuchAtomTypeException when the VDW > radii should be configured (line 318). I circumvented this by > assigning the VDW radii to the Protein as in the > ProteinPocketFinder.java file (function assignVdwRadiiToProtein) prior > to calling NumericalSurface(). However, I was wondering if there is an > easy way to use the configVDW of the NumericalSurface class?
I've just committed some changes to NumericalSurface and now there is a constructor in which you can supply a filename of a file that contains VDW radii. So one way to use this is to make a copy of the Jmol atom types file (org/openscience/cdk/config/jmol_atomtypes.txt), edit it to whatever you want and specify the new file. ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- I'm related to people I don't relate to." -Calvin ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
