On Friday 09 February 2007, sushil ronghe wrote: > I have finally installed the CDK in netbeans5.5 .
Excellent. Please feel free to add a page in the wiki [1], on how to set it up in NetBeans, so that other users may take advantage of it... or to just share experiences (I use Eclipse...). > And i wish to use the fileconvertor and substructure search application in > my program. > > While doing so i got few errors. > > 1) While converting XYZ file to mol i got this error > java.lang.NumberFormatException: For input string: "C" > at sun.misc.FloatingDecimal.readJavaFormatString( > FloatingDecimal.java:1224) > at java.lang.Double.valueOf(Double.java:447) > at java.lang.Double.<init>(Double.java:539) > at > org.openscience.cdk.io.XYZReader.readChemFile(XYZReader.java:177) at > org.openscience.cdk.io.XYZReader.read(XYZReader.java:120) at > chemfile.Main.main(Main.java:337) Please give the file content, so that I can see what goes wrong. > 2 ) Other files are converting well but the connection tabel is not present > in any of the converted file. > though i have kept this boolean true: > applyHAdding = true; > applyHRemoval = true; > apply2DCleanup = true; > apply3DRebonding = true; XYZ files do not contain bond information, and CDK does not do anything you did not ask for. Please have a look at the cdk.graph.rebond.RebondTool, which allows creating bonds from 3D coordinates. > 3) While doing the substructure search,when i input the smart with > logical operator (ref:: > http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) I got the > warning the "string" is not valid smart. > I have tried the operators , & ; ! . Only a subset of SMARTS is implemented in the CDK, pending an MQL implementation. Adding features is not too difficult, but requires some explanation. If interested, please let me know. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
