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On Apr 17, 2008, at 8:45 AM, Andreas Schüller wrote: > Hello all! > > On 17/04/2008, Egon Willighagen <[EMAIL PROTECTED]> wrote: >>> Any more requests? :) >>> >>> Seriously, these are easy things to do, with quick usability >>> effects >>> for the user... > > I've got one. > The simple task of reading a molecule from a mol2 file is overly > complicated and actually only manageable for a CDK expert. Here's an > example: > > IChemModel chemModel = (IChemModel) mol2Reader.read( > DefaultChemObjectBuilder.getInstance().newChemModel()); > > IAtomContainer atomContainer = (IAtomContainer) > ChemModelManipulator.getAllAtomContainers(chemModel).get(0); > > IMolecule molecule = > DefaultChemObjectBuilder.getInstance().newMolecule > (atomContainer); Indeed this is a hassle. See http://cheminfo.informatics.indiana.edu/~rguha/code/java/#fread for a code snippet that automatically detects the format and loads all the available molecules at one go into an array. Not a great idea for large multi-molecule SDF's or SMI's (you should use the Iterating*Reader), but much easier than going through the multiple levels of abstraction - ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Heisenberg may have slept here... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgHbKEACgkQZqGSLFHnnoSdkACfUJJOm+AFWRhyF0r32fItCvy1 5wkAoLNhUirvupqTOr2zVAn0CZRTZc6W =4qf5 -----END PGP SIGNATURE----- ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
