OK, thanks. Behaviour is good with 2.0. Timm
On 26/06/2017 09:51, John Mayfield wrote:
Use version 2.0 :-)On 26 June 2017 at 08:31, Tim Dudgeon <[email protected] <mailto:[email protected]>> wrote:Here's what I see: IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser parser = new SmilesParser(bldr); IAtomContainer mol1 = parser.parseSmiles("CCO"); IAtomContainer mol2 = parser.parseSmiles("CCO ethanol"); SDFWriter sdf = new SDFWriter(System.out); sdf.write(mol1); sdf.write(mol2); Outputs: CDK 0626170823 3 2 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 M END > <cdk:Title> null $$$$ ethanol CDK 0626170823 3 2 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 M END > <cdk:Title> ethanol $$$$ Note that for mol1 no title is set but a property named cdk:Title is output with a value of "null". For mol2 the title is set and output correctly, but the property cdk:Title is also output. This is with version 1.5.14. Tim On 25/06/2017 15:40, John Mayfield wrote:I'm planning on rewriting the CTab readers to fix issues like the cdk:Remark nastyness but the title lines should still be working. IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser smipar = new SmilesParser(bldr); IAtomContainer mol = smipar.parseSmiles("CCO ethanol"); new MDLV2000Writer(System.out).write(mol); System.out.println("//"); try (SDFWriter sdf = new SDFWriter(System.out)) { sdf.write(mol); } Result: ethanol CDK 0625171540 3 2 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 01 2 1 0 0 0 0 2 3 1 0 0 0 0M END // ethanol CDK 0625171540 3 2 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 01 2 1 0 0 0 0 2 3 1 0 0 0 0M END $$$$ How are you using them Tim? John On 24 June 2017 at 17:19, Tim Dudgeon <[email protected] <mailto:[email protected]>> wrote: One possibility might be to use the value of IChemObject.getID() for the title line. Not sure if that would be a good or a bad idea. But I tried it and it doesn't work. Another thing I noticed is that CDK has a bad habit of adding an empty cdk:Remark property for no particular reason. But if you know about this then you can remove it before exporting so its not a major problem. Tim On 24/06/2017 15:45, Egon Willighagen wrote: Mmm... I'd consider that a regression, as that was the intended behavior... John, do you agree we should restore that behavior, or do you have a better solution? Egon On Sat, Jun 24, 2017 at 4:23 PM, Tim Dudgeon <[email protected] <mailto:[email protected]>> wrote: Hi All, I'm needing to write the title line (the first line in the record) for MDL formats. I'm using SDFWriter.write(mol) to write out the SD file. I've found that you can do this be setting the property CDKConstants.TITLE (which has a value of "cdk:Title") of the IAtomContainer to the value you want in the title line , but you also get this written as a SD file property, which is not what I want. Is there a way of better controlling this? Tim ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Cdk-user mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/cdk-user <https://lists.sourceforge.net/lists/listinfo/cdk-user> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Cdk-user mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/cdk-user <https://lists.sourceforge.net/lists/listinfo/cdk-user>------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Cdk-user mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/cdk-user <https://lists.sourceforge.net/lists/listinfo/cdk-user>
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