Hi Egon >sorry for not having replied earlier, but I am at a conference right >now (google:goslar chemoinformatics GCC). Thank you for your comment. I also attended to the QSAR symposium in Niigata until yesterday.
>I haven't had time to look into it yet, so don't know exactly which >method is using what data. >Additionally, I do not know if the given IUPAC mass is correct either. Latest IUPAC ATOMIC WEIGHTS OF THE ELEMENTS can be obtained form http://www.chem.qmul.ac.uk/iupac/AtWt/ For example List of Elements in Atomic Number Order. At No Symbol Name Atomic Wt Notes 1 H Hydrogen 1.00794(7) 1, 2, 3 6 C Carbon 12.0107(8) 1, 2 7 N Nitrogen 14.0067(2) 1, 2 8 O Oxygen 15.9994(3) 1, 2 >Takayuki, if you like, you could download BODR 4 from the CDK download webpage, and compare the isotopic masses and >natural abundances that IUPAC gives and which BODR gives. BODR uses (mostly) primary literature, and should have, that's >why that project is set up, high quality data. Thank you for information. I will try to use BODR. Does BODR require the latest cdk? >I will need to look at this too; do I understand correctly that when parsing that SMILES, the molecular formula is on hydrogen short? When I use "CN(CC2=CC=CO2)C1=CC=CC=C1" to parse SMILES, and calculated molecular formula using getMolecularFormula() or getHTMLMolecularFormula() at MFAnalyser class, they give the correct formula (C12H13NO). However getCanonicalMass() gives the incorrect value. At a glance of the java code, I guess, getHydrogenCount() would be some problem. I think that the pursing of SMILES would be a cause of the problem, but getMolecularFormula() recovered the hydrogen loss ( it does not give C12H12NO), so getMolecularFormula() gives some idea to solve pursing of SMILES more precisely. >> getMass() and getNaturalMass() are also including the same problems. >The problem of having one hydrogen short, or ...? Yes, one hydrogen short. Takayuki KOTANI ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
