On Fri, May 27, 2011 at 12:23 PM, Andrew Dalke <da...@dalkescientific.com> wrote: > Hi Greg, > >> My reading of the SMARTS theory manual >> (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) says >> that [0*] means "any atom with a mass of 0", so [!0*] would be "any >> atom that doesn't have a mass of 0". What am I missing? > > In the Daylight, OpenEye, and OpenBabel data models, an > incoming atom which doesn't have an assigned isotope number > is given the isotope number of 0. > > That is, they treat [0S] the same as [S].
That is definitely wrong according to the Daylight theory manual: "Isotopic specifications are indicated by preceding the atomic symbol with a number equal to the desired integral atomic mass. An atomic mass can only be specified inside brackets." So [0S] would be S with an atomic mass of 0. > I just posted an email to the BlueObelisk-SMILES list on this topic. > The OpenSMILES spec says that these two atoms should be different, > but I don't think that's right. We can agree to change it, but it's certainly consistent with what Daylight says in the theory manual. -greg ------------------------------------------------------------------------------ vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
