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]. 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. A problem with the Daylight docs is that they don't distinguish between atomic weight/atomic mass and isotope number. For example, at the API level, to get the isotope number you call dt_weight http://www.daylight.com/dayhtml/doc/man/man3/dt_weight.html dt_weight(dt_Handle) => dt_Integer meaning that mass == weight == isotope is always treated as an int. I see that RDKit doesn't store the isotope, but instead tracks the atomic mass instead. I don't believe that's the right solution. > Agreed that using the generic atomic-number form makes a lot more sense. When my updated definitions, with atomic number, are available, I'll let you know. Grrr (in a chuckling sort of way)! Now I have to resynchonize my definitions to the changes you just made! Andrew [email protected] ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
