Re: [Rdkit-discuss] MACCS SMARTS pattern definitions

[Andrew D. <da...@da...>]

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
				da...@da...