Dear Christoph,

There are no smart reasons to use SMARTS notation instead of MNA.
1. There is no reason to use 15 characters of SMARTS notation
"[H]C([H])([H])N" instead of only five of MNA "CHHHN".
2. As I understand your example:
  H
  |
H-C-N
  |
  H
 
which would translate to the SMARTS string "[H]C([H])([H])N"
 
the three another SMARTS strings can be generated:
  H
  |
N-C-H       NC([H])([H])[H]
  |
  H
 
  N
  |
H-C-H       [H]C(N)([H])[H]
  |
  H
 
  H
  |
H-C-H       [H]C([H])(N)[H]
  |
  N
 
But MNA is unique - it is "CHHHN" in all cases.
3. In general, the MNA descriptors are determined as (D. Filimonov, V.
Poroikov, Probabilistic Approaches in Activity Prediction, in
Chemoinformatics Approaches to Virtual Screening, A. Varnek and A. Tropsha,
eds., Cambridge (UK): RSC Publishing, 2008, pp. 182-216):
The 2D structural formulae of compounds were chosen as the basis for
description of chemical structure because this is the only information
available in the early stage of research. The Multilevel Neighbourhoods of
Atoms (MNA) descriptors are based on the molecular structure representation,
which includes the hydrogens according to the valences and partial charges
of other atoms and does not specify the types of bonds. MNA descriptors are
generated as recursively defined sequence:
.	zero-level MNA descriptor for each atom is the mark A of the atom
itself;
.	any next-level MNA descriptor for the atom is the sub-structure
notation A(D1D2...Di...),
where Di is the previous-level MNA descriptor for i-th immediate neighbour's
of the atom A.
The mark of atom may include not only the atomic type but also any
additional information about the atom. In particular, if the atom is not
included into the ring, it is marked by "-". The neighbour descriptors
D1D2...Di... are arranged in unique manner, e.g., in lexicographic order.
Iterative process of MNA descriptors generation can be continued covering
first, second, etc. neighbourhoods of each atom. MNA descriptors have more
general background than the descriptors, which look like MNA.
The molecular structure is represented by the set of unique MNA descriptors
of the 1st and 2nd levels.
 
So, if You wish use SMARTS then you can use this notation, but we use for
SAR/QSAR MNA about fifteen years and we concluded that MNA descriptors are
very smart, powerful and universal descriptors.

Best regards

Dmitry S. Druzhilovsky

Laboratory of Structure-Function Based Drug Design
119121, Russia, Moscow, Pogodinskaya street, 10 
Phone: +7 499 255-30-29
Fax: +7 499 245-08-57


D> -----Original Message-----
D> From: development-bounces at opentox.org [mailto:development-
D> bounces at opentox.org] On Behalf Of Christoph Helma
D> Sent: Wednesday, December 22, 2010 3:43 PM
D> To: development
D> Subject: Re: [OTDev] IBMC QNA\MNA services
D> 
D> Dear Dimitry,
D> 
D> Excerpts from Druzhilovsky's message of Wed Dec 22 12:09:52 +0100
D> 2010:
D> >
D> > Dear Christoph,
D> >
D> > You have written:
D> > "I have ... suspect that some brackets around explicit hydrogens are
D> misssing."
D> >
D> > Explanation.
D> > The MNA descriptors:
D> >
D> > HO
D> 
D> I was suggesting to provide MNA descriptors in SMARTS notation. I
D> guess
D> that "CHHHN" stands for
D> 
D>   H
D>   |
D> H-C-N
D>   |
D>   H
D> 
D> which would translate to the SMARTS string "[H]C([H])([H])N".
D> 
D> Best regards,
D> Christoph
D> _______________________________________________
D> Development mailing list
D> Development at opentox.org
D> http://www.opentox.org/mailman/listinfo/development