Hi, Guillaume,
Idon't fully understand your goal.
You may fragment a molecule using certain rule(s). Rules may be
represented as positive and negative SMARTS patterns for bonds. Then you
can manually cleave only those bonds which correspond to positive SMARTS
patterns but not to negative ones.
Alternatively you may use more general SMARTS pattern to produce many
possible sets of fragments and then select that set which is optimal for
your task, e.g. fragment set having the longest alkyl chain(s) or the
lowest number of fragments, etc.
Kind regards,
Pavel
On 12/08/2016 08:43 AM, Guillaume GODIN wrote:
Dear all,
I would like to know if you have an idea on how to determine
the "real" fragment count in a molecule. I mean find one fragment with
priority and remove it from the molecule and continue until the
molecule was empty.
the complex part is related to the proper enumaration of linear or
branched alkaned substituants:
iso_Bu, iso_Pr, ter_Bu, 2_Bu, CH2, CH2CH2, CH2CH2CH2, CH2CH2CH2CH2,
CH3, CH3, Et, Pr, Bu
here few examples:
Pentylamine, CCCCCN => CH2:1 & Bu:1 & NH2:1
Isopropyl Palmitate, CCCCCCCCCCCCCCCC(=O)OC(C)C=> Bu:1 & iso_Pr:1 &
CH2CH2CH2:1 & COO:1 & CH2CH2CH2CH2:2
Di-2-Ethylhexyl Ether,CCCCC(CC)COCC(CC)CCCC =>CH2:2 & CH:2 & Bu:2
& Et:2 & O:1
any idea ?
*Dr. Guillaume GODIN*
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
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