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SMILES-based scaffold search [message #582] Tue, 25 June 2019 13:36 Go to next message
nbehrnd is currently offline  nbehrnd
Messages: 8
Registered: June 2019
Junior Member
It seems worth to add to the manual pages [1] that once DataWarrior identified
scaffolds, like the Murcko scaffolds, DataWarrior may determine their
SMILES and add this as a new column to the array. Advantageously, it is
possible to subsequently search entries in the array by setting up a new
text based filter, too.

As a word of caution, results of such a text-based search depend on how the
pull-down menu in front of the string to be deployed is set:

+ «equal», followed for example by C1CCCCC1 (capital characters) retrieves
both entries with the scaffold of cyclohexane, as well as entries with the
scaffold of benzene (for which, given the aromatization, other programs
deploy the string of c1ccccc1).

+ «matches regex» will retrieve scaffolds described by a string exactly as
described in the string entered here. Since it is case sensitive, c1ccccc1
will retrieve only entries with a scaffold of benzene; conversely, C1CCCCC1
will yield only those about the of cyclohexane. It requires backslashes
should your SMILES string contain parentheses, or brackets.

DataWarrior's SMILES occasionally differ from the output provided by other
programs, e.g. openbabel.

Norwid

http://www.openmolecules.org/help/chemistry.html#ScaffoldAna lysis

[Updated on: Tue, 25 June 2019 13:43]

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Re: SMILES-based scaffold search [message #583 is a reply to message #582] Thu, 27 June 2019 08:04 Go to previous message
thomas is currently offline  thomas
Messages: 219
Registered: June 2014
Senior Member
Alternatively, one may add a structure filter to the scaffold column...
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