Vinay M wrote:
> Hi Everyone
> Could any one help me to know the difference between
> HBA1 HBA2. I am screening the database based on L5 and other parameters.
> Secondly please help me to eliminate the molecules based on the
> functional groups.
>
If you type
babel -L descriptors verbose
you will get the SMARTS patterns HBA1 and HBA2 are based on
HBA1 [$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]
HBA2
[$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]
together with some other information. These patterns were taken from
the now unsupported JoelLib and others may be able to pick out the
subtlties better than I can.
> Secondly please help me to eliminate the molecules based on the
> functional groups.
Describe the functional group with a SMARTS pattern
(SMARTS_InteLigand.txt might help). For example, [Br,I]
To eliminate all molecules containing bromine or iodine:
babel dataset.xxx filteredset.yyy -v [Br,I]
To use multiple SMARTS patterns:
babel dataset.xxx filteredset.yyy
--filter "smarts!=[Br,I] smarts!=COO"
The filter can, if necessary, use more complex Boolean logic and other
descriptors, see http://openbabel.org/wiki/--filter_option
If the filtering criteria get inconveniently long, you can make a
CompoundFilter (L5 is one). To plugindefines.txt add an entry like:
CompoundFilter
Vinfilter # ID
smarts!=[Br,I] smarts!=COO # definition
Remove mols with Br,I,peroxide # description
Then you can use
babel dataset.xxx filteredset.yyy --filter Vinfilter
(There is a bug in 2.2.3 when using plugindefines.txt and SMARTs
containing a # character.)
Chris
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