On Thu, Jan 28, 2016 at 1:08 PM, Pshemak Maslak <n...@psu.edu> wrote:
>
> The new DSSR has base pairs and nucleotide indexed by numbers, For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp "A-T"
>
x=_M.dssr.pairs.getProperty("SELECT nt* where bp='T-A' or bp='A-T'")
select within(@x)
_M is the auxiliaryInfo for the current model.
Note that x is an array of associative arrays:
[... {
"nt1" : "|1|D|DT|12||||"
"nt2" : "|1|E|DA|27||||"
}
{
"nt1" : "|1|D|DT|15||||"
"nt2" : "|1|E|DA|24||||"
}
...]
Jmol finds those "unit ids" in there. Better is to use ( ) around the nt*:
x=_M.dssr.pairs.getProperty("SELECT (nt*) where bp='T-A' or bp='A-T'")
This creates a clean array of those unit ids:
$ x=_M.dssr.pairs.getProperty("SELECT (nt*) where bp='T-A' or bp='A-T'")
$ print x
|1|E|DT|34||||
|1|D|DA|5||||
|1|E|DT|31||||
|1|D|DA|8||||
|1|E|DT|29||||
|1|D|DA|10||||
|1|E|DA|27||||
|1|D|DT|12||||
|1|E|DA|24||||
|1|D|DT|15||||
> auxiliaryinfo.models[1].dssr.pairs[9].nt1 "|1|D|A|10||||"
auxiliaryinfo.models[1].dssr.pairs[9].nt2 "|1|E|T|29||||"
>
x = _M.dssr.pairs[9]
select within(@x)
x = _M.dssr.pairs[9].nt1
select within(@x)
x = _M.dssr.pairs[9].nt2
select within(@x)
>
> What is the proper syntax to select any one of these"
>
> Thanks,
>
> PM
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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