This is what SMARTS searching does.
rings = {*}.find("SMARTS","c1ccccc1", true) // an array of atom sets
centers = rings.xyz // centers of those atom sets; still an array
print centers[1]
print centers[2]
...
On Tue, Feb 10, 2015 at 3:59 PM, Eric Martz <ema...@microbio.umass.edu>
wrote:
> I would like to generate a list of distances between the centers of
> aromatic rings, identifying the pair of residues that each distance
> represents.
>
> I believe the following reports the center of the 6-carbon ring of Tyr3
> in 1pgb:
>
>
$ load =1pgb
IMMUNOGLOBULIN BINDING PROTEIN 23-NOV-93 1PGB
TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING
DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR
found biomolecule 1: A
// all rings:
$ rings = {*}.find("SMARTS","c1ccccc1", true)
$ print rings.xyz
{13.123668 14.505501 26.274666}
{7.7295 15.019166 20.959}
{1.7821666 16.910334 17.072166}
{7.07 8.775001 16.5255}
{15.482834 9.6655 22.505835}
{11.408334 10.879166 21.280832}
// just tyr
$ rings = {tyr}.find("SMARTS","c1ccccc1", true)
$ print rings.xyz
{13.123668 14.505501 26.274666}
{1.7821666 16.910334 17.072166}
{15.482834 9.6655 22.505835}
// with labels
for (var i = 1; i <= rings.length; i++) {
print (rings[i])[1].label("%n%r") + " " + rings[i].xyz
}
TYR3 {13.123668 14.505501 26.274666}
TYR33 {1.7821666 16.910334 17.072166}
TYR45 {15.482834 9.6655 22.505835}
If I had such lists, how would I generate a list of distances between
> the ring-centers, being able to identify the two residues for each
> distance?
>
>
// use .xyz.distance (average position...distance....)
for (var i = 1; i <= rings.length; i++) {
for (var j = i + 1; j <= rings.length; j++) {
print (rings[i])[1].label("%n%r") + "\t" + (rings[j])[1].label("%n%r")
+ "\t" + rings[i].xyz.distance(rings[j].xyz).format("%6.3f")
}
}
TYR3 TYR33 14.802
TYR3 TYR45 6.572
TYR33 TYR45 16.423
:)
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