Thanks so much, Bob! This seems to be working perfectly.
The only change I had to make is that rings.length is an array of zeros.
So I used rings.lines.count.
I was able to get His rings with
ringsh = {*}.find("SMARTS","c1cncn1", true)
and then make a single array
ringsall = rings + ringsh
Jmol continues to amaze and delight me!
Eric
On 2/10/15 5:47 PM, Robert Hanson wrote:
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 <[email protected]
<mailto:[email protected]>> 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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