Get surrounding atoms using multiple components

[leguilv]

Hi there,

I've a simple case where I've loaded a PDB and a ligand, both separately, meaning they have their own components. Now want to be able to select atoms from the ligand, and get the atoms of the protein that are at a specific distance of the ligand.

Can't find a way to do that... I tried to create a selection from the ligand component and then use it to get protein atoms using getAtomSetWithinSelection but it does not work.

Any idea ?

[fredludlow]

I do something similar with this function, this returns an AtomSet given an array of ligand structures (queryStructures) and a protein structure targetStructure.

If you want to select particular ligand atoms it would need some adaptation but hopefully this gets you started:

function atomsNear (queryStructures, targetStructure, r) {
  var atomSet = targetStructure.getAtomSet(false)
  atomSet.clearAll(0)

  for (var i = 0; i < queryStructures.length; i++) {
    queryStructures[i].eachAtom(function (ap) {
      var atomArray = targetStructure.spatialHash.within(ap.x, ap.y, ap.z, r)
      for (var j = 0; j < atomArray.length; j++) {
        atomSet.set(atomArray[j])
      }
    })
  }

  return atomSet
}

Then atomSet.toSeleString() to get the selection string

[leguilv]

Hi fredludlow

That works like a charm, and I assume that there is not much way of doing such a component to component operation (I'm also thinking about contacts...) except for doing it by hand like you suggested :)

Thanks !!

[fredludlow]

You can concatenate two molecules (see the test/concat example code) http://nglviewer.org/ngl/?script=test/concat

Source here: https://github.com/arose/ngl/blob/master/examples/scripts/test/concat.js