LocateAtomsInSpatialProximity

How can I identify atoms in a certain spatial proximity in a fast way?

Identifying atoms in a certain spatial proximity can be done with the help of BALL's HashGridBox3.

C++

#include <BALL/DATATYPE/hashGrid.h>
#include <BALL/STRUCTURE/geometricProperties.h>

#include <BALL/MATHS/vector3.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/atom.h>
using namespace BALL;


//  create and fill a grid with spacing 1.5 Angstroem containing the protein  

// create a bounding box including the proteins in the System S
BoundingBoxProcessor bp;
S.apply(bp);
	
Vector3 upper = bp.getUpper();
Vector3 lower = bp.getLower();
	
// create a grid with spacing 1.5\AA storing atom pointers limited to the bounding box
HashGrid3<Atom*> grid(lower, upper - lower, 1.5);
...

   // insert all atom pointers into the grid according to the atom positions
   grid.insert(atomN->getPosition(), atomN);

...
	
//   now get all neighbouring atoms within a distance of 1.5\AA of atom B
	
// get the box containing atom B
HashGridBox3<Atom*>* box = grid.getBox(atomB->getPosition());

// and iterate over all neighbouring boxes
for(HashGridBox3<Atom*>::BoxIterator bit = box->beginBox(); +bit; ++bit) 
{
    HashGridBox3<Atom*>::DataIterator data_it;
    for (data_it = bit->beginData(); +data_it; ++data_it)
    {
        if((*data_it)->getDistance(*atomB) <= 1.5) 
        {
            // now do something interesting
            std::cout << (*data_it)->getPosition() << std::endl;
        }
    }
}

Python

Please note that this interface is available in version 1.4!

from BALL import *

# define the HashGrid spacing
threshold = 5.
threshold_sq = threshold*threshold

# get a system
S = getSystems()[0]

# create a bounding box including the proteins in the System S
bbp = BoundingBoxProcessor()
S.apply(bbp)

# create a grid with spacing 1.5\AA storing atom pointers limited to the bounding box
grid = AtomHashGrid3(bbp.getLower()-Vector3(threshold), bbp.getUpper()-bbp.getLower()+Vector3(threshold), threshold)

# insert all aminoacid atoms into the grid according to the atom positions
for a in atoms(S):
  if ((not a.getResidue().isAminoAcid())):
    continue
  grid.insert(a.getPosition(), a)

# consider a special atom a
a = ...

# get the box containing atom a
box = grid.getBox(a.getPosition())

# and iterate over all neighbouring boxes
for neighbor_box in box.iterboxes():
    for a2 in neighbor_box.iterdata():
       # now do something interesting
       print a2.getPosition()

If you want to run the script without BALLView replace

S = getSystems()[0]

with

path = Path()
pdbfile = PDBFile(path.find("structures/bpti.pdb"))

S = System()
pdbfile.read(S)