Tom, Wanted to alert you to a couple of functions in chimera.misc that will be in the next _production_ release:

getAtoms(atomContainer) returns a list of atoms from various things (or lists of things) that can contain atoms, such as residues, sequences, molecules

atomSearchTree(atomContainer, sepVal=5.0) returns a adaptive search tree of the atoms in the atomContainer (ala arg to getAtoms()). CGLutil.AdaptiveTree has docs for these trees. Typically searched with the 'searchTree' method.

--Eric

On Mar 23, 2005, at 11:37 AM, Thomas Goddard wrote:

Hi Grant,

Below is some Python code that will create pseudobonds between all pairs of selected atoms from different molecules that are within 3 angstroms. It is quite slow for large sets of selected atoms. It could be made much faster but I chose to keep it simple.

   Tom

#

---

# Check all pairwise distances between selected atoms and connect those # atom pairs that are close by a pseudobond if the atoms belong to different # molecules. # # To run this use Tools / Programming / Idle to show the Python shell and # type # # >>> execfile('path-to-this-file.py') # # For large selected sets of atoms this will be slow. #

#

---

# def connect_close(dist):

from chimera import selection, distance
atoms = selection.currentAtoms()
atom_pairs = []
n = len(atoms)
for i1 in range(n):
    a1 = atoms[i1]
    for i2 in range(i1+1, n):
        a2 = atoms[i2]
        if a1.molecule != a2.molecule:
            if distance(a1.xformCoord().xyz, a2.xformCoord().xyz)  

<= dist: atom_pairs.append((a1,a2)) print len(atom_pairs), 'atom pairs'

from chimera import PseudoBondGroup, PseudoBondMgr_mgr, PseudoBond
pg = PseudoBondMgr_mgr().newPseudoBondGroup('close contacts')
bonds = []
for a1, a2 in atom_pairs:
    bonds.append(pg.newPseudoBond(a1, a2))

import chimera
chimera.openModels.add([pg])

selection.setCurrent(bonds)

#

---

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