Re: [Chimera-users] Zones to create inspector list of "contacts"

23 Mar 2005

      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)

# ----------------------------------------------------------------------------
#
connect_close(3)

Re: [Chimera-users] Zones to create inspector list of "contacts"

Thomas Goddard