Select atoms and bonds by location#

This example combines what is written in the Selecting nodes section and demonstrates how to select atoms and bonds based on their location.

Example: select atoms and bonds by location#
# get an indexer of all atoms in the active document
# here we use SAMSON Node Specification Language
atom_indexer = SAMSON.getNodes('node.type atom')

# two planes
x_min = SBQuantity.angstrom(0.0)
x_max = SBQuantity.angstrom(5.0)

# an indexer in which we will be adding the desired nodes
atom_selection_indexer = SBNodeIndexer()

# a loop over an indexer
for atom in atom_indexer:
    x_coord = atom.getX()
    # check whether the atom lies in between the desired planes
    if x_coord >= x_min and x_coord <= x_max:
        # add the atom to the indexer

# add bonds between the atoms to the selection
bond_selection_indexer = SBNodeIndexer()
for atom in atom_selection_indexer:
    # go through all the bonds of an atom
    for bond in atom.getBondList():
        # skip bonds that are already in the indexer
        if bond in bond_selection_indexer: continue
        # check if the opposite atom should also be selected
        if bond.getOppositeAtom(atom) in atom_selection_indexer:

# make the operation undoable
SAMSON.beginHolding('Select atoms')

# clear the current selection in the active document

# select nodes by changing their selectionFlag
for node in atom_selection_indexer:
    node.selectionFlag = True

for node in bond_selection_indexer:
    node.selectionFlag = True

# stop the undoable operation