Getting nodes

Often you need to work on specific nodes, pass them to other functions, or perform more precise selections than the built-in actions provide (see Selecting nodes). For that, you can use the getNodes functions, which return a node indexer (SBNodeIndexer, essentially a list-like collection of nodes) based on a Node Specification Language (NSL) expression:

• SAMSON.getNodes from the SAMSON interface, returns a node indexer for the active document.

• SBNode.getNodes applied to a specific node, returns a node indexer with nodes descending from this node.

See also

User Guide: Node types

User Guide: Node Specification Language

Getting nodes using NSL

# get a node indexer with all hydrogens in the active document
nodeIndexer1 = SAMSON.getNodes('Hydrogen')
# add in this node indexer all carbons in the active document
SAMSON.getNodes(nodeIndexer1, 'Carbon')

# get a node indexer with all hydrogens bonded to oxygens in the active document
nodeIndexer2 = SAMSON.getNodes('H linking O')

# get a node indexer with all nodes named "CA" that are within 5 angstrom of any sulfur atom
# in the active document
nodeIndexer3 = SAMSON.getNodes('"CA" within 5A of S')

# get a node indexer with all molecule nodes in the active document
nodeIndexer4 = SAMSON.getNodes('node.type molecule')

if len(nodeIndexer4):
    # get a node indexer with all atoms within the first molecule
    nodeIndexer5 = nodeIndexer4[0].getNodes('node.type atom')

# populate a node indexer with all residues within the molecules from nodeIndexer4
nodeIndexer6 = SBNodeIndexer()
for node in nodeIndexer4:
    node.getNodes(nodeIndexer6, 'node.type residue')

You can iterate over a node indexer much like a Python list:

# get a node indexer with all atoms in the active document
nodeIndexer = SAMSON.getNodes('node.type atom')

# print the size of the node indexer
print(len(nodeIndexer))

if len(nodeIndexer):
    # prints information on the last node (atom) in the node indexer
    print(nodeIndexer[-1])

for node in nodeIndexer:
    # do something, e.g. print info on the node
    print(node)

# usage of list comprehensions:
# construct a list of x-coordinates of atoms in nanometers
atomXCoords = [atom.getX().nm for atom in nodeIndexer]

You can delete or add a node from the indexer, or check if it is present in it:

# get a node indexer with all atoms in the active document
nodeIndexer = SAMSON.getNodes('node.type atom')

if len(nodeIndexer):
    # get the 1st atom from the node indexer
    atom = nodeIndexer[0]
    # remove the atom from the node indexer
    nodeIndexer.removeNode(atom)
    # check if the node indexer has the atom
    print(nodeIndexer.hasNode(atom))
    # add atom back to the node indexer
    nodeIndexer.addNode(atom)

The next example shows a simple use of the NSL, node indexers, and how to make changes to node attributes.

# get a node indexer with all molecule nodes in the active document
moleculeIndexer = SAMSON.getNodes('node.type molecule')

if len(moleculeIndexer):
    # print info on the 1st molecule
    print(moleculeIndexer[0])
    # get atoms that are in this molecule
    atomIndexer = moleculeIndexer[0].getNodes('node.type atom')

    if len(atomIndexer):
        # get the 1st atom in node indexer
        atom = atomIndexer[0]
        # print the atom type
        print(atom.type)
        # print the atom information
        print(atom)
        # return the atom's atomic weight
        print(atom.atomicWeight)
        # select the atom: it will be highlighted
        atom.selectionFlag = True
        # get the atom's position
        atom.getPosition()
        # shift the position of the chosen atom by 100 picometers (pm) in x-direction
        atom.setX(atom.getX() + SBQuantity.pm(100))