1.1.1.2.1.1.1.4.8. TraverseOper

class molpher.swig_wrappers.core.TraverseOper(*args)

Bases: molpher.swig_wrappers.core.TreeOperation

Parameters:*args (ExplorationTree, TraverseCallback and MolpherMol (optional)) – the exploration tree and the callback to call. Optionally we can specify a morph which will define the root of the subtree to traverse. If no root is specified, then the source molecule is selected automatically.

A tree operation that can register a TraverseCallback and call its __call__() method on every molecule it encounters in the given subtree (defined by its root).

Warning

The callback to Python is realized using SWIG’s director feature, which makes it possible to keep the implementation concurrent and efficient. However, there is a problem:

If a reference to the MolpherMol instance is saved into a variable that outlives the call to the callback function, this reference then becomes invalid when the call is finished. Therefore, doing something like this:

var = None
class MyCallback(TraverseCallback):

    def __call__(self, morph):
        if var:
            print("Previous:", var.smiles)
        var = morph

callback = MyCallback()
traverse = TraverseOper(callback)
tree.runOperation(traverse)

will likely result in a segmentation fault upon a second call to the callback function, because the object referenced by var will no longer refer to valid memory. This is likely a result of SWIG freeing the pointer without taking the existing reference from Python into account.

One way to work around this is to just use the SMILES string to fetch the reference directly using the fetchMol() method:

var = morph.tree.fetchMol(morph.smiles)

__call__()

Run the attached callback on every molecule in the subtree with the given root.