schrodinger.application.matsci.enumeration.VacancyAlchemist

Class VacancyAlchemist

An alchemist class that deletes atoms in a Structure and the hydrogens they are bound to @note: The new_items argument to the constructor for this class should have the following format: type new_items: list param new_items: Should be [None]

Instance Methods

[hide private]

schrodinger.structure.Structure

performTransmutation(self, struct, index, item)
Mark atom index for deletion, and also mark all the hydrogen atoms it is attached to.

deleteAtoms(self, struct)
Delete all atoms marked for deletion

allTransmutationsCompleted(self, struct, used)
All transmutations have been performed on struct, write it out to a file if we are keeping this result

Inherited from StructureAlchemist: __init__, runTransmutations

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

DELETE_PROPERTY = 'b_matsci_impending_vacancy'

performTransmutation(self, struct, index, item)

Mark atom index for deletion, and also mark all the hydrogen atoms it is attached to. This will happen on a copy of the input structure.

Normally this method in parent classes actually changes the structure, but in this case, deleting atoms would mess up all the atom numbering for Alchemists down the line, so we only mark those atoms for later deletion.

Parameters:

struct (schrodinger.structure.Structure) - The structure to transmute a copy of
index (int) - An index that tells what atom to delete
item (None) - None - unused

Returns: schrodinger.structure.Structure

A COPY of struct with atom index and attached hydrogens marked for deletion.

Overrides: Alchemist.performTransmutation

deleteAtoms(self, struct)

Delete all atoms marked for deletion

Parameters:

struct (schrodinger.structure.Structure) - The structure object with the transmuted atoms

allTransmutationsCompleted(self, struct, used)

All transmutations have been performed on struct, write it out to a file if we are keeping this result

Parameters:

struct (schrodinger.structure.Structure) - The structure object with the transmuted atoms
used (list of int) - The atom indexes of the transmuted atoms

Overrides: Alchemist.allTransmutationsCompleted