schrodinger.application.matsci.enumeration.ElementAlchemist

Class ElementAlchemist

object --+ | Alchemist --+ | StructureAlchemist --+ | ElementAlchemist

An alchemist class that transmutes elements in a Structure @note: The new_items argument to the constructor for this class should have the following format: type new_items: list of tuple param new_items: Each item of the list is an (element, color) tuple, where element is the atomic symbol of the element to mutate to, and color is the new color for that atom in a form accepted by the _StructAtom.color property

Instance Methods

[hide private]

schrodinger.structure.Structure

performTransmutation(self, struct, index, item)
Perform a transmutation on a copy of struct at index.

fixHydrogens(self, struct, used)
Correct the number of hydrogens bonded to each transmuted atom

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__

Properties

[hide private]

Inherited from object: __class__

performTransmutation(self, struct, index, item)

Perform a transmutation on a copy of struct at index. It is very important that this happen on a copy of struct, not struct itself.

Parameters:

struct (schrodinger.structure.Structure) - The structure to transmute a copy of
index (int) - An index that tells what atom to transmute
item (tuple) - An (element, color) tuple, where element is the atomic symbol of the element to mutate to, and color is the new color for that atom in a form accepted by the _StructAtom.color property

Returns: schrodinger.structure.Structure

A COPY of struct with atom index transmuted

Overrides: Alchemist.performTransmutation

fixHydrogens(self, struct, used)

Correct the number of hydrogens bonded to each transmuted atom

Parameters:

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