schrodinger.application.matsci.etatoggle module¶

Utilities for toggle eta style.

class schrodinger.application.matsci.etatoggle.Maker(struct)¶

Bases: object

Base class for classes that change Eta complex bonding

__init__(struct)¶

Create a Maker instance

Parameters:	struct (`schrodinger.structure.Structure`) – The structure to operate on

class schrodinger.application.matsci.etatoggle.PerAtomMaker(dummies, *args, **kwargs)¶

Class that changes Eta bonding to have one bond per atom

__init__(dummies, *args, **kwargs)¶

Create a PerAtomMaker instance

Parameters:	dummies (list) – The atom objects of each dummy atom in the structure

convert()¶

Convert the complex to have one bond per atom

Raises:	ValueError – Too many metal-to-ligand bonds

class schrodinger.application.matsci.etatoggle.DummyMaker(struct)¶

Class that changes Eta bonding to have one dummy bond per Eta ligand

__init__(struct)¶

Create a Maker instance

Parameters:	struct (`schrodinger.structure.Structure`) – The structure to operate on

findEtaGroups(dummy_style=True)¶

Find each Eta group

We define an Eta group as 2 or more atoms that are bound together and also bound to a metal atom

Parameters:	dummy_style (bool) – Whether to also find eta ligands that are bound by bonding all the ligand atoms to a dummy and then the dummy to the metal. If False, only those ligands that have all eta atoms bound directly to the metal will be found.
Note:	The function assumes that the self.metals property is set to a list of metal atoms and it creates the self.eta_groups and self_all_eta_atoms properties

schrodinger.application.matsci.etatoggle.get_dummy_atoms(struct)¶

Find all dummy atoms in the structure

Parameters:	struct (`schrodinger.structure.Structure`) – The structure containing the dummy atoms
Return type:	list
Returns:	The atom objects of the dummy atoms in the structure

schrodinger.application.matsci.etatoggle.toggle_structure(struct)¶

Toggle the Eta bonding between dummy style and per atom style

Parameters:	struct (`schrodinger.structure.Structure`) – The structure to toggle the style of