Class ReactantMolecule

Create an instance.

Parameters:

• molecule (schrodinger.structure._Molecule) - reactant molecule to be extracted from the reactants structure

Overrides: object.__init__

Set the two lists of reactive indicies attributes using the provided list of original reactive indicies

Parameters:

• reactive_inds_orig (list) - original reactive indicies for this reactant molecule

Return the new to orig atom reordering map for this molecule extended by that of the other molecule by offsetting the keys of the map of the other molecule.

Parameters:

• other_molecule (schrodinger.structure._Molecule) - molecule whose new to orig atom reordering map will be combined with that of the current molecule

Returns: dict

final_map, the combined new to original atom reordering maps of this molecule and the other molecule

Add a temporary hydrogen to the reactive atom of this molecule to act as a bond handle for performing the reaction. All traces of this temporary hydrogen will be removed from this instance once the reactions are complete. Note that the family of functions that handles the temporary hydrogens are put in place so that all reaction channels can be handled just like the bond-bond double displacement type, i.e. the association and single displacement types then become nothing more than double displacement with a fake hydrogen.

React this molecule with the provided other molecule according to their reactive indicies and return the product object.

Parameters:

• other_molecule (ReactantMolecule) - the input molecule that this molecule will react with
• reverse (bool) - specifies to reverse the order of reactive indicies for the other molecule

Returns: Products

Dissociate this molecule according to its reactive indicies.

Parameters:

• dissociation_bond_length (float) - final bond length to use for dissociative reaction channels

Returns: Products