Class Dimer

Create a Dimer object

Parameters:

• stindex (int) - The index of the structure this dimer comes from
• mol1 (int) - The molecule number in the structure of the first molecule in this dimer
• mol2 (int) - The molecule number in the structure of the second molecule in this dimer
• neighbor_info (Neighbor) - The Neighbor information for this dimer
• pbc (schrodinger.infra.structure.PBC) - The PBC object to use for this dimer, if any

Overrides: object.__init__

Check whether this dimer meets the species criterium - sets the meets_species_criterium property.

Parameters:

• crit_species (SpeciesData) - The species the criterium applies to
• crit (str) - The criterium - should be one of the constants NO_MOLS, ONE_ONLY_MOL, AT_LEAST_ONE_MOL, TWO_MOLS
• species (dict) - The dictionary containing information for all species. Keys are unique SMILES strings for a species, values are SpeciesData for the species with that SMILES string.

Create the dimer structure

Parameters:

• struct (schrodinger.structure.Structure) - The structure containing the dimer molecules

Returns: schrodinger.structure.Structure

The structure object for the dimer

Get a structure that is the dimer surrounded by all nearest neighbor molecules. The dimer and all molecules are positioned at their nearest neighbor images to the original position of the first molecule in the dimer.

Parameters:

• struct (schrodinger.structure.Structure) - The structure containing this Dimer and all neighbor molecules
• cell (schrodinger.infra.structure.DistanceCell) - The DistanceCell to use when finding nearest neighbors. If not given, will be calculated based on struct and distance. Either cell or distance must be given.
• distance (float) - The distance to use when creating a new distance cell if needed. Either cell or distance must be given.

Returns: schrodinger.structure.Structure

The structure of the dimer with nearest neighbor molecules. The dimer molecules appear first in the cluster.

Create a dimer structure for a pair of molecules that takes into account the periodic boundary condition.

If | represents a cell boundary, and .... represents some long distance, imagine two molecules X and Y on opposite sides of the cell.

Y|X....Y|X

We need to extract coordinates for Y that represent the Y|X case, not the X....Y case.

Parameters:

• struct (schrodinger.structure.Structure) - The structure containing the dimer molecules

Returns: schrodinger.structure.Structure

The structure object for the dimer

Create a dimer structure for a pair of molecules in a non-periodic system

Parameters:

• struct (schrodinger.structure.Structure) - The structure containing the dimer molecules

Returns: schrodinger.structure.Structure

The structure object for the dimer