schrodinger.application.matsci.nano.tools module¶

Tools for periodic systems (crystals, slabs) manipulation.

schrodinger.application.matsci.nano.tools.origin_shift_maestro(struct, atom_index, shift_to_origin=True)¶

Shift origin of the structure to origin or center.

Parameters

struct (schrodinger.structure.Structure) – Input structure
atom_index (int) – Atom index to shift to
shift_to_origin (bool) – If True, shift to origin, if False shift to middle of the cell ([0.5, 0.5, 0.5])

schrodinger.application.matsci.nano.tools.find_polygon_vertices(structures)¶

Find the vertices for a regular polygon with N number of structures placed at each vertex.

Parameters: structures (list) – The structures to combine into a single structure
Return type: list
Returns: Each item is a numpy array of XYZ coordinates of a polygon vertex

schrodinger.application.matsci.nano.tools.polygonize_structures(structures)¶

Combine the individual component structures into an overall structure where each molecule is placed at the vertices of a polygon for better visualization.

Parameters: structures (list) – The structures to combine into a single structure
Return type: structure.Structure
Returns: The combined structure with all component structures placed