schrodinger.application.matsci.nano.util module

Utility functions for nanostructures.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.nano.util.get_atomic_element_symbols()

Return a set of symbols of atomic elements in the periodic table.

Return type:set of strs
Returns:symbols, set of atomic elements
schrodinger.application.matsci.nano.util.get_rotated_vector(invector, angle, length=None, axis=None)

Return a rotated vector of a given length.

Parameters:
  • invector (numpy.array) – input vector
  • angle (float) – rotation angle in radians
  • length (float) – length of output vector
  • axis (numpy.array) – rotation axis
Return type:

numpy.array

Returns:

outvector, output vector

schrodinger.application.matsci.nano.util.rotate_double_bonds(structure)

For a six-membered ring rotate the three double bonds, i.e. the first double bond will be moved from the atom pair (1, 2) to the atom pair (2, 3).

Parameters:structure (schrodinger.structure.Structure) – structure
schrodinger.application.matsci.nano.util.get_inversion_index(index)

Return the atom index obtained by applying an inversion operation to the given index in a given hexagon.

Parameters:index (int) – atom index of an atom in a honeycomb cell
Return type:invindex, int
Returns:invindex, atom index after inversion