pyvibdmc.simulation_utilities.xyz_npy
=====================================

.. py:module:: pyvibdmc.simulation_utilities.xyz_npy


Classes
-------

.. autoapisummary::

   pyvibdmc.simulation_utilities.xyz_npy.XYZNPY


Module Contents
---------------

.. py:class:: XYZNPY

   Handler of xyz <-> npy conversion, like a personal version of openBabel.


   .. py:method:: extract_xyz(file_name, num_atoms)
      :staticmethod:


      Extracts the coordinates from an xyz file and returns it as an np array of dimension nxmx3,
      where n = number of geometries, m = number of atoms, and 3 = cartesian coordinates

      :param file_name: Name of the .xyz file, including extension
      :type file_name: str
      :param num_atoms: Number of atoms in molecule.
      :type num_atoms: int
      :return: nxmx3 numpy array of coordinates



   .. py:method:: write_xyz(coords, fname, atm_strings, cmt=None)
      :staticmethod:


      Writes a numpy array of x,y,z coordinates to a .xyz file

      :param fname: name of xyz file
      :param coords: numpy array, either mx3 or nxmx3, where n = number of geometries and m = number of atoms
      :param atm_strings: list of strings that correspond to the atom type e.g. ["H","H","O"]
      :return: np.ndarray