class_docstr: Generate molecule conformers.
  
  Notes
  -----
  Procedure
  1. Generate a pool of conformers.
  2. Minimize conformers.
  3. Prune conformers using an RMSD threshold.
  
  Note that pruning is done _after_ minimization, which differs from the
  protocol described in the references [1]_ [2]_.
  
  References
  ----------
  .. [1] http://rdkit.org/docs/GettingStartedInPython.html#working-with-3d-molecules
  .. [2] http://pubs.acs.org/doi/full/10.1021/ci2004658
  
  Notes
  -----
  This class requires RDKit to be installed.
docstr: Calculate conformer-conformer RMSD.
  
  Parameters
  ----------
  mol: rdkit.Chem.rdchem.Mol
      RDKit Mol object
  
  Returns
  -------
  rmsd: np.ndarray
      A conformer-conformer RMSD value. The shape is `(NumConformers, NumConformers)`
docstr_tok: ["Calculate","conformer-conformer","RMSD",".","Parameters","--","--","--","--","--","mol",":","rdkit.Chem.rdchem.Mol","RDKit","Mol","object","Returns","--","--","--","-","rmsd",":","np.ndarray","A","conformer-conformer","RMSD","value",".","The","shape","is","`","(","NumConformers",",","NumConformers",")","`"]
code: def get_conformer_rmsd(mol: RDKitMol) -> np.ndarray:
      """
      Calculate conformer-conformer RMSD.
  
      Parameters
      ----------
      mol: rdkit.Chem.rdchem.Mol
          RDKit Mol object
  
      Returns
      -------
      rmsd: np.ndarray
          A conformer-conformer RMSD value. The shape is `(NumConformers, NumConformers)`
      """
      try:
          from rdkit.Chem import AllChem
      except ModuleNotFoundError:
          raise ImportError(
              "This function requires RDKit to be installed."
          )
  
      rmsd = np.zeros(
          (mol.GetNumConformers(), mol.GetNumConformers()), dtype=float
      )
      for i, ref_conf in enumerate(mol.GetConformers()):
          for j, fit_conf in enumerate(mol.GetConformers()):
              if i >= j:
                  continue
              rmsd[i, j] = AllChem.GetBestRMS(
                  mol, mol, ref_conf.GetId(), fit_conf.GetId()
              )
              rmsd[j, i] = rmsd[i, j]
      return rmsd
  
file_path: deepchem/deepchem/utils/conformers.py
imports: import numpy
  from typing import Any, List, Optional
  from deepchem.utils.typing import RDKitMol
label_desc: Use image node_id 9 for calling the ConformerGenerator obj's underlying member method code with example usage: obj.get_conformer_rmsd(mol) and returns: rmsd