gflownet.utils.molecule.conformer_base
======================================

.. py:module:: gflownet.utils.molecule.conformer_base


Attributes
----------

.. autoapisummary::

   gflownet.utils.molecule.conformer_base.rmol


Classes
-------

.. autoapisummary::

   gflownet.utils.molecule.conformer_base.ConformerBase


Functions
---------

.. autoapisummary::

   gflownet.utils.molecule.conformer_base.get_torsion_angles_atoms_list
   gflownet.utils.molecule.conformer_base.get_torsion_angles_values
   gflownet.utils.molecule.conformer_base.get_all_torsion_angles
   gflownet.utils.molecule.conformer_base.get_dummy_ad_atom_positions
   gflownet.utils.molecule.conformer_base.get_dummy_ad_conf_base


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

.. py:function:: get_torsion_angles_atoms_list(mol)

.. py:function:: get_torsion_angles_values(conf, torsion_angles_atoms_list)

.. py:function:: get_all_torsion_angles(mol, conf)

.. py:function:: get_dummy_ad_atom_positions()

.. py:function:: get_dummy_ad_conf_base()

.. py:class:: ConformerBase(atom_positions, smiles, freely_rotatable_tas=None)

   :param atom_positions: numpy.ndarray of shape [num_atoms, 3] of dtype float64


   .. py:attribute:: smiles


   .. py:attribute:: rdk_mol


   .. py:attribute:: rdk_conf


   .. py:attribute:: freely_rotatable_tas
      :value: None



   .. py:method:: __deepcopy__(memo)


   .. py:method:: get_mol_from_smiles(smiles)

      Create RDKit molecule from SMILES string
      :param smiles: python string
      :returns: rdkit.Chem.rdchem.Mol object



   .. py:method:: embed_mol_and_get_conformer(mol, extra_opt=False)

      Embed RDkit mol with a conformer and return the RDKit conformer object
      (which is synchronized with the RDKit molecule object)
      :param mol: rdkit.Chem.rdchem.Mol object defining the molecule
      :param extre_opt: bool, if True, an additional optimisation of the conformer will be performed



   .. py:method:: set_atom_positions(atom_positions)

      Set atom positions of the self.rdk_conf to the input atom_positions values
      :param atom_positions: 2d numpy array of shape [num atoms, 3] with new atom positions



   .. py:method:: get_atom_positions()

      :returns: numpy array of atom positions of shape [num_atoms, 3]



   .. py:method:: get_atomic_numbers()

      Get atomic numbers of the atoms as 1d numpy array
      :returns: numpy array of atomic numbers of shape [num_atoms,]



   .. py:method:: get_n_atoms()


   .. py:method:: set_torsion_angle(torsion_angle, value)


   .. py:method:: get_all_torsion_angles()

      :returns: a dict of all tostion angles in the molecule with their values



   .. py:method:: get_freely_rotatable_tas_values()

      :returns: a list of values of self.freely_rotatable_tas



   .. py:method:: randomize_freely_rotatable_tas()

      Uniformly randomize torsion angles defined by self.freely_rotatable_tas



   .. py:method:: increment_torsion_angle(torsion_angle, increment)

      :param torsion_angle: tuple of 4 integers defining the torsion angle
      :param increment: a float value of the increment of the angle (in radians)



.. py:data:: rmol