move doc of old stereo checks into own deprecated section

modules/mol/alg/doc/stereochemistry_deprecated.rst

+:orphan:
+
+Stereochemistry (deprecated)
+================================================================================
+
+
+.. function:: CheckStructure(ent, \
+                             bond_table, \
+                             angle_table, \
+                             nonbonded_table, \
+                             bond_tolerance, \
+                             angle_tolerance)
+
+  Perform structural checks and filters the structure.
+
+  :param ent: Structure to check
+  :type ent: :class:`~ost.mol.EntityView`
+  :param bond_table: List of bond stereo chemical parameters obtained from
+    :class:`~ost.io.StereoChemicalParamsReader` or :func:`FillStereoChemicalParams`
+  :type bond_table: :class:`~ost.mol.alg.StereoChemicalParams`
+  :param angle_table: List of angle stereo chemical parameters obtained from
+    :class:`~ost.io.StereoChemicalParamsReader` or :func:`FillStereoChemicalParams`
+  :type angle_table: :class:`~ost.mol.alg.StereoChemicalParams`
+  :param nonbonded_table: Information about the clashing distances obtained from
+    :class:`~ost.io.StereoChemicalParamsReader` or :func:`FillClashingDistances`
+  :type nonbonded_table: :class:`~ost.mol.alg.ClashingDistances`
+  :param bond_tolerance: Tolerance in stddev for bonds
+  :type bond_tolerance: :class:`float`
+  :param angle_tolerance: Tolerance in stddev for angles
+  :type angle_tolerance: :class:`float`
+
+    
+.. class:: StereoChemicalProps(bond_table, angle_table, nonbonded_table)
+  
+  Object containing the stereo-chemical properties read form stereochmical_props.txt
+  file.
+
+  :param bond_table: Sets :attr:`bond_table`
+  :param angle_table: Sets :attr:`angle_table`
+  :param nonbonded_table: Sets :attr:`nonbonded_table`
+
+  .. attribute:: bond_table
+  
+    Object containing bond parameters
+    
+    :type: :class:`~ost.mol.alg.StereoChemicalParams`
+
+  .. attribute:: angle_table
+    
+    Object containing angle parameters
+    
+    :type: :class:`~ost.mol.alg.StereoChemicalParams`
+
+  .. attribute:: nonbonded_table
+    
+    Object containing clashing distances parameters
+    
+    :type: :class:`~ost.mol.alg.ClashingDistances`
\ No newline at end of file