From 2a4ffecbc09856aa3b4da91598b8fa146dd935e7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 16 Nov 2022 09:23:51 +0100
Subject: [PATCH] move doc of old stereo checks into own deprecated section

---
 .../alg/doc/stereochemistry_deprecated.rst    | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 modules/mol/alg/doc/stereochemistry_deprecated.rst

diff --git a/modules/mol/alg/doc/stereochemistry_deprecated.rst b/modules/mol/alg/doc/stereochemistry_deprecated.rst
new file mode 100644
index 000000000..3a4802a7a
--- /dev/null
+++ b/modules/mol/alg/doc/stereochemistry_deprecated.rst
@@ -0,0 +1,58 @@
+: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
-- 
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