#310 Support stereo CIP calculation in Ket format (#1054)

* ket commons

* CIP

* CIP

* CIP int cast

* tests split

* clang fix

* static fix

* stack fix

* stack fix

* stack fix

* python exception

* python exception

* python exception

* python exception

* stack fix

* python format fix

* test fix

* multiple CIP fixes

* wasm fix

* black py fix

* test fix

* comment removed

---------

Co-authored-by: Roman Porozhnetov <roman_porozhnetov@epam.com>

api/tests/integration/ref/basic/ketfile_stereo_desc.py.out

@@ -0,0 +1,41 @@
+1910.mol:SUCCEED
+C14_R_iso.mol:SUCCEED
+C14_R_iso_2.mol:SUCCEED
+CIP_issue.mol:SUCCEED
+P-9.5.2.2_ex3.mol:SUCCEED
+P-92.5.1.mol:SUCCEED
+P-92.5.3.mol:SUCCEED
+P-92.6.mol:SUCCEED
+P-92.6_2.mol:SUCCEED
+P-92.6_ex2.mol:SUCCEED
+P-92_2_1_1_3_ex1.mol:SUCCEED
+P-92_2_1_1_3_ex2.mol:SUCCEED
+P-92_2_1_2_1_ex1.mol:SUCCEED
+P-92_2_1_2_1_ex2.mol:SUCCEED
+P-92_2_1_2_1_ex3.mol:SUCCEED
+P-92_2_1_3_ex1.mol:SUCCEED
+P-92_2_1_3_ex2.mol:SUCCEED
+RS-symmetrical-structure.mol:SUCCEED
+RS.mol:SUCCEED
+RS_for_incorrect_valence.mol:SUCCEED
+S-R diff.mol:SUCCEED
+StereochemComplexTester_AllAbs.mol:SUCCEED
+all-trans-inositol.mol:SUCCEED
+atom_any.mol:SUCCEED
+cis.mol:SUCCEED
+different stereo 2.mol:SUCCEED
+different stereo 3.mol:SUCCEED
+different stereo 4.mol:SUCCEED
+different stereo 5.mol:SUCCEED
+different stereo.mol:SUCCEED
+ketcher.mol:SUCCEED
+stereo-different-ketcher-marvin.mol:SUCCEED
+stereo-different-ketcher-marvin2.mol:SUCCEED
+t4_R.mol:SUCCEED
+t4_R_iso.mol:SUCCEED
+t4_S.mol:SUCCEED
+t4_S_iso.mol:SUCCEED
+trans.mol:SUCCEED
+without_stereo_label.mol:SUCCEED
+crazystereo.rxn:SUCCEED
+

api/tests/integration/tests/basic/ketfile_stereo_desc.py

@@ -0,0 +1,99 @@
+import difflib
+import os
+import sys
+
+
+def find_diff(a, b):
+    return "\n".join(difflib.unified_diff(a.splitlines(), b.splitlines()))
+
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+
+from env_indigo import *
+
+threading.stack_size(2 * 1024 * 1024)
+
+
+def stereo_desc_test(py_file, out_queue):
+    str_res = ""
+    ref_path = joinPathPy("ref/", __file__)
+    root = joinPathPy("molecules/CIP/", __file__)
+
+    indigo = Indigo()
+    indigo.setOption("json-saving-pretty", True)
+
+    for filename in sorted(os.listdir(root)):
+        ketfile = joinPathPy(
+            os.path.join(ref_path, filename[:-4] + ".ket"), __file__
+        )
+        mol = indigo.loadMoleculeFromFile(os.path.join(root, filename))
+        with open(ketfile, "r") as file:
+            ket_ref = file.read()
+        mol_json_no_cip = mol.json()
+        indigo.setOption("json-saving-add-stereo-desc", True)
+        mol_json_cip = mol.json()
+        diff = find_diff(ket_ref, mol_json_cip)
+        if not diff:
+            diff = find_diff(mol_json_no_cip, mol_json_cip)
+            indigo.setOption("json-saving-add-stereo-desc", False)
+            mol = indigo.loadMoleculeFromFile(
+                os.path.join(root, filename)
+            )  # reload to reset CIP
+            if diff:
+                diff = find_diff(mol.json(), mol_json_no_cip)
+                if diff:
+                    str_res += (
+                        "mismatch: json-saving-add-stereo-desc = false:\n"
+                    )
+                else:
+                    # check conversion
+                    indigo.setOption("molfile-saving-add-stereo-desc", True)
+                    mol_cip = indigo.loadMolecule(
+                        mol.molfile()
+                    )  # mol_cip should contain CIP as properties of atoms and bonds
+                    diff = find_diff(
+                        mol_cip.json(), mol_json_cip
+                    )  # check if molecule has CIP
+                    if diff:
+                        str_res += "mismatch: molfile loader doesn't convert CIP SGroups:\n"
+                    else:
+                        str_res += filename + ":SUCCEED\n"
+                        continue
+            str_res += filename + ":FAILED\n"
+            str_res += diff + "\n"
+
+    indigo.setOption("ignore-stereochemistry-errors", "true")
+    filename = "crazystereo.rxn"
+
+    rxn = indigo.loadReactionFromFile(
+        os.path.join(joinPathPy("reactions/", __file__), filename)
+    )
+
+    ketfile = joinPathPy(os.path.join(ref_path, "crazystereo.ket"), __file__)
+    with open(ketfile, "r") as file:
+        ket_ref = file.read()
+        diff = find_diff(ket_ref, rxn.json())
+        if not diff:
+            str_res += filename + ":SUCCEED\n"
+        else:
+            str_res += filename + ":FAILED\n"
+            str_res += diff + "\n"
+    out_queue.put(str_res)
+
+
+if isJython():
+    from Queue import Queue
+else:
+    from queue import Queue
+
+th_queue = Queue()
+test_thread = threading.Thread(
+    target=stereo_desc_test, args=(os.path.abspath(__file__), th_queue)
+)
+test_thread.start()
+test_thread.join()
+print(th_queue.get())