#2412 - User can't correctly save (or make a layout) to RDF/RXN react…

…ion several products or with separate positioned molecules (#2717)
epam · Feb 18, 2025 · 9132b83 · 9132b83
1 parent 62e515e
commit 9132b83
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Showing 85 changed files with 17,029 additions and 1,283 deletions.
diff --git a/api/tests/integration/ref/formats/ket_to_ket.py.out b/api/tests/integration/ref/formats/ket_to_ket.py.out
@@ -6,3 +6,4 @@ ambiguous_monomer.ket mol loadQueryMolecule: SUCCEED
 monomer_shape.ket doc loadKetDocument: SUCCEED
 monomer_shape.ket mol loadMolecule: SUCCEED
 monomer_shape.ket mol loadQueryMolecule: SUCCEED
+multi_merge4.ket:SUCCEED
diff --git a/api/tests/integration/ref/formats/ket_to_rdf.py.out b/api/tests/integration/ref/formats/ket_to_rdf.py.out
@@ -1,6 +1,12 @@
 *** KET to RDF ***
 2404-metadata_detect.rdf:SUCCEED
 multi.rdf:SUCCEED
+multi_merge1.rdf:SUCCEED
+multi_merge2.rdf:SUCCEED
+multi_merge3.rdf:SUCCEED
+multi_merge4.rdf:SUCCEED
+multi_merge5.rdf:SUCCEED
+multi_merge6.rdf:SUCCEED
 pathway1.rdf:SUCCEED
 pathway10.rdf:SUCCEED
 pathway11.rdf:SUCCEED
@@ -13,3 +19,5 @@ pathway6.rdf:SUCCEED
 pathway7.rdf:SUCCEED
 pathway8.rdf:SUCCEED
 pathway9.rdf:SUCCEED
+pathway_merge1.rdf:SUCCEED
+pathway_merge2.rdf:SUCCEED
diff --git a/api/tests/integration/ref/formats/ket_to_rxn.py.out b/api/tests/integration/ref/formats/ket_to_rxn.py.out
@@ -0,0 +1,13 @@
+*** KET to RXN ***
+merge_test1.rxn:SUCCEED
+merge_test1a.rxn:SUCCEED
+merge_test2.rxn:SUCCEED
+merge_test2a.rxn:SUCCEED
+merge_test3.rxn:SUCCEED
+merge_test3a.rxn:SUCCEED
+merge_test4.rxn:SUCCEED
+merge_test5.rxn:SUCCEED
+merge_test6.rxn:SUCCEED
+merge_test7.rxn:SUCCEED
+merge_test8.rxn:SUCCEED
+merge_test9.rxn:SUCCEED
diff --git a/api/tests/integration/tests/formats/ket_to_ket.py b/api/tests/integration/tests/formats/ket_to_ket.py
@@ -22,6 +22,7 @@ def find_diff(a, b):
 
 root = joinPathPy("molecules/", __file__)
 ref_path = joinPathPy("ref/", __file__)
+root_rea = joinPathPy("reactions/", __file__)
 
 files = [
     "images",
@@ -73,3 +74,25 @@ def check_res(filename, format, ket_ref, ket):
             #     file.write(mol.json())
             ket = mol.json()
             check_res(filename, format + " " + loader.__name__, ket_ref, ket)
+
+files = [
+    "multi_merge4",
+]
+
+files.sort()
+for filename in files:
+    rea = indigo.loadReactionFromFile(
+        os.path.join(root_rea, filename + ".ket")
+    )
+
+    # with open(os.path.join(ref_path, filename) + ".ket", "w") as file:
+    #     file.write(rea.json())
+    with open(os.path.join(ref_path, filename) + ".ket", "r") as file:
+        ket_ref = file.read()
+    ket = rea.json()
+    diff = find_diff(ket_ref, ket)
+    if not diff:
+        print(filename + ".ket:SUCCEED")
+    else:
+        print(filename + ".ket:FAILED")
+        print(diff)
diff --git a/api/tests/integration/tests/formats/ket_to_rdf.py b/api/tests/integration/tests/formats/ket_to_rdf.py
@@ -39,6 +39,14 @@ def find_diff(a, b):
     "pathway10",
     "pathway11",
     "pathway12",
+    "pathway_merge1",
+    "pathway_merge2",
+    "multi_merge1",
+    "multi_merge2",
+    "multi_merge3",
+    "multi_merge4",
+    "multi_merge5",
+    "multi_merge6",
 ]
 
 files.sort()
@@ -64,7 +72,7 @@ def find_diff(a, b):
     rdf = buffer.toString()
 
     # with open(os.path.join(ref_path, filename) + ".rdf", "w") as file:
-    #     file.write(rdf)
+    #    file.write(rdf)
 
     with open(os.path.join(ref_path, filename) + ".rdf", "r") as file:
         rdf_ref = file.read()

diff --git a/api/tests/integration/tests/formats/ket_to_rxn.py b/api/tests/integration/tests/formats/ket_to_rxn.py
@@ -0,0 +1,56 @@
+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 Indigo, joinPathPy  # noqa
+
+indigo = Indigo()
+indigo.setOption("json-saving-pretty", True)
+indigo.setOption("ignore-stereochemistry-errors", True)
+indigo.setOption("molfile-saving-skip-date", True)
+
+print("*** KET to RXN ***")
+
+root = joinPathPy("reactions/", __file__)
+ref_path = joinPathPy("ref/", __file__)
+
+files = [
+    "merge_test1",
+    "merge_test1a",
+    "merge_test2",
+    "merge_test2a",
+    "merge_test3",
+    "merge_test3a",
+    "merge_test4",
+    "merge_test5",
+    "merge_test6",
+    "merge_test7",
+    "merge_test8",
+    "merge_test9",
+]
+
+files.sort()
+for filename in files:
+    rea = indigo.loadReactionFromFile(os.path.join(root, filename + ".ket"))
+
+    # with open(os.path.join(ref_path, filename) + ".rxn", "w") as file:
+    #     file.write(rea.rxnfile())
+    with open(os.path.join(ref_path, filename) + ".rxn", "r") as file:
+        rxn_ref = file.read()
+    rxn = rea.rxnfile()
+    diff = find_diff(rxn_ref, rxn)
+    if not diff:
+        print(filename + ".rxn:SUCCEED")
+    else:
+        print(filename + ".rxn:FAILED")
+        print(diff)
diff --git a/api/tests/integration/tests/formats/reactions/ket_retro_arrow.ket b/api/tests/integration/tests/formats/reactions/ket_retro_arrow.ket
@@ -31,34 +31,26 @@
         "type": "molecule",
         "atoms": [
             {
-                "label": "C",
-                "location": [
-                    1.366025,
-                    -0.75,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
+                "label": "O",
                 "location": [
-                    1.366025,
+                    5.232051,
                     0.25,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    0.5,
-                    0.75,
+                    6.098076,
+                    -0.25,
                     0.0
                 ]
             },
             {
-                "label": "N",
+                "label": "O",
                 "location": [
-                    2.232051,
-                    0.75,
+                    6.964102,
+                    0.25,
                     0.0
                 ]
             }
@@ -77,40 +69,41 @@
                     1,
                     2
                 ]
-            },
-            {
-                "type": 1,
-                "atoms": [
-                    1,
-                    3
-                ]
             }
         ]
     },
     "mol1": {
         "type": "molecule",
         "atoms": [
             {
-                "label": "O",
+                "label": "C",
                 "location": [
-                    5.232051,
+                    1.366025,
+                    -0.75,
+                    0.0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    1.366025,
                     0.25,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    6.098076,
-                    -0.25,
+                    0.5,
+                    0.75,
                     0.0
                 ]
             },
             {
-                "label": "O",
+                "label": "N",
                 "location": [
-                    6.964102,
-                    0.25,
+                    2.232051,
+                    0.75,
                     0.0
                 ]
             }
@@ -129,6 +122,13 @@
                     1,
                     2
                 ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    1,
+                    3
+                ]
             }
         ]
     }