#1183 Support monomer templates import from KET-format (#1335)

epam · Oct 17, 2023 · eb6c27a · eb6c27a
1 parent 94bce83
commit eb6c27a
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Showing 16 changed files with 1,871 additions and 3 deletions.
diff --git a/api/tests/integration/ref/formats/ket_to_mol.py.out b/api/tests/integration/ref/formats/ket_to_mol.py.out
@@ -1,4 +1,10 @@
 *** KET to MOL ***
+chem.ket:SUCCEED
+cysteine.ket:SUCCEED
+dala.ket:SUCCEED
+dcysteine.ket:SUCCEED
+dthymine.ket:SUCCEED
 suplabel.ket:SUCCEED
+thymine.ket:SUCCEED
 empty_apid.ket:SUCCEED
 ket-reaction-arrow.ket:SUCCEED
diff --git a/api/tests/integration/tests/formats/ket_to_mol.py b/api/tests/integration/tests/formats/ket_to_mol.py
@@ -24,11 +24,22 @@ def find_diff(a, b):
 ref_path = joinPathPy("ref/", __file__)
 root_rea = joinPathPy("reactions/", __file__)
 
-files = ["suplabel"]
+files = [
+    "suplabel",
+    "cysteine",
+    "dcysteine",
+    "thymine",
+    "dthymine",
+    "dala",
+    "chem",
+]
 
 files.sort()
 for filename in files:
     mol = indigo.loadMoleculeFromFile(os.path.join(root, filename + ".ket"))
+    # with open(os.path.join(ref_path, filename) + ".mol", "w") as file:
+    #     file.write(mol.molfile())
+
     with open(os.path.join(ref_path, filename) + ".mol", "r") as file:
         ket_ref = file.read()
     ket = mol.molfile()

diff --git a/api/tests/integration/tests/formats/molecules/chem.ket b/api/tests/integration/tests/formats/molecules/chem.ket
@@ -0,0 +1,183 @@
+{
+    "root": {
+        "nodes": [],
+        "templates": [
+            {
+                "$ref": "monomerTemplate-cch_3"
+            }
+        ]
+    },
+    "monomerTemplate-cch_3": {
+        "type": "monomerTemplate",
+        "id": "cch_3",
+        "class": "Chem",
+        "classHELM": "CHEM",
+        "alias": "cch",
+        "attachmentPoints": [
+            {
+                "type": "right",
+                "label": "R2",
+                "attachmentAtom": 8,
+                "leavingGroup": {
+                    "atoms": [
+                        1
+                    ]
+                }
+            },
+            {
+                "type": "side",
+                "label": "R3",
+                "attachmentAtom": 6,
+                "leavingGroup": {
+                    "atoms": [
+                        2
+                    ]
+                }
+            },
+            {
+                "type": "side",
+                "label": "R5",
+                "attachmentAtom": 3,
+                "leavingGroup": {
+                    "atoms": [
+                        0
+                    ]
+                }
+            }
+        ],
+        "atoms": [
+            {
+                "label": "H",
+                "location": [
+                    9.201199531555176,
+                    -7.158699989318848,
+                    0.0
+                ]
+            },
+            {
+                "label": "H",
+                "location": [
+                    8.374699592590332,
+                    -7.985400199890137,
+                    0.0
+                ]
+            },
+            {
+                "label": "O",
+                "location": [
+                    10.02810001373291,
+                    -7.985400199890137,
+                    0.0
+                ]
+            },
+            {
+                "label": "S",
+                "location": [
+                    9.718199729919434,
+                    -6.737199783325195,
+                    0.0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    9.194899559020996,
+                    -7.6427001953125,
+                    0.0
+                ],
+                "stereoLabel": "abs"
+            },
+            {
+                "label": "O",
+                "location": [
+                    9.698399543762207,
+                    -8.580300331115723,
+                    0.0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    9.698399543762207,
+                    -7.97629976272583,
+                    0.0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    9.194899559020996,
+                    -7.03879976272583,
+                    0.0
+                ]
+            },
+            {
+                "label": "N",
+                "location": [
+                    8.704099655151368,
+                    -7.994699954986572,
+                    0.0
+                ]
+            }
+        ],
+        "bonds": [
+            {
+                "type": 1,
+                "atoms": [
+                    3,
+                    0
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    6,
+                    2
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    8,
+                    1
+                ]
+            },
+            {
+                "type": 2,
+                "atoms": [
+                    6,
+                    5
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    4,
+                    7
+                ],
+                "stereo": 1
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    7,
+                    3
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    4,
+                    6
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    8,
+                    4
+                ]
+            }
+        ]
+    }
+}
diff --git a/api/tests/integration/tests/formats/molecules/chem.mol b/api/tests/integration/tests/formats/molecules/chem.mol
@@ -37,7 +37,7 @@ M  V30 2 SUP 2 ATOMS=(1 3) XBONDS=(1 2) LABEL=OH CSTATE=(4 2 -0.825 0 0) -
 M  V30 CLASS=LGRP
 M  V30 3 SUP 3 ATOMS=(1 1) XBONDS=(1 1) LABEL=H CSTATE=(4 1 0 -0.8267 0) -
 M  V30 CLASS=LGRP
-M  V30 4 SUP 4 ATOMS=(6 4 5 6 7 8 9) XBONDS=(3 1 2 3) LABEL=Cys CSTATE=(4 3 -
+M  V30 4 SUP 4 ATOMS=(6 4 5 6 7 8 9) XBONDS=(3 1 2 3) LABEL=cch CSTATE=(4 3 -
 M  V30 -0.8265 0 0) CSTATE=(4 2 0.825 0 0) CSTATE=(4 1 0 0.8267 0) CLASS=AA -
 M  V30 SAP=(3 9 2 Br) SAP=(3 7 3 Cx) SAP=(3 4 1 Ex)
 M  V30 END SGROUP