Backmerge: #1449 No naturalAnalogShort in KET for basic aminoacids du…

…ring conversion MOLV3000 -> KET (#1457)
epam · Dec 27, 2023 · faa03d1 · faa03d1
1 parent 7b958a4
commit faa03d1
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Showing 10 changed files with 108 additions and 2 deletions.
diff --git a/api/tests/integration/tests/formats/ref/anacyclamide.ket b/api/tests/integration/tests/formats/ref/anacyclamide.ket
@@ -288,6 +288,7 @@
         "classHELM": "PEPTIDE",
         "alias": "Q",
         "name": "Gln",
+        "naturalAnalogShort": "Q",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -501,6 +502,7 @@
         "classHELM": "PEPTIDE",
         "alias": "S",
         "name": "Ser",
+        "naturalAnalogShort": "S",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -669,6 +671,7 @@
         "classHELM": "PEPTIDE",
         "alias": "T",
         "name": "Thr",
+        "naturalAnalogShort": "T",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -854,6 +857,7 @@
         "classHELM": "PEPTIDE",
         "alias": "P",
         "name": "Pro",
+        "naturalAnalogShort": "P",
         "attachmentPoints": [
             {
                 "attachmentAtom": 7,
@@ -1021,6 +1025,7 @@
         "classHELM": "PEPTIDE",
         "alias": "V",
         "name": "Val",
+        "naturalAnalogShort": "V",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1181,6 +1186,7 @@
         "classHELM": "PEPTIDE",
         "alias": "G",
         "name": "Gly",
+        "naturalAnalogShort": "G",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1294,6 +1300,7 @@
         "classHELM": "PEPTIDE",
         "alias": "W",
         "name": "Trp",
+        "naturalAnalogShort": "W",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1596,6 +1603,7 @@
         "classHELM": "PEPTIDE",
         "alias": "I",
         "name": "Ile",
+        "naturalAnalogShort": "I",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,

diff --git a/api/tests/integration/tests/formats/ref/apamine.ket b/api/tests/integration/tests/formats/ref/apamine.ket
@@ -590,6 +590,7 @@
         "classHELM": "PEPTIDE",
         "alias": "H",
         "name": "His",
+        "naturalAnalogShort": "H",
         "attachmentPoints": [
             {
                 "attachmentAtom": 5,
@@ -825,6 +826,7 @@
         "classHELM": "PEPTIDE",
         "alias": "Q",
         "name": "Gln",
+        "naturalAnalogShort": "Q",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1038,6 +1040,7 @@
         "classHELM": "PEPTIDE",
         "alias": "R",
         "name": "Arg",
+        "naturalAnalogShort": "R",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1281,6 +1284,7 @@
         "classHELM": "PEPTIDE",
         "alias": "A",
         "name": "Ala",
+        "naturalAnalogShort": "A",
         "attachmentPoints": [
             {
                 "attachmentAtom": 2,
@@ -1411,6 +1415,7 @@
         "classHELM": "PEPTIDE",
         "alias": "L",
         "name": "Leu",
+        "naturalAnalogShort": "L",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1586,6 +1591,7 @@
         "classHELM": "PEPTIDE",
         "alias": "T",
         "name": "Thr",
+        "naturalAnalogShort": "T",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1771,6 +1777,7 @@
         "classHELM": "PEPTIDE",
         "alias": "E",
         "name": "Glu",
+        "naturalAnalogShort": "E",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1984,6 +1991,7 @@
         "classHELM": "PEPTIDE",
         "alias": "P",
         "name": "Pro",
+        "naturalAnalogShort": "P",
         "attachmentPoints": [
             {
                 "attachmentAtom": 7,
@@ -2151,6 +2159,7 @@
         "classHELM": "PEPTIDE",
         "alias": "K",
         "name": "Lys",
+        "naturalAnalogShort": "K",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2364,6 +2373,7 @@
         "classHELM": "PEPTIDE",
         "alias": "N",
         "name": "Asn",
+        "naturalAnalogShort": "N",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2562,6 +2572,7 @@
         "classHELM": "PEPTIDE",
         "alias": "C",
         "name": "C",
+        "naturalAnalogShort": "C",
         "attachmentPoints": [
             {
                 "attachmentAtom": 4
@@ -2670,6 +2681,7 @@
         "classHELM": "PEPTIDE",
         "alias": "C",
         "name": "C",
+        "naturalAnalogShort": "C",
         "attachmentPoints": [
             {
                 "attachmentAtom": 4
@@ -2778,6 +2790,7 @@
         "classHELM": "PEPTIDE",
         "alias": "C",
         "name": "C",
+        "naturalAnalogShort": "C",
         "attachmentPoints": [
             {
                 "attachmentAtom": 4
@@ -2886,6 +2899,7 @@
         "classHELM": "PEPTIDE",
         "alias": "C",
         "name": "C",
+        "naturalAnalogShort": "C",
         "attachmentPoints": [
             {
                 "attachmentAtom": 4

diff --git a/api/tests/integration/tests/formats/ref/conjugate.ket b/api/tests/integration/tests/formats/ref/conjugate.ket
@@ -2231,6 +2231,7 @@
         "classHELM": "PEPTIDE",
         "alias": "D",
         "name": "Asp",
+        "naturalAnalogShort": "D",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2429,6 +2430,7 @@
         "classHELM": "PEPTIDE",
         "alias": "F",
         "name": "Phe",
+        "naturalAnalogShort": "F",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2656,6 +2658,7 @@
         "classHELM": "PEPTIDE",
         "alias": "G",
         "name": "Gly",
+        "naturalAnalogShort": "G",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2769,6 +2772,7 @@
         "classHELM": "PEPTIDE",
         "alias": "H",
         "name": "His",
+        "naturalAnalogShort": "H",
         "attachmentPoints": [
             {
                 "attachmentAtom": 5,
@@ -3004,6 +3008,7 @@
         "classHELM": "PEPTIDE",
         "alias": "I",
         "name": "Ile",
+        "naturalAnalogShort": "I",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3181,6 +3186,7 @@
         "classHELM": "PEPTIDE",
         "alias": "K",
         "name": "Lys",
+        "naturalAnalogShort": "K",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3562,6 +3568,7 @@
         "classHELM": "PEPTIDE",
         "alias": "V",
         "name": "Val",
+        "naturalAnalogShort": "V",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3722,6 +3729,7 @@
         "classHELM": "PEPTIDE",
         "alias": "E",
         "name": "Glu",
+        "naturalAnalogShort": "E",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3935,6 +3943,7 @@
         "classHELM": "PEPTIDE",
         "alias": "C",
         "name": "Cys",
+        "naturalAnalogShort": "C",
         "attachmentPoints": [
             {
                 "attachmentAtom": 8,
@@ -4370,6 +4379,7 @@
         "classHELM": "PEPTIDE",
         "alias": "E",
         "name": "E",
+        "naturalAnalogShort": "E",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0

diff --git a/api/tests/integration/tests/formats/ref/cysteine.ket b/api/tests/integration/tests/formats/ref/cysteine.ket
@@ -15,6 +15,7 @@
         "classHELM": "PEPTIDE",
         "alias": "C",
         "name": "cys",
+        "naturalAnalogShort": "C",
         "attachmentPoints": [
             {
                 "attachmentAtom": 8,

diff --git a/api/tests/integration/tests/formats/ref/fmoc.ket b/api/tests/integration/tests/formats/ref/fmoc.ket
@@ -856,6 +856,7 @@
         "classHELM": "PEPTIDE",
         "alias": "H",
         "name": "His",
+        "naturalAnalogShort": "H",
         "attachmentPoints": [
             {
                 "attachmentAtom": 5,
@@ -1091,6 +1092,7 @@
         "classHELM": "PEPTIDE",
         "alias": "A",
         "name": "Ala",
+        "naturalAnalogShort": "A",
         "attachmentPoints": [
             {
                 "attachmentAtom": 2,
@@ -1221,6 +1223,7 @@
         "classHELM": "PEPTIDE",
         "alias": "E",
         "name": "Glu",
+        "naturalAnalogShort": "E",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1434,6 +1437,7 @@
         "classHELM": "PEPTIDE",
         "alias": "G",
         "name": "Gly",
+        "naturalAnalogShort": "G",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1547,6 +1551,7 @@
         "classHELM": "PEPTIDE",
         "alias": "T",
         "name": "Thr",
+        "naturalAnalogShort": "T",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1732,6 +1737,7 @@
         "classHELM": "PEPTIDE",
         "alias": "F",
         "name": "Phe",
+        "naturalAnalogShort": "F",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -1959,6 +1965,7 @@
         "classHELM": "PEPTIDE",
         "alias": "S",
         "name": "Ser",
+        "naturalAnalogShort": "S",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2127,6 +2134,7 @@
         "classHELM": "PEPTIDE",
         "alias": "D",
         "name": "Asp",
+        "naturalAnalogShort": "D",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2325,6 +2333,7 @@
         "classHELM": "PEPTIDE",
         "alias": "V",
         "name": "Val",
+        "naturalAnalogShort": "V",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2485,6 +2494,7 @@
         "classHELM": "PEPTIDE",
         "alias": "Y",
         "name": "Tyr",
+        "naturalAnalogShort": "Y",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2750,6 +2760,7 @@
         "classHELM": "PEPTIDE",
         "alias": "L",
         "name": "Leu",
+        "naturalAnalogShort": "L",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -2925,6 +2936,7 @@
         "classHELM": "PEPTIDE",
         "alias": "Q",
         "name": "Gln",
+        "naturalAnalogShort": "Q",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3138,6 +3150,7 @@
         "classHELM": "PEPTIDE",
         "alias": "K",
         "name": "Lys",
+        "naturalAnalogShort": "K",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3351,6 +3364,7 @@
         "classHELM": "PEPTIDE",
         "alias": "I",
         "name": "Ile",
+        "naturalAnalogShort": "I",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3528,6 +3542,7 @@
         "classHELM": "PEPTIDE",
         "alias": "W",
         "name": "Trp",
+        "naturalAnalogShort": "W",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,
@@ -3830,6 +3845,7 @@
         "classHELM": "PEPTIDE",
         "alias": "R",
         "name": "Arg",
+        "naturalAnalogShort": "R",
         "attachmentPoints": [
             {
                 "attachmentAtom": 0,