Backmerge: #2257 - Unable to save CHEM SS3 to IDT format (#2502)

epam · Oct 4, 2024 · 98beb22 · 98beb22
1 parent d4233f9
commit 98beb22
Show file tree

Hide file tree

Showing 5 changed files with 265 additions and 13 deletions.
diff --git a/api/tests/integration/ref/formats/ket_to_idt.py.out b/api/tests/integration/ref/formats/ket_to_idt.py.out
@@ -15,6 +15,7 @@ idt_i2moera_32moera.ket:SUCCEED
 idt_i2moera_sp.ket:SUCCEED
 idt_i2moera_sp_32moera.ket:SUCCEED
 idt_i2moera_t.ket:SUCCEED
+idt_issue_2257.ket:SUCCEED
 idt_many_molecules.ket:SUCCEED
 idt_mixed.ket:SUCCEED
 idt_mixed_custom.ket:SUCCEED

diff --git a/api/tests/integration/tests/formats/ket_to_idt.py b/api/tests/integration/tests/formats/ket_to_idt.py
@@ -65,6 +65,7 @@ def find_diff(a, b):
     "idt_mixed_custom": "(N1:10203050)(N1)N",
     "idt_rna_dna_mixed_custom": "r(R1:50003000)(R1)",
     "idt_mixed_ketcher": "KrK(K1:00003070)r(K2:00003070)",
+    "idt_issue_2257": "/3ThioMC3-D/",
 }
 
 for filename in sorted(idt_data.keys()):

diff --git a/api/tests/integration/tests/formats/ref/idt_issue_2257.ket b/api/tests/integration/tests/formats/ref/idt_issue_2257.ket
@@ -0,0 +1,236 @@
+{
+    "root": {
+        "nodes": [
+            {
+                "$ref": "monomer0"
+            }
+        ],
+        "connections": [],
+        "templates": [
+            {
+                "$ref": "monomerTemplate-SS3___Dipropanol-disulfide"
+            }
+        ]
+    },
+    "monomer0": {
+        "type": "monomer",
+        "id": "0",
+        "position": {
+            "x": 14.424999999999997,
+            "y": -5.899999999999998
+        },
+        "alias": "SS3",
+        "templateId": "SS3___Dipropanol-disulfide"
+    },
+    "monomerTemplate-SS3___Dipropanol-disulfide": {
+        "type": "monomerTemplate",
+        "atoms": [
+            {
+                "label": "H",
+                "location": [
+                    -6.8609,
+                    -0.665,
+                    0
+                ]
+            },
+            {
+                "label": "O",
+                "location": [
+                    -5.862,
+                    0,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    -4.5166,
+                    -0.6653,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    -3.2673,
+                    0.1663,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    -1.922,
+                    -0.499,
+                    0
+                ]
+            },
+            {
+                "label": "S",
+                "location": [
+                    -0.6726,
+                    0.3327,
+                    0
+                ]
+            },
+            {
+                "label": "S",
+                "location": [
+                    0.6726,
+                    -0.3327,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    1.922,
+                    0.499,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    3.2673,
+                    -0.1663,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    4.5166,
+                    0.6653,
+                    0
+                ]
+            },
+            {
+                "label": "O",
+                "location": [
+                    5.862,
+                    0,
+                    0
+                ]
+            },
+            {
+                "label": "H",
+                "location": [
+                    6.8609,
+                    0.665,
+                    0
+                ]
+            }
+        ],
+        "bonds": [
+            {
+                "type": 1,
+                "atoms": [
+                    5,
+                    6
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    1,
+                    2
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    6,
+                    7
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    7,
+                    8
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    2,
+                    3
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    8,
+                    9
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    9,
+                    10
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    3,
+                    4
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    10,
+                    11
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    0,
+                    1
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    4,
+                    5
+                ]
+            }
+        ],
+        "class": "CHEM",
+        "classHELM": "CHEM",
+        "id": "SS3___Dipropanol-disulfide",
+        "fullName": "Dipropanol-disulfide",
+        "alias": "SS3",
+        "attachmentPoints": [
+            {
+                "attachmentAtom": 1,
+                "leavingGroup": {
+                    "atoms": [
+                        0
+                    ]
+                },
+                "type": "left"
+            },
+            {
+                "attachmentAtom": 10,
+                "leavingGroup": {
+                    "atoms": [
+                        11
+                    ]
+                },
+                "type": "right"
+            }
+        ],
+        "idtAliases": {
+            "base": "ThioMC3-D",
+            "modifications": {
+                "endpoint3": "3ThioMC3-D"
+            }
+        }
+    }
+}
diff --git a/api/tests/integration/tests/formats/ref/monomer_library.ket b/api/tests/integration/tests/formats/ref/monomer_library.ket
@@ -45012,6 +45012,12 @@
     "id": "SS3___Dipropanol-disulfide",
     "fullName": "Dipropanol-disulfide",
     "alias": "SS3",
+    "idtAliases": {
+        "base": "ThioMC3-D",
+        "modifications": {
+            "endpoint3": "3ThioMC3-D"
+        }
+    },
     "attachmentPoints": [
       {
         "attachmentAtom": 1,

diff --git a/core/indigo-core/molecule/src/sequence_saver.cpp b/core/indigo-core/molecule/src/sequence_saver.cpp
@@ -869,8 +869,12 @@ void SequenceSaver::saveIdt(KetDocument& doc, std::vector<std::deque<std::string
             std::string sugar;
             std::string base;
             std::string phosphate;
-            if (seq_string.size() > 0 && sequence.size() == 0)
-                modification = IdtModification::THREE_PRIME_END;
+            IdtModification possible_modification = modification;
+            if (sequence.size() == 0) // last monomer
+                if (seq_string.size() > 0)
+                    modification = IdtModification::THREE_PRIME_END;
+                else // corner case - only one monomer
+                    possible_modification = IdtModification::THREE_PRIME_END;
 
             if (monomer_class == MonomerClass::Phosphate)
             {
@@ -898,17 +902,25 @@ void SequenceSaver::saveIdt(KetDocument& doc, std::vector<std::deque<std::string
             }
             else if (monomer_class == MonomerClass::CHEM || monomer_class == MonomerClass::DNA || monomer_class == MonomerClass::RNA)
             {
+                auto write_name = [&](const IdtAlias& idtAlias) -> bool {
+                    bool has_modification = idtAlias.hasModification(modification);
+                    if (has_modification || (possible_modification != modification && idtAlias.hasModification(possible_modification)))
+                    {
+                        const std::string& idt_alias =
+                            has_modification ? idtAlias.getModification(modification) : idtAlias.getModification(possible_modification);
+                        seq_string += '/';
+                        seq_string += idt_alias;
+                        seq_string += '/';
+                        return true;
+                    }
+                    return false;
+                };
                 // Try to find in library
                 const std::string& lib_monomer_id = _library.getMonomerTemplateIdByAlias(monomer_class, monomer);
                 if (lib_monomer_id.size()) // Monomer in library
                 {
-                    const MonomerTemplate& templ = _library.getMonomerTemplateById(lib_monomer_id);
-                    if (templ.idtAlias().hasModification(modification))
+                    if (write_name(_library.getMonomerTemplateById(lib_monomer_id).idtAlias()))
                     {
-                        const std::string& idt_alias = templ.idtAlias().getModification(modification);
-                        seq_string += '/';
-                        seq_string += idt_alias;
-                        seq_string += '/';
                         if (modification == IdtModification::FIVE_PRIME_END)
                             modification = IdtModification::INTERNAL;
                         continue;
@@ -917,12 +929,8 @@ void SequenceSaver::saveIdt(KetDocument& doc, std::vector<std::deque<std::string
 
                 // Check template for IdtAlias
                 auto& monomer_template = doc.getMonomerTemplate(monomers.at(monomer_id)->templateId());
-
-                if (monomer_template.idtAlias().hasModification(modification))
+                if (write_name(monomer_template.idtAlias()))
                 {
-                    seq_string.push_back('/');
-                    seq_string.append(monomer_template.idtAlias().getModification(modification));
-                    seq_string.push_back('/');
                     modification = IdtModification::INTERNAL;
                     continue;
                 }