#2722 Monomer could be saved to RDF V3000 format but can't be loaded back - exception (#2876)

Author: even1024

api/tests/integration/ref/formats/pathway.py.out

@@ -10,3 +10,4 @@ pathway9.rdf:SUCCEED
 pathway10.rdf:SUCCEED
 pathway11.rdf:SUCCEED
 pathway12.rdf:SUCCEED
+pathway_mon.rdf:SUCCEED

api/tests/integration/tests/formats/pathway.py

@@ -31,6 +31,7 @@ def find_diff(a, b):
     "pathway10",
     "pathway11",
     "pathway12",
+    "pathway_mon",
 ]
 
 for filename in files:

api/tests/integration/tests/formats/reactions/rdf/pathway_mon.rdf

@@ -0,0 +1,58 @@
+$RDFILE 1
+$DATM    04/25/25 10:02
+$RFMT
+$RXN V3000
+
+ -INDIGO- 0425251002
+
+M  V30 COUNTS 1 0
+M  V30 BEGIN REACTANT
+M  V30 BEGIN CTAB
+M  V30 COUNTS 1 0 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 A 10.2 -7.775 0.0 0 CLASS=AA SEQID=1
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 END BOND
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 1 AA/Ala/A/ NATREPLACE=AA/A
+M  V30 BEGIN CTAB
+M  V30 COUNTS 7 6 3 0 0
+M  V30 BEGIN ATOM
+M  V30 1 N -0.866 -0.25 0.0 0
+M  V30 2 C 0.0 0.25 0.0 0 CFG=2
+M  V30 3 H -1.732 0.25 0.0 0
+M  V30 4 C 0.866 -0.25 0.0 0
+M  V30 5 O 1.732 0.25 0.0 0
+M  V30 6 O 0.866 -1.25 0.0 0
+M  V30 7 C 0.0 1.25 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 1 3
+M  V30 3 1 2 4
+M  V30 4 1 4 5
+M  V30 5 2 4 6
+M  V30 6 1 2 7 CFG=1
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(1 2)
+M  V30 END COLLECTION
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(1 3) XBONDS=(1 2) BRKXYZ=(9 0.433000 -0.250000 0.000000-
+M  V30  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=-
+M  V30 LGRP
+M  V30 2 SUP 2 ATOMS=(1 5) XBONDS=(1 4) BRKXYZ=(9 -0.433000 -0.250000 0.00000-
+M  V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLAS-
+M  V30 S=LGRP
+M  V30 3 SUP 3 ATOMS=(5 1 2 4 6 7) XBONDS=(2 2 4) BRKXYZ=(9 -0.433000 0.25000-
+M  V30 0 0.000000 0.433000 0.250000 0.000000 0.000000 0.000000 0.000000) LABE-
+M  V30 L=A CLASS=AA SAP=(3 1 3 Al) SAP=(3 4 5 Br) NATREPLACE=AA/A
+M  V30 END SGROUP
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  V30 END REACTANT
+M  V30 BEGIN PRODUCT
+M  V30 END PRODUCT
+M  END

api/tests/integration/tests/formats/ref/pathway_mon.ket

@@ -0,0 +1 @@
+{"root":{"nodes":[{"type":"arrow","data":{"mode":"filled-triangle","pos":[{"x":2.694444417953491,"y":-2.0,"z":0.0},{"x":9.69444465637207,"y":-2.0,"z":0.0}]}},{"$ref":"monomer0"}],"connections":[],"templates":[{"$ref":"monomerTemplate-Ala_1"}]},"monomer0":{"type":"monomer","id":"0","seqid":1,"position":{"x":1.0,"y":-2.0},"alias":"A","templateId":"Ala_1"},"monomerTemplate-Ala_1":{"type":"monomerTemplate","id":"Ala_1","class":"AminoAcid","classHELM":"PEPTIDE","alias":"A","name":"Ala","naturalAnalogShort":"A","naturalAnalog":"Ala","attachmentPoints":[{"attachmentAtom":0,"leavingGroup":{"atoms":[2]}},{"attachmentAtom":3,"leavingGroup":{"atoms":[4]}}],"atoms":[{"label":"N","location":[-0.8659999966621399,-0.25,0.0]},{"label":"C","location":[0.0,0.25,0.0],"stereoLabel":"abs"},{"label":"H","location":[-1.7319999933242798,0.25,0.0]},{"label":"C","location":[0.8659999966621399,-0.25,0.0]},{"label":"O","location":[1.7319999933242798,0.25,0.0]},{"label":"O","location":[0.8659999966621399,-1.25,0.0]},{"label":"C","location":[0.0,1.25,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[0,2]},{"type":1,"atoms":[1,3]},{"type":1,"atoms":[3,4]},{"type":2,"atoms":[3,5]},{"type":1,"atoms":[1,6],"stereo":1}]}}

core/indigo-core/molecule/inchi_wrapper.h

@@ -60,7 +60,7 @@ namespace indigo
 
         void parseInchiOutput(const InchiOutput& inchi_output, Molecule& mol);
 
-        void generateInchiInput(Molecule& mol, inchi_Input& input, Array<inchi_Atom>& atoms, Array<inchi_Stereo0D>& stereo);
+        void generateInchiInput(Molecule& input_mol, inchi_Input& input, Array<inchi_Atom>& atoms, Array<inchi_Stereo0D>& stereo);
 
         void neutralizeV5Nitrogen(Molecule& mol);
 

core/indigo-core/molecule/src/inchi_wrapper.cpp

@@ -404,8 +404,16 @@ void InchiWrapper::parseInchiOutput(const InchiOutput& inchi_output, Molecule& m
     }
 }
 
-void InchiWrapper::generateInchiInput(Molecule& mol, inchi_Input& input, Array<inchi_Atom>& atoms, Array<inchi_Stereo0D>& stereo)
+void InchiWrapper::generateInchiInput(Molecule& input_mol, inchi_Input& input, Array<inchi_Atom>& atoms, Array<inchi_Stereo0D>& stereo)
 {
+    Molecule tmol;
+    auto tcount = input_mol.tgroups.getTGroupCount();
+    Molecule& mol = tcount ? tmol : input_mol;
+    if (tcount)
+    {
+        tmol.clone_KeepIndices(input_mol);
+        tmol.transformSCSRtoFullCTAB();
+    }
     QS_DEF(Array<int>, mapping);
     mapping.clear_resize(mol.vertexEnd());
     mapping.fffill();
@@ -425,7 +433,8 @@ void InchiWrapper::generateInchiInput(Molecule& mol, inchi_Input& input, Array<i
             throw Error("Molecule with pseudoatom (%s) cannot be converted into InChI", mol.getPseudoAtom(v));
         if (atom_number == ELEM_RSITE)
             throw Error("Molecule with RGroups cannot be converted into InChI");
-        strncpy(atom.elname, Element::toString(atom_number), ATOM_EL_LEN);
+
+        strncpy(atom.elname, atom_number == ELEM_TEMPLATE ? mol.getTemplateAtom(v) : Element::toString(atom_number), ATOM_EL_LEN);
 
         Vec3f& c = mol.getAtomXyz(v);
         atom.x = c.x;
@@ -471,7 +480,14 @@ void InchiWrapper::generateInchiInput(Molecule& mol, inchi_Input& input, Array<i
 
         // Other properties
         atom.isotopic_mass = mol.getAtomIsotope(v);
-        atom.radical = mol.getAtomRadical(v);
+        try
+        {
+            atom.radical = mol.getAtomRadical(v);
+        }
+        catch (Molecule::Error&)
+        {
+            atom.radical = 0;
+        }
         atom.charge = mol.getAtomCharge(v);
 
         // Hydrogens

core/indigo-core/molecule/src/molecule_tgroups.cpp

@@ -208,7 +208,8 @@ int MoleculeTGroups::findTGroup(const char* name)
         TGroup& tgroup = *_tgroups.at(i);
         if (tgroup.tgroup_name.size() > 0 && name != 0)
         {
-            if (strncmp(tgroup.tgroup_name.ptr(), name, tgroup.tgroup_name.size()) == 0)
+            if (strncmp(tgroup.tgroup_name.ptr(), name, tgroup.tgroup_name.size()) == 0 ||
+                strncmp(tgroup.tgroup_alias.ptr(), name, tgroup.tgroup_alias.size()) == 0)
                 return i;
         }
     }