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#1371 Chirality symbol is added to the SMARTS when 'single up/down' or 'double cis/trans' bond type is set up #1382

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Oct 26, 2023
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#1371 Chirality symbol is added to the SMARTS when 'single up/down' or 'double cis/trans' bond type is set up #1382

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bc6c397
#1371 Chirality symbol is added to the SMARTS when
AliaksandrDziarkach Oct 26, 2023
4aa11eb
Use constants
AliaksandrDziarkach Oct 26, 2023
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2 changes: 2 additions & 0 deletions api/tests/integration/ref/formats/custom_query.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,5 @@
ket_with_rb_as_drawn.ket OK. Smarts equals expected string '[#6](-[#6])(-[#6;x0])-[#6]'
**** #1337 wrong smarts for ring bond count as drawn ****
ket_with_custom_query_with_list.ket OK. Smarts equals expected string '[#6]1-[#6]=[Cl,Br,I,Na,O]-[#6]=[#6]-[#6]=1'
**** #1371Chirality symbol is added to the SMARTS when 'single up/down' or 'double cis/trans' bond type is set up wrong smarts for ring bond count as drawn ****
ket_with_bond_stereo_ether.ket OK. Smarts equals expected string '[#6]1-[#6]=[#6]-[#6]=[#6]\[#6]=1'
9 changes: 9 additions & 0 deletions api/tests/integration/tests/formats/custom_query.py
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Expand Up @@ -50,3 +50,12 @@ def test_ket_to_smarts(filename, expected_str):
fname = "ket_with_custom_query_with_list.ket"
expected = "[#6]1-[#6]=[Cl,Br,I,Na,O]-[#6]=[#6]-[#6]=1"
test_ket_to_smarts(fname, expected)

print(
"**** #1371Chirality symbol is added to the SMARTS when "
"'single up/down' or 'double cis/trans' bond type is set up"
" wrong smarts for ring bond count as drawn ****"
)
fname = "ket_with_bond_stereo_ether.ket"
expected = "[#6]1-[#6]=[#6]-[#6]=[#6]\[#6]=1"
test_ket_to_smarts(fname, expected)
108 changes: 108 additions & 0 deletions api/tests/integration/tests/formats/ref/ket_with_bond_stereo_ether.ket
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Original file line number Diff line number Diff line change
@@ -0,0 +1,108 @@
{
"root": {
"nodes": [
{
"$ref": "mol0"
}
]
},
"mol0": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [
2.9673491521285666,
-16.35007441717461,
0
]
},
{
"label": "C",
"location": [
4.697650847871435,
-16.349589229177205,
0
],
"stereoLabel": "abs"
},
{
"label": "C",
"location": [
3.8341375094912395,
-15.849966888850188,
0
]
},
{
"label": "C",
"location": [
4.697650847871435,
-17.35053206782215,
0
]
},
{
"label": "C",
"location": [
2.9673491521285666,
-17.35502005679814,
0
]
},
{
"label": "C",
"location": [
3.836320855479559,
-17.850033111149813,
0
]
}
],
"bonds": [
{
"type": 2,
"atoms": [
2,
0
]
},
{
"type": 1,
"atoms": [
0,
4
]
},
{
"type": 2,
"atoms": [
4,
5
]
},
{
"type": 1,
"atoms": [
5,
3
]
},
{
"type": 2,
"atoms": [
3,
1
]
},
{
"type": 1,
"atoms": [
1,
2
],
"stereo": 6
}
]
}
}
5 changes: 3 additions & 2 deletions core/indigo-core/molecule/query_molecule.h
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Expand Up @@ -334,8 +334,9 @@ namespace indigo

static std::string getSmartsBondStr(QueryMolecule::Bond* bond);
static void writeSmartsBond(Output& output, QueryMolecule::Bond* bond, bool has_or_parent);
static std::string getSmartsAtomStr(QueryMolecule::Atom* atom);
static void writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent);
static std::string getSmartsAtomStr(QueryMolecule::Atom* atom, int original_format);
static void writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent,
int original_format);

enum QUERY_ATOM
{
Expand Down
2 changes: 1 addition & 1 deletion core/indigo-core/molecule/src/molecule_json_saver.cpp
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Expand Up @@ -830,7 +830,7 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
if (needCustomQuery)
{
QueryMolecule::Atom& atom = _pqmol->getAtom(i);
std::string customQuery = QueryMolecule::getSmartsAtomStr(&atom);
std::string customQuery = QueryMolecule::getSmartsAtomStr(&atom, _pqmol->original_format);
writer.Key("customQuery");
writer.String(customQuery.c_str());
}
Expand Down
29 changes: 19 additions & 10 deletions core/indigo-core/molecule/src/query_molecule.cpp
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Expand Up @@ -404,11 +404,11 @@ void QueryMolecule::writeSmartsBond(Output& output, Bond* bond, bool has_or_pare
}
}

std::string QueryMolecule::getSmartsAtomStr(QueryMolecule::Atom* atom)
std::string QueryMolecule::getSmartsAtomStr(QueryMolecule::Atom* atom, int original_format)
{
Array<char> out;
ArrayOutput output(out);
writeSmartsAtom(output, atom, -1, -1, 1, false, false);
writeSmartsAtom(output, atom, -1, -1, 1, false, false, original_format);
std::string result{out.ptr(), static_cast<std::size_t>(out.size())};
return result;
}
Expand Down Expand Up @@ -438,7 +438,7 @@ static void writeAnd(Output& _output, QueryMolecule::Node* node, bool has_or_par
_output.writeChar(';');
}

void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent)
void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent, int original_format)
{
int i;

Expand All @@ -454,7 +454,7 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
break;
}
output.writeChar('!');
writeSmartsAtom(output, atom->child(0), aam, chirality, depth + 1, has_or_parent, true);
writeSmartsAtom(output, atom->child(0), aam, chirality, depth + 1, has_or_parent, true, original_format);
break;
}
case OP_AND: {
Expand Down Expand Up @@ -498,7 +498,7 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
output.writeChar(has_or_parent ? '&' : ';');
cur_pos = output.tell();
}
writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, has_or_parent, has_not_parent);
writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, has_or_parent, has_not_parent, original_format);
}
break;
}
Expand All @@ -512,7 +512,7 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi

if (i > 0)
output.printf(has_not_parent ? "!" : ",");
writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, true, has_not_parent);
writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, true, has_not_parent, original_format);
}
break;
}
Expand All @@ -521,10 +521,19 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
break;
case ATOM_NUMBER: {
output.printf("#%d", atom->value_max);
if (chirality == 1)
output.printf("@");
else if (chirality == 2)
output.printf("@@");
switch (original_format)
{
case SMARTS:
case KET:
// SMARTS and ket save chirality in ATOM_CHIRALITY for query molecule
break;
default:
if (chirality == 1)
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output.printf("@");
else if (chirality == 2)
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output.printf("@@");
break;
}

if (aam > 0)
output.printf(":%d", aam);
Expand Down
2 changes: 1 addition & 1 deletion core/indigo-core/molecule/src/smiles_saver.cpp
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Expand Up @@ -601,7 +601,7 @@ void SmilesSaver::_saveMolecule()
else if (_qmol != 0)
{
int aam = _bmol->reaction_atom_mapping[v_idx];
QueryMolecule::writeSmartsAtom(_output, &_qmol->getAtom(v_idx), aam, _atoms[v_idx].chirality, 0, false, false);
QueryMolecule::writeSmartsAtom(_output, &_qmol->getAtom(v_idx), aam, _atoms[v_idx].chirality, 0, false, false, _qmol->original_format);
}
else
throw Error("SMARTS format available for query only!");
Expand Down