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#3435 Tautomers strict mode #3436

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5ea6560
tautomers
even1024 Jan 6, 2026
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even1024 Jan 6, 2026
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6 changes: 4 additions & 2 deletions api/c/bingo-nosql/src/bingo_matcher.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -572,7 +572,8 @@ bool MoleculeSubMatcher::_tryCurrent() // const

matcher.arom_options = indigo.arom_options;
matcher.setRulesList(&indigo.tautomer_rules);
matcher.setRules(_tautomer_params.conditions, _tautomer_params.force_hydrogens, _tautomer_params.ring_chain, _tautomer_params.method);
matcher.setRules(_tautomer_params.conditions, _tautomer_params.force_hydrogens, _tautomer_params.ring_chain, _tautomer_params.method,
_tautomer_params.strict);
matcher.setQuery(query_mol);
return matcher.find();
}
Expand Down Expand Up @@ -1411,7 +1412,8 @@ bool MolExactMatcher::_tryCurrent() /* const */

matcher.arom_options = indigo.arom_options;
matcher.setRulesList(&indigo.tautomer_rules);
matcher.setRules(_tautomer_params.conditions, _tautomer_params.force_hydrogens, _tautomer_params.ring_chain, _tautomer_params.method);
matcher.setRules(_tautomer_params.conditions, _tautomer_params.force_hydrogens, _tautomer_params.ring_chain, _tautomer_params.method,
_tautomer_params.strict);
matcher.setQuery(query_mol);
return matcher.find();
}
Expand Down
6 changes: 3 additions & 3 deletions api/c/indigo/src/indigo_match.cpp
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Expand Up @@ -130,7 +130,7 @@ DLLEXPORT bool _indigoParseTautomerFlags(const char* flags, IndigoTautomerParams
if (strcasecmp(word.ptr(), "TAU") != 0)
return false;

MoleculeTautomerMatcher::parseConditions(flags, params.conditions, params.force_hydrogens, params.ring_chain, params.method);
MoleculeTautomerMatcher::parseConditions(flags, params.conditions, params.force_hydrogens, params.ring_chain, params.method, params.strict);

return true;
}
Expand Down Expand Up @@ -266,7 +266,7 @@ CEXPORT int indigoExactMatch(int handler1, int handler2, const char* flags)

matcher.arom_options = self.arom_options;
matcher.setRulesList(&self.tautomer_rules);
matcher.setRules(params.conditions, params.force_hydrogens, params.ring_chain, params.method);
matcher.setRules(params.conditions, params.force_hydrogens, params.ring_chain, params.method, params.strict);
matcher.setQuery(mol1);

if (!matcher.find())
Expand Down Expand Up @@ -709,7 +709,7 @@ bool IndigoMoleculeSubstructureMatcher::findTautomerMatch(QueryMolecule& query,
}

tau_matcher->setRulesList(&tautomer_rules);
tau_matcher->setRules(tau_params.conditions, tau_params.force_hydrogens, tau_params.ring_chain, tau_params.method);
tau_matcher->setRules(tau_params.conditions, tau_params.force_hydrogens, tau_params.ring_chain, tau_params.method, tau_params.strict);
tau_matcher->setQuery(query);
tau_matcher->arom_options = indigo.arom_options;
if (!tau_matcher->find())
Expand Down
1 change: 1 addition & 0 deletions api/c/indigo/src/indigo_match.h
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Expand Up @@ -46,6 +46,7 @@ struct IndigoTautomerParams
int conditions;
bool force_hydrogens;
bool ring_chain;
bool strict;
TautomerMethod method;
};

Expand Down
147 changes: 147 additions & 0 deletions api/c/tests/unit/tests/tautomers.cpp
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@@ -0,0 +1,147 @@
#include <gtest/gtest.h>

#include "common.h"
#include <indigo.h>
#include <indigo_internal.h>

using namespace indigo;

class IndigoApiTautomersTest : public IndigoApiTest
{
};

TEST_F(IndigoApiTautomersTest, testExactTau)
{
try
{
const char* flags = "TAU STRICT";
// 2-Penten-2-ol
int mol1 = indigoLoadMoleculeFromString("CC(O)=CCC");

// 2-Pentanone
int mol2 = indigoLoadMoleculeFromString("CC(CCC)=O");

int match = indigoExactMatch(mol1, mol2, flags);
ASSERT_NE(0, match) << "Expected match between 2-Penten-2-ol and 2-Pentanone";
if (match)
indigoFree(match);

// 3-Penten-2-ol
int mol3 = indigoLoadMoleculeFromString("CC(O)/C=C/C");
match = indigoExactMatch(mol1, mol3, flags);
ASSERT_EQ(0, match) << "Expected NO match between 2-Penten-2-ol and 3-Penten-2-ol with restricted rules";
int mol4 = indigoLoadMoleculeFromString("CC(/C=C(\\O)/C)O");
match = indigoExactMatch(mol1, mol4, flags);
ASSERT_EQ(0, match) << "Expected NO match between 2-Penten-2-ol and 3-Penten-2-ol with restricted rules";
if (match)
indigoFree(match);

indigoFree(mol1);
indigoFree(mol2);
indigoFree(mol3);
}
catch (Exception& e)
{
ASSERT_STREQ("", e.message());
}
}

TEST_F(IndigoApiTautomersTest, testSpecificTautomers)
{
const char* flags = "TAU STRICT";
int mol1 = indigoLoadMoleculeFromString("C(/C)(\\O)=C\\C(CC)O");
int mol2 = indigoLoadMoleculeFromString("C(C)(O)/C=C(/CC)\\O");

int match = indigoExactMatch(mol1, mol2, flags);
ASSERT_NE(0, match) << "Expected match between specified tautomers";

if (match)
indigoFree(match);

indigoFree(mol1);
indigoFree(mol2);
}

TEST_F(IndigoApiTautomersTest, testExpandedTautomerRules)
{
const char* flags = "TAU STRICT";

// 1. NOT MATCHED: Allylic Isomerization (Simple Alkene Shift)
// C=CCCC (1-Pentene) vs CC=CCC (2-Pentene)
// Shift C1-C2 to C2-C3. Proton shift involved. Neither C1 nor C3 activated.
int mol1 = indigoLoadMoleculeFromString("C=CCCC");
int mol2 = indigoLoadMoleculeFromString("CC=CCC");
int match = indigoExactMatch(mol1, mol2, flags);
ASSERT_EQ(0, match) << "Allylic Isomerization should NOT match";
if (match)
indigoFree(match);
indigoFree(mol1);
indigoFree(mol2);

// 2. NOT MATCHED: Allylic Alcohol Isomerization
// CC(O)=CCC (Enol) vs CC(O)C=CC (Allylic Alcohol)
mol1 = indigoLoadMoleculeFromString("CC(O)=CCC");
mol2 = indigoLoadMoleculeFromString("CC(O)C=CC");
match = indigoExactMatch(mol1, mol2, flags);
ASSERT_EQ(0, match) << "Allylic Alcohol Isomerization should NOT match";
if (match)
indigoFree(match);
indigoFree(mol1);
indigoFree(mol2);

// 3. MATCHED: Keto-Enol Tautomerism
// CC(=O)C (Acetone) vs CC(O)=C (Propen-2-ol)
mol1 = indigoLoadMoleculeFromString("CC(=O)C");
mol2 = indigoLoadMoleculeFromString("CC(O)=C");
match = indigoExactMatch(mol1, mol2, flags);
ASSERT_NE(0, match) << "Keto-Enol should MATCH";
if (match)
indigoFree(match);
indigoFree(mol1);
indigoFree(mol2);

// 4. MATCHED: Imine-Enamine Tautomerism
// CC=N (Imine) vs C=CN (Enamine)
mol1 = indigoLoadMoleculeFromString("CC=N");
mol2 = indigoLoadMoleculeFromString("C=CN");
match = indigoExactMatch(mol1, mol2, flags);
ASSERT_NE(0, match) << "Imine-Enamine should MATCH";
if (match)
indigoFree(match);
indigoFree(mol1);
indigoFree(mol2);

// 5. MATCHED: Enediol Tautomerism
// O-C=C(O) (Enediol) vs O=C-C(O) (Hydroxyketone)
mol1 = indigoLoadMoleculeFromString("OC=C(O)");
mol2 = indigoLoadMoleculeFromString("O=CC(O)");
match = indigoExactMatch(mol1, mol2, flags);
ASSERT_NE(0, match) << "Enediol should MATCH";
if (match)
indigoFree(match);
indigoFree(mol1);
indigoFree(mol2);

// 6. MATCHED: 1,3-Dicarbonyl Tautomerism (Activated Methylene)
// CC(=O)CC(=O)C (Pentane-2,4-dione) vs CC(=O)C=C(O)C (Enol form)
mol1 = indigoLoadMoleculeFromString("CC(=O)CC(=O)C");
mol2 = indigoLoadMoleculeFromString("CC(=O)C=C(O)C");
match = indigoExactMatch(mol1, mol2, flags);
ASSERT_NE(0, match) << "1,3-Dicarbonyl should MATCH";
if (match)
indigoFree(match);
indigoFree(mol1);
indigoFree(mol2);

// 7. MATCHED: Nitro-Aci-Nitro Tautomerism
// [O-][N+](=O)C (Nitromethane) vs [O-][N+](=C)O (Aci-nitro zwitterion)
// Ensures valence compatibility (N+ in both).
mol1 = indigoLoadMoleculeFromString("[O-][N+](=O)C");
mol2 = indigoLoadMoleculeFromString("[O-][N+](=C)O");
match = indigoExactMatch(mol1, mol2, flags);
ASSERT_NE(0, match) << "Nitro-Aci-Nitro should MATCH";
if (match)
indigoFree(match);
indigoFree(mol1);
indigoFree(mol2);
}
4 changes: 3 additions & 1 deletion core/indigo-core/molecule/molecule_tautomer.h
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Expand Up @@ -81,6 +81,7 @@ namespace indigo

bool force_hydrogens;
bool ring_chain;
bool strict;
int rules;
TautomerMethod method;
bool substructure;
Expand Down Expand Up @@ -123,11 +124,12 @@ namespace indigo
bool isFeasiblePair(int n1, int n2, int& h_diff);
void restore();

static bool matchAtomsTau(BaseMolecule& g1, BaseMolecule& g2, int n1, int n2);
static bool matchAtomsTau(BaseMolecule& g1, BaseMolecule& g2, int n1, int n2, bool strict);
static bool matchBondsTau(Graph& subgraph, Graph& supergraph, int sub_idx, int super_idx, void* userdata);
static bool matchBondsTauSub(Graph& subgraph, Graph& supergraph, int sub_idx, int super_idx, void* userdata);

static bool fixBondsNotInChains(TautomerSearchContext& context, const int* core1, const int* core2);
static bool isTautomerActivatedCarbon(BaseMolecule& mol, int atom_idx);

private:
bool _checkInterPathBonds();
Expand Down
5 changes: 3 additions & 2 deletions core/indigo-core/molecule/molecule_tautomer_matcher.h
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Expand Up @@ -48,13 +48,13 @@ namespace indigo
void setQuery(BaseMolecule& query);

void setRulesList(const PtrArray<TautomerRule>* rules_list);
void setRules(int rules_set, bool force_hydrogens, bool ring_chain, TautomerMethod method);
void setRules(int rules_set, bool force_hydrogens, bool ring_chain, TautomerMethod method, bool strict);

bool find();

const int* getQueryMapping();

static void parseConditions(const char* tautomer_text, int& rules, bool& force_hydrogens, bool& ring_chain, TautomerMethod& method);
static void parseConditions(const char* tautomer_text, int& rules, bool& force_hydrogens, bool& ring_chain, TautomerMethod& method, bool& strict);

static int countNonHydrogens(BaseMolecule& molecule);

Expand All @@ -66,6 +66,7 @@ namespace indigo
bool _substructure;
bool _force_hydrogens;
bool _ring_chain;
bool _strict;
TautomerMethod _method;
int _rules;

Expand Down
10 changes: 5 additions & 5 deletions core/indigo-core/molecule/src/molecule_tautomer_chain.cpp
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Expand Up @@ -113,7 +113,7 @@ bool TautomerChainFinder::nextPair(int& n1, int& n2, int& e1, int& e2, int prev_
if (_context.core_2[n2] != EmbeddingEnumerator::UNMAPPED)
continue;

if (TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2))
if (TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2, _context.strict))
return true;
}

Expand Down Expand Up @@ -144,7 +144,7 @@ bool TautomerChainFinder::nextPair(int& n1, int& n2, int& e1, int& e2, int prev_
if (_context.core_2[n2] != EmbeddingEnumerator::UNMAPPED)
continue;

if (TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2))
if (TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2, _context.strict))
return true;
}

Expand Down Expand Up @@ -175,7 +175,7 @@ bool TautomerChainFinder::nextPair(int& n1, int& n2, int& e1, int& e2, int prev_
if (_context.core_2[n2] != EmbeddingEnumerator::UNMAPPED)
continue;

if (TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2))
if (TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2, _context.strict))
return true;
}

Expand Down Expand Up @@ -490,7 +490,7 @@ bool TautomerChainChecker::isFeasibleStartingPair(int n1, int n2, int& h_diff)
return true;
}

if (!TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2))
if (!TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2, _context.strict))
return false;

int h_count_2 = _context.g2.getAtomTotalH(n2);
Expand Down Expand Up @@ -751,7 +751,7 @@ int TautomerChainChecker::isFeasiblePair(int n1, int n2, TautomerChainChecker& n

if (n1 != -1)
{
if (!TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2))
if (!TautomerMatcher::matchAtomsTau(_context.g1, _context.g2, n1, n2, _context.strict))
return 0;

int h_rep_1 = 0;
Expand Down
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