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Fix EPAM Indigo parsing so that the S groups needs to saved before collection block #3531

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Fix EPAM Indigo parsing so that the S groups needs to saved before collection block #3531

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1cefbfb
[Sapio] [CHEMBUGS-184] In molfile_saver.cpp, we need to change it so …
sapiosciences-dev May 14, 2024
4b0267b
[Sapio] [CHEMBUGS-184] removed old hack on turning off implicit hydro…
sapiosciences-dev Mar 6, 2026
e4ce543
clang format and windows env fix.
sapiosciences-dev Mar 12, 2026
4efd18b
CHEMBUGS-184 Merge Up Fixes.
sapiosciences-dev Mar 12, 2026
6addc56
CHEMBUGS-184 Fixed merge up on commons.cpp my changes.
sapiosciences-dev Mar 12, 2026
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41 changes: 30 additions & 11 deletions core/indigo-core/molecule/src/molfile_saver.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
#include <ctime>
#include <map>
#include <sstream>
#include <string>

#include "base_cpp/locale_guard.h"
#include "base_cpp/output.h"
Expand Down Expand Up @@ -787,11 +788,29 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)

output.writeStringCR("M V30 END BOND");

QS_DEF(Array<int>, sgs_sorted);
_checkSGroupIndices(mol, sgs_sorted);

//[Sapio] [CHEMBUGS-184] S-GROUP needs to be before COLLECTION when S GROUP is used.
const bool has_sgroups = (mol.countSGroups() > 0);
MoleculeStereocenters& stereocenters = mol.stereocenters;
const bool has_collection = (stereocenters.begin() != stereocenters.end() || mol.hasHighlighting() || mol.custom_collections.size() > 0);
const bool sgroup_collection_order_reversed = (has_sgroups && has_collection);

// Default order: COLLECTION before SGROUP.
// When sgroup_collection_order_reversed, write SGROUP then COLLECTION (CT spec) page 22.
std::string collection_str;
StringOutput collection_buf(collection_str);
Output* collection_dest_ptr;
if (sgroup_collection_order_reversed)
collection_dest_ptr = static_cast<Output*>(&collection_buf);
else
collection_dest_ptr = &output;
Output& collection_dest = *collection_dest_ptr;

if (stereocenters.begin() != stereocenters.end() || mol.hasHighlighting())
if (has_collection)
{
output.writeStringCR("M V30 BEGIN COLLECTION");
collection_dest.writeStringCR("M V30 BEGIN COLLECTION");

QS_DEF(Array<int>, processed);

Expand Down Expand Up @@ -832,7 +851,7 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
out.printf(" %d", _atom_mapping[list[j]]);
out.writeChar(')');

_writeMultiString(output, buf.ptr(), buf.size());
_writeMultiString(collection_dest, buf.ptr(), buf.size());
}

if (mol.hasHighlighting())
Expand All @@ -848,7 +867,7 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
out.printf(" %d", _bond_mapping[i]);
out.writeChar(')');

_writeMultiString(output, buf.ptr(), buf.size());
_writeMultiString(collection_dest, buf.ptr(), buf.size());
}
if (mol.countHighlightedAtoms() > 0)
{
Expand All @@ -859,7 +878,7 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
out.printf(" %d", _atom_mapping[i]);
out.writeChar(')');

_writeMultiString(output, buf.ptr(), buf.size());
_writeMultiString(collection_dest, buf.ptr(), buf.size());
}
}
if (mol.custom_collections.size() > 0)
Expand All @@ -868,17 +887,14 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
{
ArrayOutput out(buf);
out.printf("%s", mol.custom_collections.at(i));
_writeMultiString(output, buf.ptr(), buf.size());
_writeMultiString(collection_dest, buf.ptr(), buf.size());
}
}

output.writeStringCR("M V30 END COLLECTION");
collection_dest.writeStringCR("M V30 END COLLECTION");
}

QS_DEF(Array<int>, sgs_sorted);
_checkSGroupIndices(mol, sgs_sorted);

if (mol.countSGroups() > 0)
if (has_sgroups)
{
MoleculeSGroups* sgroups = &mol.sgroups;
int idx = 1;
Expand Down Expand Up @@ -1074,6 +1090,9 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
_removeImplicitSGroups(mol, implicit_sgroups_indexes);
}

if (sgroup_collection_order_reversed)
output.write(collection_str.data(), static_cast<int>(collection_str.size()));

output.writeStringCR("M V30 END CTAB");

int n_rgroups = mol.rgroups.getRGroupCount();
Expand Down
2 changes: 2 additions & 0 deletions core/indigo-core/tests/common.cpp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
#include "common.h"
#include "reaction/reaction.h"
#include "reaction/reaction_auto_loader.h"
#include "reaction/reaction_cml_saver.h"
#include "reaction/reaction_json_saver.h"
#include "reaction/rxnfile_saver.h"
Expand Down
249 changes: 249 additions & 0 deletions core/indigo-core/tests/tests/molecule.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,13 @@
#include <molecule/hybridization.h>
#include <molecule/lipinski.h>
#include <molecule/molecule_mass.h>
#include <molecule/molfile_loader.h>
#include <molecule/smiles_loader.h>
#include <molecule/smiles_saver.h>
#include <molecule/tpsa.h>

#include "common.h"
#include "molecule/elements.h"

using namespace std;
using namespace indigo;
Expand Down Expand Up @@ -352,3 +354,250 @@ TEST_F(IndigoCoreMoleculeTest, dearomatize_smarts)
// printf("%s", sm.c_str());
EXPECT_STREQ("c1-c=c-c=c-c=1", sm.c_str());
}

// [Sapio] [CHEMBUGS-184] Stereo reaction molecules (from former stereo_reaction.rxn): load as mol blocks to verify parsing.
namespace
{
const char* const stereoReactionReactant1 = R"(
Mrv2305 05232323372D

18 19 0 0 0 0 999 V2000
-6.9420 -0.0902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.6565 -0.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.6565 -1.3278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.9420 -1.7402 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-6.2275 -1.3278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.2275 -0.5027 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-5.5357 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-4.7511 -0.2549 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.2661 0.4125 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
-4.7510 1.0800 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-5.5356 0.8250 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
-3.4411 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.2031 1.3100 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-4.4961 1.8646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.4066 1.6399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.3709 -1.7403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.5130 -1.7403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8891 1.0256 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
9 10 1 0 0 0 0
10 11 1 0 0 0 0
7 11 1 0 0 0 0
9 12 1 1 0 0 0
3 16 2 0 0 0 0
5 17 2 0 0 0 0
8 9 1 0 0 0 0
7 8 1 0 0 0 0
10 14 1 6 0 0 0
12 18 1 0 0 0 0
11 15 1 1 0 0 0
11 13 1 6 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
7 6 1 1 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
M STY 1 1 SUP
M SAL 1 1 15
M SBL 1 1 13
M SMT 1 Me
M SAP 1 1 15 11 1
M END
)";
const char* const stereoReactionReactant2 = R"(
Mrv2305 05232323372D

24 26 0 0 0 0 999 V2000
-4.7105 -3.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1382 -0.2125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-4.7106 -2.2750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.9961 -1.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9961 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2816 -0.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5671 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5671 -1.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2816 -2.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8527 -0.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8527 0.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5672 0.6126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5671 1.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8527 1.8500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1382 1.4376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1382 0.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1382 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4237 -0.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2907 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2907 -1.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0052 -2.2750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7197 -1.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4237 -2.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1382 -1.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
4 9 1 0 0 0 0
5 6 1 0 0 0 0
6 7 2 0 0 0 0
7 8 1 0 0 0 0
7 10 1 0 0 0 0
8 9 2 0 0 0 0
10 11 1 0 0 0 0
10 17 1 0 0 0 0
11 12 2 0 0 0 0
11 16 1 0 0 0 0
12 13 1 0 0 0 0
13 14 2 0 0 0 0
14 15 1 0 0 0 0
15 16 2 0 0 0 0
17 18 2 0 0 0 0
17 24 1 0 0 0 0
18 19 1 0 0 0 0
19 20 2 0 0 0 0
20 21 1 0 0 0 0
20 23 1 0 0 0 0
21 22 1 0 0 0 0
23 24 2 0 0 0 0
M STY 1 1 SUP
M SAL 1 15 1 3 4 5 6 7 8 9 10 11 12 13 14 15 16
M SAL 1 8 17 18 19 20 21 22 23 24
M SBL 1 1 1
M SMT 1 DMTr
M SAP 1 1 10 2 1
M END
)";
const char* const stereoReactionProduct = R"(
Mrv2305 05232323372D

41 45 0 0 0 0 999 V2000
2.9291 -0.1300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2146 -0.5425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2146 -1.3676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9291 -1.7800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.6436 -1.3676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6436 -0.5425 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.3354 -0.0398 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
5.1200 -0.2947 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.6049 0.3727 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
5.1200 1.0402 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
4.3354 0.7852 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
6.4299 0.3727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6680 1.2701 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
5.3749 1.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.4645 1.6000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5002 -1.7801 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3581 -1.7801 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.9820 0.9858 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.5195 1.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.1070 0.9858 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.2820 0.9858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8695 0.2713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0445 0.2713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6320 0.9858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0445 1.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8695 1.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8070 0.9858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3945 0.2713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8070 -0.4432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3945 -1.1576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5695 -1.1576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1570 -0.4432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5695 0.2713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3945 1.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5695 1.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1570 2.4147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5695 3.1292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1570 3.8437 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.3320 3.8437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3945 3.1292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8070 2.4147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
9 10 1 0 0 0 0
10 11 1 0 0 0 0
7 11 1 0 0 0 0
9 12 1 1 0 0 0
3 16 2 0 0 0 0
5 17 2 0 0 0 0
8 9 1 0 0 0 0
7 8 1 0 0 0 0
10 14 1 6 0 0 0
12 18 1 0 0 0 0
11 15 1 1 0 0 0
11 13 1 6 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
7 6 1 1 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
18 27 1 0 0 0 0
19 20 1 0 0 0 0
20 21 1 0 0 0 0
21 22 2 0 0 0 0
21 26 1 0 0 0 0
22 23 1 0 0 0 0
23 24 2 0 0 0 0
24 25 1 0 0 0 0
24 27 1 0 0 0 0
25 26 2 0 0 0 0
27 28 1 0 0 0 0
27 34 1 0 0 0 0
28 29 2 0 0 0 0
28 33 1 0 0 0 0
29 30 1 0 0 0 0
30 31 2 0 0 0 0
31 32 1 0 0 0 0
32 33 2 0 0 0 0
34 35 2 0 0 0 0
34 41 1 0 0 0 0
35 36 1 0 0 0 0
36 37 2 0 0 0 0
37 38 1 0 0 0 0
37 40 1 0 0 0 0
38 39 1 0 0 0 0
40 41 2 0 0 0 0
M STY 2 1 SUP 2 SUP
M SAL 1 1 15
M SBL 1 1 13
M SMT 1 Me
M SAP 1 1 15 11 1
M SAL 2 15 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33
M SAL 2 8 34 35 36 37 38 39 40 41
M SBL 2 1 20
M SMT 2 DMTr
M SAP 2 1 27 18 1
M END
)";
}

TEST_F(IndigoCoreMoleculeTest, stereoReactionReactant1)
{
Molecule mol;
BufferScanner scanner(stereoReactionReactant1);
MolfileLoader loader(scanner);
loader.loadMolecule(mol);
EXPECT_EQ(18, mol.vertexCount());
EXPECT_EQ(19, mol.edgeCount());
}

TEST_F(IndigoCoreMoleculeTest, stereoReactionReactant2)
{
Molecule mol;
BufferScanner scanner(stereoReactionReactant2);
MolfileLoader loader(scanner);
loader.loadMolecule(mol);
EXPECT_EQ(24, mol.vertexCount());
EXPECT_EQ(26, mol.edgeCount());
}

TEST_F(IndigoCoreMoleculeTest, stereoReactionProduct)
{
Molecule mol;
BufferScanner scanner(stereoReactionProduct);
MolfileLoader loader(scanner);
loader.loadMolecule(mol);
EXPECT_EQ(41, mol.vertexCount());
EXPECT_EQ(45, mol.edgeCount());
}
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