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#2707 - Atom Query feature export: System lost MOST "Substitution co…
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…unt" values (#2779)
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@AliaksandrDziarkach
AliaksandrDziarkach authored Feb 20, 2025
1 parent c037ec2 commit 6bf742c
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Showing 13 changed files with 161 additions and 24 deletions.
2 changes: 2 additions & 0 deletions api/tests/integration/ref/formats/ket_to_ket.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,6 @@ ambiguous_monomer.ket mol loadQueryMolecule: SUCCEED
monomer_shape.ket doc loadKetDocument: SUCCEED
monomer_shape.ket mol loadMolecule: SUCCEED
monomer_shape.ket mol loadQueryMolecule: SUCCEED
2707_subst_count.ket ket: SUCCEED
2707_subst_count.ket mol: SUCCEED
multi_merge4.ket:SUCCEED
19 changes: 16 additions & 3 deletions api/tests/integration/tests/formats/ket_to_ket.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ def find_diff(a, b):
indigo = Indigo()
indigo.setOption("json-saving-pretty", True)
indigo.setOption("ignore-stereochemistry-errors", True)
indigo.setOption("molfile-saving-skip-date", True)

print("*** KET to KET ***")

Expand Down Expand Up @@ -59,22 +60,34 @@ def check_res(filename, format, ket_ref, ket):
"monomer_shape",
"ambiguous_monomer",
]
formats = {
savers = {
"doc": [indigo.loadKetDocument],
"mol": [indigo.loadMolecule, indigo.loadQueryMolecule],
}
for filename in sorted(files):
for format in sorted(formats.keys()):
for format in sorted(savers.keys()):
file_path = os.path.join(ref_path, filename)
with open("{}_{}.ket".format(file_path, format), "r") as file:
ket_ref = file.read()
for loader in formats[format]:
for loader in savers[format]:
mol = loader(ket_ref)
# with open("{}_{}.ket".format(file_path, format), "w") as file:
# file.write(mol.json())
ket = mol.json()
check_res(filename, format + " " + loader.__name__, ket_ref, ket)

filename = "2707_subst_count"
file_path = os.path.join(ref_path, filename)
mol = indigo.loadQueryMoleculeFromFile("{}.ket".format(file_path))
savers = {"ket": mol.json, "mol": mol.molfile}
for format in sorted(savers.keys()):
data = savers[format]()
# with open("{}.{}".format(file_path, format), "w") as file:
# file.write(data)
with open("{}.{}".format(file_path, format), "r") as file:
data_ref = file.read()
check_res(filename, format, data_ref, data)

files = [
"multi_merge4",
]
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96 changes: 96 additions & 0 deletions api/tests/integration/tests/formats/ref/2707_subst_count.ket
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@@ -0,0 +1,96 @@
{
"root": {
"nodes": [
{
"$ref": "mol0"
}
]
},
"mol0": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [
7.300000,
-8.930000,
0.000000
],
"substitutionCount": 5
},
{
"label": "C",
"location": [
7.800000,
-10.470000,
0.000000
],
"substitutionCount": 7
},
{
"label": "C",
"location": [
8.110000,
-9.525000,
0.000000
],
"substitutionCount": 6
},
{
"label": "C",
"location": [
6.800000,
-10.470000,
0.000000
],
"substitutionCount": 8
},
{
"label": "C",
"location": [
6.490000,
-9.520000,
0.000000
],
"substitutionCount": 9
}
],
"bonds": [
{
"type": 1,
"atoms": [
0,
4
]
},
{
"type": 2,
"atoms": [
4,
3
]
},
{
"type": 1,
"atoms": [
3,
1
]
},
{
"type": 2,
"atoms": [
1,
2
]
},
{
"type": 1,
"atoms": [
2,
0
]
}
]
}
}
16 changes: 16 additions & 0 deletions api/tests/integration/tests/formats/ref/2707_subst_count.mol
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@@ -0,0 +1,16 @@

-INDIGO-01000000002D

5 5 0 0 0 0 0 0 0 0999 V2000
7.3000 -8.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8000 -10.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1100 -9.5250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8000 -10.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4900 -9.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
5 4 2 0 0 0 0
4 2 1 0 0 0 0
2 3 2 0 0 0 0
3 1 1 0 0 0 0
M SUB 5 1 5 2 6 3 6 4 6 5 6
M END
1 change: 1 addition & 0 deletions core/indigo-core/molecule/molfile_saver.h
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Expand Up @@ -54,6 +54,7 @@ namespace indigo
MODE_3000 // force saving to v3000 format
};
constexpr static int MAX_RING_BOND_COUNT = 4;
constexpr static int MAX_SUBSTITUTION_COUNT = 6;

MolfileSaver(Output& output);

Expand Down
2 changes: 2 additions & 0 deletions core/indigo-core/molecule/query_molecule.h
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Expand Up @@ -189,6 +189,8 @@ namespace indigo
virtual void _optimize(){};
};

constexpr static int MAX_ATOM_VALUE = 100;

class DLLEXPORT Atom : public Node
{
public:
Expand Down
3 changes: 1 addition & 2 deletions core/indigo-core/molecule/src/cml_loader.cpp
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Expand Up @@ -683,8 +683,7 @@ void CmlLoader::_loadMoleculeElement(XMLHandle& handle)
}
else if (subst > 0)
{
atom.reset(QueryMolecule::Atom::und(
atom.release(), new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, subst, (subst < 6 ? subst : 100))));
atom.reset(QueryMolecule::Atom::und(atom.release(), new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, subst)));
}
}
else if (strncmp(qf.ptr(), "u", 1) == 0)
Expand Down
5 changes: 2 additions & 3 deletions core/indigo-core/molecule/src/molecule_json_loader.cpp
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Expand Up @@ -477,9 +477,8 @@ void MoleculeJsonLoader::parseAtoms(const rapidjson::Value& atoms, BaseMolecule&
_pqmol->getVertex(atom_idx).degree())));
}
else if (sub_count > 0)
_pqmol->resetAtom(atom_idx,
QueryMolecule::Atom::und(_pqmol->releaseAtom(atom_idx), new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, sub_count,
(sub_count < 6 ? sub_count : 100))));
_pqmol->resetAtom(
atom_idx, QueryMolecule::Atom::und(_pqmol->releaseAtom(atom_idx), new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, sub_count)));
else
throw Error("invalid SUB value: %d", sub_count);
}
Expand Down
10 changes: 4 additions & 6 deletions core/indigo-core/molecule/src/molecule_savers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -93,12 +93,10 @@ bool MoleculeSavers::getSubstitutionCountFlagValue(QueryMolecule& qmol, int idx,
value = -1;
return true;
}
int values[1] = {6};
if (atom.sureValueBelongs(QueryMolecule::ATOM_SUBSTITUENTS, values, 1))
{
value = 6;
return true;
}
// Some data stored as min=value, max=100(e.g. MOL format)
auto subst_node = atom.sureConstraint(QueryMolecule::ATOM_SUBSTITUENTS);
if (subst_node != nullptr)
return subst_node->value_min;
}
else if (atom.sureValue(QueryMolecule::ATOM_SUBSTITUENTS_AS_DRAWN, v))
{
Expand Down
21 changes: 14 additions & 7 deletions core/indigo-core/molecule/src/molfile_loader.cpp
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Expand Up @@ -27,6 +27,7 @@
#include "molecule/molecule_3d_constraints.h"
#include "molecule/molecule_stereocenters.h"
#include "molecule/molfile_loader.h"
#include "molecule/molfile_saver.h"
#include "molecule/monomer_commons.h"
#include "molecule/parse_utils.h"
#include "molecule/query_molecule.h"
Expand Down Expand Up @@ -836,9 +837,11 @@ void MolfileLoader::_readCtab2000()
_qmol->getVertex(atom_idx).degree())));
}
else if (sub_count > 0)
_qmol->resetAtom(atom_idx, QueryMolecule::Atom::und(_qmol->releaseAtom(atom_idx),
new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, sub_count,
(sub_count < 6 ? sub_count : 100))));
_qmol->resetAtom(atom_idx, QueryMolecule::Atom::und(
_qmol->releaseAtom(atom_idx),
new QueryMolecule::Atom(
QueryMolecule::ATOM_SUBSTITUENTS, sub_count,
(sub_count < MolfileSaver::MAX_SUBSTITUTION_COUNT ? sub_count : QueryMolecule::MAX_ATOM_VALUE))));
else
throw Error("invalid SUB value: %d", sub_count);
}
Expand Down Expand Up @@ -2817,8 +2820,11 @@ void MolfileLoader::_readCtab3000()
new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS_AS_DRAWN, _qmol->getVertex(i).degree())));
}
else if (subst > 0)
_qmol->resetAtom(i, QueryMolecule::Atom::und(_qmol->releaseAtom(i), new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, subst,
(subst < 6 ? subst : 100))));
_qmol->resetAtom(
i, QueryMolecule::Atom::und(
_qmol->releaseAtom(i),
new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, subst,
(subst < MolfileSaver::MAX_SUBSTITUTION_COUNT ? subst : QueryMolecule::MAX_ATOM_VALUE))));
else
throw Error("invalid SUBST value: %d", subst);
}
Expand Down Expand Up @@ -2865,8 +2871,9 @@ void MolfileLoader::_readCtab3000()
new QueryMolecule::Atom(QueryMolecule::ATOM_RING_BONDS_AS_DRAWN, rbonds)));
}
else if (rb > 1)
_qmol->resetAtom(i, QueryMolecule::Atom::und(_qmol->releaseAtom(i),
new QueryMolecule::Atom(QueryMolecule::ATOM_RING_BONDS, rb, (rb < 4 ? rb : 100))));
_qmol->resetAtom(
i, QueryMolecule::Atom::und(_qmol->releaseAtom(i), new QueryMolecule::Atom(QueryMolecule::ATOM_RING_BONDS, rb,
(rb < 4 ? rb : QueryMolecule::MAX_ATOM_VALUE))));
else
throw Error("invalid RBCNT value: %d", rb);
}
Expand Down
2 changes: 1 addition & 1 deletion core/indigo-core/molecule/src/molfile_saver.cpp
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Expand Up @@ -1388,7 +1388,7 @@ void MolfileSaver::_writeCtab2000(Output& output, BaseMolecule& mol, bool query)
{
int* s = substitution_count.push();
s[0] = i;
s[1] = subst;
s[1] = subst > MAX_SUBSTITUTION_COUNT ? MAX_SUBSTITUTION_COUNT : subst;
}
}

Expand Down
4 changes: 4 additions & 0 deletions core/indigo-core/molecule/src/query_molecule.cpp
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Expand Up @@ -157,6 +157,10 @@ int QueryMolecule::getAtomSubstCount(int idx)
return res;
if (_atoms[idx]->sureValue(ATOM_SUBSTITUENTS_AS_DRAWN, res))
return res;
// Some data stored as min=value, max=100(e.g. MOL format)
auto atom = _atoms[idx]->sureConstraint(ATOM_SUBSTITUENTS);
if (atom != nullptr)
return atom->value_min;

return -1;
}
Expand Down
4 changes: 2 additions & 2 deletions core/indigo-core/molecule/src/smiles_loader.cpp
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Expand Up @@ -1356,8 +1356,8 @@ void SmilesLoader::_readOtherStuff()
_qmol->getVertex(atom_idx).degree())));
break;
default:
_qmol->resetAtom(atom_idx, QueryMolecule::Atom::und(_qmol->releaseAtom(atom_idx), new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS,
subs, (subs < 6 ? subs : 100))));
_qmol->resetAtom(atom_idx,
QueryMolecule::Atom::und(_qmol->releaseAtom(atom_idx), new QueryMolecule::Atom(QueryMolecule::ATOM_SUBSTITUENTS, subs)));
break;
}
if (_scanner.lookNext() == ',')
Expand Down

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