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Enable chemist-friendly depiction of R-groups (#6866)

Browse Source 
* - added a convenience function to relabel R-groups in a chemist-friendly fashion
- exposed functionality to MinimalLib through a JSON option at molecule creation time
- added relevant unit tests

* changes in response to review

* added missing library

* fixed Python test

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
2023-11-11 07:16:54 +01:00
committed by GitHub
parent b58b8f1397
commit 08cc96336c
9 changed files with 406 additions and 9 deletions
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40
Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp
View File

@@ -208,4 +208,44 @@ std::string toJSON(const RGroupColumns &cols, const std::string &prefix) {
return res;
}
void relabelMappedDummies(ROMol &mol, unsigned int inputLabels,
unsigned int outputLabels) {
for (auto &atom : mol.atoms()) {
if (atom->getAtomicNum()) {
continue;
}
unsigned int atomMapNum = 0;
if (inputLabels & AtomMap) {
atomMapNum = static_cast<unsigned int>(abs(atom->getAtomMapNum()));
}
if (!atomMapNum && (inputLabels & Isotope)) {
atomMapNum = atom->getIsotope();
}
if (!atomMapNum && (inputLabels & MDLRGroup)) {
atom->getPropIfPresent(common_properties::_MolFileRLabel, atomMapNum);
}
if (!atomMapNum) {
continue;
}
auto rLabel = "R" + std::to_string(atomMapNum);
if (outputLabels & AtomMap) {
atom->setAtomMapNum(atomMapNum);
} else {
atom->setAtomMapNum(0);
}
if (outputLabels & Isotope) {
atom->setIsotope(atomMapNum);
} else {
atom->setIsotope(0);
}
if (outputLabels & MDLRGroup) {
atom->setProp(common_properties::_MolFileRLabel, atomMapNum);
atom->setProp(common_properties::dummyLabel, rLabel);
} else {
atom->clearProp(common_properties::_MolFileRLabel);
atom->clearProp(common_properties::dummyLabel);
}
}
}
} // namespace RDKit

14
Code/GraphMol/RGroupDecomposition/RGroupUtils.h
View File

@@ -93,6 +93,20 @@ RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(
const RGroupColumns &rgr, const std::string &prefix = "");
//! Relabel dummy atoms bearing an R-group mapping (as
/// atom map number, isotope or MDLRGroup label) such that
/// they will be displayed by the rendering code as R# rather
/// than #*, *:#, #*:#, etc. By default, only the MDLRGroup label
/// is retained on output; this may be configured through the
/// outputLabels parameter.
/// In case there are multiple potential R-group mappings,
/// the priority on input is Atom map number > Isotope > MDLRGroup.
/// The inputLabels parameter allows to configure which mappings
/// are taken into consideration.
RDKIT_RGROUPDECOMPOSITION_EXPORT void relabelMappedDummies(
ROMol &mol, unsigned int inputLabels = AtomMap | Isotope | MDLRGroup,
unsigned int outputLabels = MDLRGroup);
} // namespace RDKit
#endif

29
Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
View File

@@ -43,6 +43,7 @@
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RGroupDecomposition/RGroupDecomp.h>
#include <GraphMol/RGroupDecomposition/RGroupUtils.h>
#include <RDBoost/Wrap.h>
#include <RDBoost/python_streambuf.h>
@@ -186,7 +187,13 @@ python::object RGroupDecomp(python::object cores, python::object mols,
} else {
return make_tuple(decomp.GetRGroupsAsColumn(asSmiles), unmatched);
}
} // namespace RDKit
}
void relabelMappedDummiesHelper(ROMol &mol, unsigned int inputLabels,
unsigned int outputLabels) {
relabelMappedDummies(mol, static_cast<RGroupLabelling>(inputLabels),
static_cast<RGroupLabelling>(outputLabels));
}
struct rgroupdecomp_wrapper {
static void wrap() {
@@ -405,11 +412,29 @@ struct rgroupdecomp_wrapper {
"\n"
" unmatched is a vector of indices in the input mols that were not "
"matched.\n";
python::def("RGroupDecompose", RDKit::RGroupDecomp,
python::def("RGroupDecompose", RGroupDecomp,
(python::arg("cores"), python::arg("mols"),
python::arg("asSmiles") = false, python::arg("asRows") = true,
python::arg("options") = RGroupDecompositionParameters()),
docString.c_str());
docString =
"Relabel dummy atoms bearing an R-group mapping (as\n"
"atom map number, isotope or MDLRGroup label) such that\n"
"they will be displayed by the rendering code as R# rather\n"
"than #*, *:#, #*:#, etc. By default, only the MDLRGroup label\n"
"is retained on output; this may be configured through the\n"
"outputLabels parameter.\n"
"In case there are multiple potential R-group mappings,\n"
"the priority on input is Atom map number > Isotope > MDLRGroup.\n"
"The inputLabels parameter allows to configure which mappings\n"
"are taken into consideration.\n";
python::def("RelabelMappedDummies", relabelMappedDummiesHelper,
(python::arg("mol"),
python::arg("inputLabels") = static_cast<RGroupLabelling>(
AtomMap | Isotope | MDLRGroup),
python::arg("outputLabels") = MDLRGroup),
docString.c_str());
};
};
} // namespace RDKit

125
Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py
View File

@@ -30,10 +30,6 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
import copy
import os
import pickle
import sys
import unittest
from collections import OrderedDict
@@ -43,7 +39,9 @@ from rdkit.Chem.rdRGroupDecomposition import (RGroupCoreAlignment,
RGroupDecompose,
RGroupDecomposition,
RGroupDecompositionParameters,
RGroupLabels)
RGroupLabels,
RGroupLabelling,
RelabelMappedDummies)
RDLogger.DisableLog("rdApp.warning")
@@ -725,6 +723,123 @@ M END
self.assertEqual(len(cmol_h.GetSubstructMatch(core)), core.GetNumAtoms())
self.assertFalse(nmol_h.HasSubstructMatch(core))
def testRelabelMappedDummies(self):
p = Chem.SmilesWriteParams()
p.canonical = False
allDifferentCore = Chem.MolFromMolBlock("""
RDKit 2D
8 8 0 0 0 0 0 0 0 0999 V2000
1.0808 -0.8772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0827 0.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2177 0.6246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2198 1.6246 0.0000 R# 0 0 0 0 0 15 0 0 0 4 0 0
-0.6493 0.1262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5142 0.6280 0.0000 R# 0 0 0 0 0 15 0 0 0 3 0 0
-0.6513 -0.8736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2137 -1.3754 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 0
3 5 2 0
5 6 1 0
5 7 1 0
7 8 2 0
8 1 1 0
M RGP 2 4 2 6 1
M END
)CTAB
""")
allDifferentCore.RemoveConformer(0)
allDifferentCore.GetAtomWithIdx(3).SetIsotope(6)
allDifferentCore.GetAtomWithIdx(5).SetIsotope(5)
self.assertEqual(Chem.MolToCXSmiles(allDifferentCore, p), "c1cc([6*:4])c([5*:3])cn1 |atomProp:3.dummyLabel.R2:3.molAtomMapNumber.4:5.dummyLabel.R1:5.molAtomMapNumber.3|")
# AtomMap in, MDLRGroup out
core = Chem.MolFromSmiles("c1cc([*:2])c([*:1])cn1")
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([*:2])c([*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|")
RelabelMappedDummies(core)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|")
# Isotope in, MDLRGroup out
core = Chem.MolFromSmiles("c1cc([2*])c([1*])cn1")
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([2*])c([1*])cn1 |atomProp:3.dummyLabel.*:5.dummyLabel.*|")
RelabelMappedDummies(core)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|")
# MDLRGroup in, MDLRGroup out
core = Chem.MolFromMolBlock("""
RDKit 2D
8 8 0 0 0 0 0 0 0 0999 V2000
1.0808 -0.8772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0827 0.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2177 0.6246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2198 1.6246 0.0000 R# 0 0 0 0 0 1 0 0 0 0 0 0
-0.6493 0.1262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5142 0.6280 0.0000 R# 0 0 0 0 0 1 0 0 0 0 0 0
-0.6513 -0.8736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2137 -1.3754 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 0
3 5 2 0
5 6 1 0
5 7 1 0
7 8 2 0
8 1 1 0
M RGP 2 4 2 6 1
M END
)CTAB
""")
core.RemoveConformer(0)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([2*])c([1*])cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|")
RelabelMappedDummies(core)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|")
# AtomMap and Isotope in, MDLRGroup out - AtomMap has priority
core = Chem.MolFromSmiles("c1cc([4*:2])c([3*:1])cn1")
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([4*:2])c([3*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|")
RelabelMappedDummies(core)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|")
# AtomMap and Isotope in, MDLRGroup out - force Isotope priority
core = Chem.MolFromSmiles("c1cc([4*:2])c([3*:1])cn1")
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([4*:2])c([3*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|")
RelabelMappedDummies(core, RGroupLabelling.Isotope)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R4:5.dummyLabel.R3|")
# AtomMap, Isotope and MDLRGroup in, MDLRGroup out - AtomMap has priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R4:5.dummyLabel.R3|")
# AtomMap, Isotope and MDLRGroup in, MDLRGroup out - force Isotope priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, RGroupLabelling.Isotope)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R6:5.dummyLabel.R5|")
# AtomMap, Isotope and MDLRGroup in, MDLRGroup out - force MDLRGroup priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, RGroupLabelling.MDLRGroup)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|")
# AtomMap, Isotope and MDLRGroup in, AtomMap out - AtomMap has priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, outputLabels=RGroupLabelling.AtomMap)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([*:4])c([*:3])cn1 |atomProp:3.molAtomMapNumber.4:5.molAtomMapNumber.3|")
# AtomMap, Isotope and MDLRGroup in, Isotope out - AtomMap has priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, outputLabels=RGroupLabelling.Isotope)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([4*])c([3*])cn1")
# AtomMap, Isotope and MDLRGroup in, AtomMap out - Isotope has priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, inputLabels=(RGroupLabelling.Isotope | RGroupLabelling.MDLRGroup), outputLabels=RGroupLabelling.AtomMap)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([*:6])c([*:5])cn1 |atomProp:3.molAtomMapNumber.6:5.molAtomMapNumber.5|")
# AtomMap, Isotope and MDLRGroup in, Isotope out - Isotope has priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, inputLabels=(RGroupLabelling.Isotope | RGroupLabelling.MDLRGroup), outputLabels=RGroupLabelling.Isotope)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([6*])c([5*])cn1")
# AtomMap, Isotope and MDLRGroup in, AtomMap out - MDLRGroup has priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, inputLabels=RGroupLabelling.MDLRGroup, outputLabels=RGroupLabelling.AtomMap)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([*:2])c([*:1])cn1 |atomProp:3.molAtomMapNumber.2:5.molAtomMapNumber.1|")
# AtomMap, Isotope and MDLRGroup in, Isotope out - MDLRGroup has priority
core = Chem.Mol(allDifferentCore)
RelabelMappedDummies(core, inputLabels=RGroupLabelling.MDLRGroup, outputLabels=RGroupLabelling.Isotope)
self.assertEqual(Chem.MolToCXSmiles(core, p), "c1cc([2*])c([1*])cn1")
if __name__ == '__main__':
rdBase.DisableLog("rdApp.debug")

163
Code/GraphMol/RGroupDecomposition/catch_rgd.cpp
View File

@@ -808,3 +808,166 @@ TEST_CASE("Mol matches core") {
match.clear();
CHECK(!SubstructMatch(*nmol, *core, match));
}
TEST_CASE("relabelMappedDummies") {
SmilesWriteParams p;
p.canonical = false;
auto allDifferentCore = R"CTAB(
RDKit 2D
8 8 0 0 0 0 0 0 0 0999 V2000
1.0808 -0.8772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0827 0.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2177 0.6246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2198 1.6246 0.0000 R# 0 0 0 0 0 15 0 0 0 4 0 0
-0.6493 0.1262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5142 0.6280 0.0000 R# 0 0 0 0 0 15 0 0 0 3 0 0
-0.6513 -0.8736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2137 -1.3754 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 0
3 5 2 0
5 6 1 0
5 7 1 0
7 8 2 0
8 1 1 0
M RGP 2 4 2 6 1
M END
)CTAB"_ctab;
allDifferentCore->removeConformer(0);
allDifferentCore->getAtomWithIdx(3)->setIsotope(6);
allDifferentCore->getAtomWithIdx(5)->setIsotope(5);
CHECK(
MolToCXSmiles(*allDifferentCore, p) ==
"c1cc([6*:4])c([5*:3])cn1 |atomProp:3.dummyLabel.R2:3.molAtomMapNumber.4:5.dummyLabel.R1:5.molAtomMapNumber.3|");
SECTION("AtomMap in, MDLRGroup out") {
auto core = "c1cc([*:2])c([*:1])cn1"_smiles;
CHECK(
MolToCXSmiles(*core, p) ==
"c1cc([*:2])c([*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|");
relabelMappedDummies(*core);
CHECK(MolToCXSmiles(*core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|");
}
SECTION("Isotope in, MDLRGroup out") {
auto core = "c1cc([2*])c([1*])cn1"_smiles;
CHECK(MolToCXSmiles(*core, p) ==
"c1cc([2*])c([1*])cn1 |atomProp:3.dummyLabel.*:5.dummyLabel.*|");
relabelMappedDummies(*core);
CHECK(MolToCXSmiles(*core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|");
}
SECTION("MDLRGroup in, MDLRGroup out") {
auto core = R"CTAB(
RDKit 2D
8 8 0 0 0 0 0 0 0 0999 V2000
1.0808 -0.8772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0827 0.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2177 0.6246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2198 1.6246 0.0000 R# 0 0 0 0 0 1 0 0 0 0 0 0
-0.6493 0.1262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5142 0.6280 0.0000 R# 0 0 0 0 0 1 0 0 0 0 0 0
-0.6513 -0.8736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2137 -1.3754 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 0
3 5 2 0
5 6 1 0
5 7 1 0
7 8 2 0
8 1 1 0
M RGP 2 4 2 6 1
M END
)CTAB"_ctab;
core->removeConformer(0);
CHECK(MolToCXSmiles(*core, p) ==
"c1cc([2*])c([1*])cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|");
relabelMappedDummies(*core);
CHECK(MolToCXSmiles(*core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|");
}
SECTION("AtomMap and Isotope in, MDLRGroup out - AtomMap has priority") {
auto core = "c1cc([4*:2])c([3*:1])cn1"_smiles;
CHECK(
MolToCXSmiles(*core, p) ==
"c1cc([4*:2])c([3*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|");
relabelMappedDummies(*core);
CHECK(MolToCXSmiles(*core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|");
}
SECTION("AtomMap and Isotope in, MDLRGroup out - force Isotope priority") {
auto core = "c1cc([4*:2])c([3*:1])cn1"_smiles;
CHECK(
MolToCXSmiles(*core, p) ==
"c1cc([4*:2])c([3*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|");
relabelMappedDummies(*core, Isotope);
CHECK(MolToCXSmiles(*core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R4:5.dummyLabel.R3|");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, MDLRGroup out - AtomMap has priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core);
CHECK(MolToCXSmiles(core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R4:5.dummyLabel.R3|");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, MDLRGroup out - force Isotope priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, Isotope);
CHECK(MolToCXSmiles(core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R6:5.dummyLabel.R5|");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, MDLRGroup out - force MDLRGroup priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, MDLRGroup);
CHECK(MolToCXSmiles(core, p) ==
"c1cc(*)c(*)cn1 |atomProp:3.dummyLabel.R2:5.dummyLabel.R1|");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, AtomMap out - AtomMap has priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, AtomMap | Isotope | MDLRGroup, AtomMap);
CHECK(
MolToCXSmiles(core, p) ==
"c1cc([*:4])c([*:3])cn1 |atomProp:3.molAtomMapNumber.4:5.molAtomMapNumber.3|");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, Isotope out - AtomMap has priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, AtomMap | Isotope | MDLRGroup, Isotope);
CHECK(MolToCXSmiles(core, p) == "c1cc([4*])c([3*])cn1");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, AtomMap out - Isotope has priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, Isotope | MDLRGroup, AtomMap);
CHECK(
MolToCXSmiles(core, p) ==
"c1cc([*:6])c([*:5])cn1 |atomProp:3.molAtomMapNumber.6:5.molAtomMapNumber.5|");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, Isotope out - Isotope has priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, Isotope | MDLRGroup, Isotope);
CHECK(MolToCXSmiles(core, p) == "c1cc([6*])c([5*])cn1");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, AtomMap out - MDLRGroup has priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, MDLRGroup, AtomMap);
CHECK(
MolToCXSmiles(core, p) ==
"c1cc([*:2])c([*:1])cn1 |atomProp:3.molAtomMapNumber.2:5.molAtomMapNumber.1|");
}
SECTION(
"AtomMap, Isotope and MDLRGroup in, Isotope out - MDLRGroup has priority") {
ROMol core(*allDifferentCore);
relabelMappedDummies(core, MDLRGroup, Isotope);
CHECK(MolToCXSmiles(core, p) == "c1cc([2*])c([1*])cn1");
}
}

5
Code/MinimalLib/CMakeLists.txt
View File

@@ -5,7 +5,8 @@ if(RDK_BUILD_MINIMAL_LIB)
set(MINIMAL_LIB_LIBRARIES "MolInterchange_static;Abbreviations_static;"
"CIPLabeler_static;MolDraw2D_static;Depictor_static;RDInchiLib_static;"
"SubstructMatch_static;FileParsers_static;"
"SmilesParse_static;GraphMol_static;RDGeometryLib_static;RDGeneral_static")
"SmilesParse_static;GraphMol_static;RDGeometryLib_static;"
"RDGeneral_static;RGroupDecomposition_static")
if(RDK_BUILD_MINIMAL_LIB_RXN)
add_definitions(-DRDK_BUILD_MINIMAL_LIB_RXN)
set(MINIMAL_LIB_LIBRARIES "${MINIMAL_LIB_LIBRARIES};ChemReactions_static")
@@ -40,7 +41,7 @@ if(RDK_BUILD_CFFI_LIB)
MolInterchange Abbreviations CIPLabeler
MolDraw2D Depictor
RDInchiLib SubstructMatch FileParsers
SmilesParse GraphMol RDGeometryLib RDGeneral )
SmilesParse GraphMol RDGeometryLib RDGeneral RGroupDecomposition)
if(RDK_URF_LIBS)
list(APPEND LIBS_TO_USE RingDecomposerLib)
endif()

23
Code/MinimalLib/cffi_test.c
View File

@@ -2213,6 +2213,28 @@ void test_capture_logs() {
}
}
void test_relabel_mapped_dummies() {
printf("--------------------------\n");
printf(" test_relabel_mapped_dummies\n");
char *mpkl;
size_t mpkl_size;
char *smiles;
mpkl = get_mol("c1cc([4*:2])c([3*:1])cn1", &mpkl_size, "");
smiles = get_cxsmiles(mpkl, mpkl_size, NULL);
assert(!strcmp(
smiles,
"c1cc([4*:2])c([3*:1])cn1 |atomProp:3.molAtomMapNumber.2:3.dummyLabel.*:5.molAtomMapNumber.1:5.dummyLabel.*|"));
free(smiles);
free(mpkl);
mpkl = get_mol("c1cc([4*:2])c([3*:1])cn1", &mpkl_size,
"{\"mappedDummiesAreRGroups\":true}");
smiles = get_cxsmiles(mpkl, mpkl_size, NULL);
assert(
!strcmp(smiles, "*c1ccncc1* |atomProp:0.dummyLabel.R2:7.dummyLabel.R1|"));
free(smiles);
free(mpkl);
}
int main() {
enable_logging();
char *vers = version();
@@ -2240,5 +2262,6 @@ int main() {
test_alignment_r_groups_aromatic_ring();
test_partial_sanitization();
test_capture_logs();
test_relabel_mapped_dummies();
return 0;
}

6
Code/MinimalLib/common.h
View File

@@ -47,6 +47,7 @@
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/ChemReactions/SanitizeRxn.h>
#include <GraphMol/RGroupDecomposition/RGroupUtils.h>
#include <RDGeneral/RDLog.h>
#include <sstream>
@@ -104,6 +105,7 @@ RWMol *mol_from_input(const std::string &input,
bool setAromaticity = true;
bool fastFindRings = true;
bool assignStereo = true;
bool mappedDummiesAreRGroups = false;
RWMol *res = nullptr;
boost::property_tree::ptree pt;
if (!details_json.empty()) {
@@ -117,6 +119,7 @@ RWMol *mol_from_input(const std::string &input,
LPT_OPT_GET(setAromaticity);
LPT_OPT_GET(fastFindRings);
LPT_OPT_GET(assignStereo);
LPT_OPT_GET(mappedDummiesAreRGroups);
}
try {
if (input.find("M END") != std::string::npos) {
@@ -170,6 +173,9 @@ RWMol *mol_from_input(const std::string &input,
if (mergeQueryHs) {
MolOps::mergeQueryHs(*res);
}
if (mappedDummiesAreRGroups) {
relabelMappedDummies(*res);
}
} catch (...) {
delete res;
res = nullptr;

10
Code/MinimalLib/tests/tests.js
View File

@@ -2690,6 +2690,15 @@ M END
fentanylScaffold.delete();
}
function test_relabel_mapped_dummies() {
var core = RDKitModule.get_mol("c1cc([4*:2])c([3*:1])cn1");
assert.equal(core.get_cxsmiles(), "c1cc([4*:2])c([3*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|");
core.delete();
core = RDKitModule.get_mol("c1cc([4*:2])c([3*:1])cn1", JSON.stringify({mappedDummiesAreRGroups: true}));
assert.equal(core.get_cxsmiles(), "*c1ccncc1* |atomProp:0.dummyLabel.R2:7.dummyLabel.R1|");
core.delete();
}
initRDKitModule().then(function(instance) {
var done = {};
const waitAllTestsFinished = () => {
@@ -2759,6 +2768,7 @@ initRDKitModule().then(function(instance) {
test_capture_logs();
test_rgroup_match_heavy_hydro_none_charged();
test_get_sss_json();
test_relabel_mapped_dummies();
waitAllTestsFinished().then(() =>
console.log("Tests finished successfully")
);