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rdkit/Code/GraphMol/catch_canon.cpp
Greg Landrum a8c8e9a8e1 Add canonicalization of stereo groups (enhanced stereo) (#6051) 
* add function to canonicalize enhanced stereo representations

* use enhanced stereo in canonicalization

* Fixes #6045
enables the doc tests for EnumerateStereoisomers.py
Re-enables the BRICS tests

* some things work... tests need to be updated

* c++ and python tests pass

* update expected psql results

* run the canonicalization on SMILES generation;
c++ and python tests pass

* cartridge and java tests pass

* update doctests
2023-02-08 04:21:51 +01:00

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//
// Copyright (C) 2022 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/StereoGroup.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/new_canon.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Canon.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
using namespace RDKit;
TEST_CASE("chirality and canonicalization") {
SECTION("basics") {
auto mol = "F[C@](O)(Cl)C[C@](F)(O)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(5)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "R");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[5]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(5)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[5]);
}
SECTION("same") {
auto mol = "F[C@](O)(Cl)C[C@](O)(F)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(5)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(5)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
}
SECTION("dependent") {
auto mol = "F[C@](O)(Cl)[C@](F)(O)[C@](F)(O)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(7)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "R");
CHECK(mol->getAtomWithIdx(4)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "R");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[7]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(4)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(7)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[7]);
}
SECTION("dependent non-chiral") {
auto mol = "F[C@](O)(Cl)[C@](F)(O)[C@](O)(F)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = false;
bool force = true;
mol->getAtomWithIdx(4)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(7)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[7]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(7)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[7]);
}
SECTION("swap parity") {
auto mol = "F[C@](O)(Cl)C[C@@](O)(Cl)F"_smiles;
REQUIRE(mol);
bool cleanIt = false;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(5)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(5)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
}
}
TEST_CASE("double bond stereo and canonicalization") {
SECTION("basics") {
auto mol = "CC=C(F)C(B)C(F)=CC"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(1)->setStereoAtoms(0, 4);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOTRANS);
mol->getBondWithIdx(7)->setStereoAtoms(4, 9);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOCIS);
bool breakTies = false;
std::vector<unsigned int> ranks;
Canon::rankMolAtoms(*mol, ranks, breakTies);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOCIS);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOTRANS);
std::vector<unsigned int> ranks2;
Canon::rankMolAtoms(*mol, ranks2, breakTies);
CHECK(ranks[0] == ranks2[9]);
CHECK(ranks[1] == ranks2[8]);
CHECK(ranks[2] == ranks2[6]);
CHECK(ranks[3] == ranks2[7]);
CHECK(ranks[4] == ranks2[4]);
CHECK(ranks[5] == ranks2[5]);
// same as previous example, different controlling atoms
mol->getBondWithIdx(7)->setStereoAtoms(7, 9);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOCIS);
std::vector<unsigned int> ranks3;
Canon::rankMolAtoms(*mol, ranks3, breakTies);
CHECK(ranks2 == ranks3);
}
SECTION("STEREOANY is higher priority than STEREONONE") {
auto mol = "CC=C(F)C(B)C(F)=CC"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(7)->setStereoAtoms(4, 9);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOANY);
bool breakTies = false;
std::vector<unsigned int> ranks;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[0] < ranks[9]);
}
}
TEST_CASE("enhanced stereo canonicalization") {
SECTION("simple chiral tags") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)Cl |&1:1|", "C[C@@H](F)Cl |&1:1|"},
{"C[C@H](F)Cl |o1:1|", "C[C@@H](F)Cl |o1:1|"},
};
for (const auto& [smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() ==
mol2->getAtomWithIdx(1)->getChiralTag());
}
}
SECTION("abs groups are not modified") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)Cl |a:1|", "C[C@@H](F)Cl |a:1|"},
};
for (const auto& [smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() !=
mol2->getAtomWithIdx(1)->getChiralTag());
}
}
SECTION("relative chiral tags") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)[C@H](Br)O |&1:1,3|", "C[C@@H](F)[C@@H](Br)O |&1:1,3|"},
{"C[C@H](F)[C@@H](Br)O |&1:1,3|", "C[C@@H](F)[C@H](Br)O |&1:1,3|"},
{"O[C@H](Br)[C@H](F)C |&1:1,3|", "O[C@@H](Br)[C@@H](F)C |&1:1,3|"},
{"O[C@H](Br)[C@@H](F)C |&1:1,3|", "O[C@@H](Br)[C@H](F)C |&1:1,3|"},
};
for (const auto& [smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() ==
mol2->getAtomWithIdx(1)->getChiralTag());
CHECK(mol1->getAtomWithIdx(3)->getChiralTag() ==
mol2->getAtomWithIdx(3)->getChiralTag());
}
}
SECTION("multiple groups") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)[C@H](Br)O |&1:1,o2:3|",
"C[C@@H](F)[C@@H](Br)O |&1:1,o2:3|"},
{"C[C@H](F)[C@H](Br)O |&1:1,o2:3|",
"C[C@@H](F)[C@@H](Br)O |o1:3,&1:1|"},
};
for (const auto& [smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() ==
mol2->getAtomWithIdx(1)->getChiralTag());
CHECK(mol1->getAtomWithIdx(3)->getChiralTag() ==
mol2->getAtomWithIdx(3)->getChiralTag());
}
}
}
TEST_CASE("using enhanced stereo in rankMolAtoms") {
SECTION("basics: different ranks") {
std::vector<std::string> smis{
"C[C@H](F)[C@@H](F)C |a:1|",
"C[C@H](F)[C@@H](F)C |&1:1|"
"C[C@H](F)[C@@H](F)C |o1:1|",
"C[C@H](F)[C@@H](F)C |o1:1,a:3|",
"C[C@H](F)[C@@H](F)C |o1:1,&:3|",
"C[C@H](F)[C@@H](F)C |a:1,&2:3|",
};
for (auto& smi : smis) {
INFO(smi);
std::unique_ptr<RWMol> mol{SmilesToMol(smi)};
REQUIRE(mol);
bool breakTies = false;
std::vector<unsigned int> atomRanks;
Canon::rankMolAtoms(*mol, atomRanks, breakTies);
CHECK(atomRanks[1] != atomRanks[3]);
}
}
SECTION("basics: same ranks") {
std::vector<std::string> smis{
"C[C@H](F)[C@@H](F)C |o1:1,o2:3|",
"C[C@H](F)[C@@H](F)C |&1:1,&2:3|",
"C[C@H](F)[C@@H](F)C |a:1,a:3|",
};
for (auto& smi : smis) {
INFO(smi);
std::unique_ptr<RWMol> mol{SmilesToMol(smi)};
REQUIRE(mol);
bool breakTies = false;
std::vector<unsigned int> atomRanks;
Canon::rankMolAtoms(*mol, atomRanks, breakTies);
CHECK(atomRanks[1] == atomRanks[3]);
}
}
SECTION("more complex, include group membership") {
auto m1 =
"C[C@@H]1CC(C[C@@H](C)[C@@H](C)O)C[C@H](C)C1 |o1:1,7,o2:5,11|"_smiles;
REQUIRE(m1);
std::vector<unsigned int> atomRanks;
bool breakTies = false;
Canon::rankMolAtoms(*m1, atomRanks, breakTies);
CHECK(atomRanks[11] > atomRanks[1]);
auto m2 =
"C[C@H](O)[C@H](C)CC1C[C@H](C)C[C@@H](C)C1 |o1:1,8;o2:3,11|"_smiles;
REQUIRE(m2);
Canon::rankMolAtoms(*m2, atomRanks, breakTies);
CHECK(atomRanks[11] > atomRanks[8]);
}
}
TEST_CASE("more enhanced stereo canonicalization") {
// FIX: add tests for ring stereo in an s group
SECTION("case 1") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)F |a:3,&1:1,7,&2:5,r|"_smiles;
REQUIRE(m1);
auto m2 = "C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)F |a:3,&1:1,7,&2:5,r|"_smiles;
REQUIRE(m2);
Canon::canonicalizeEnhancedStereo(*m1);
Canon::canonicalizeEnhancedStereo(*m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
}
SECTION("case 2") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,o1:7,&2:1,r|"_smiles;
REQUIRE(m1);
auto m2 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,&2:7,o1:1,r|"_smiles;
REQUIRE(m2);
Canon::canonicalizeEnhancedStereo(*m1);
Canon::canonicalizeEnhancedStereo(*m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
}
}
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