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rdkit/Code/GraphMol/CIPLabeler/catch_tests.cpp
Ricardo Rodriguez 86902488e9 Store CIP-ranked anchors after CIP labeling. (#9056) 
* add the _CIPNeighborRanks property

* store CIP-ranked chiral neighbors

* store CIP-ranked SP2 bond and atropisomer anchors

* add a test

* boost headers in test

* add Atom::NOATOM

* add NOATOM test

* amend and clarify implicit H in Tetrahedral

* rename property

* rename property to _CIPNeighborOrder

* deprecate Chirality::StereoInfo::NOATOM
2026-01-29 18:23:44 +01:00

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//
// Copyright (C) 2020-2025 Schrödinger, LLC 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 <bitset>
#include <list>
#include <string>
#include <vector>
#include <strstream>
#ifdef RDK_TEST_MULTITHREADED
#include <csignal>
#include <thread>
#include <chrono>
#endif
#include <RDGeneral/BoostStartInclude.h>
#include <boost/algorithm/string.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <catch2/catch_all.hpp>
#include <GraphMol/Atropisomers.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/MarvinParse/MarvinParser.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/test_fixtures.h>
#include "CIPLabeler.h"
#include "Digraph.h"
#include "rules/Pairlist.h"
#include "rules/Rule1a.h"
#include "rules/Rule2.h"
#include "CIPMol.h"
using namespace RDKit;
using namespace RDKit::CIPLabeler;
std::string toBinaryString(PairList::pairing_t value) {
return std::bitset<PairList::numPairingBits>(value).to_string();
}
TEST_CASE("Descriptor lists", "[accurateCIP]") {
auto descriptors = PairList();
SECTION("IgnoreConstructionNulls") {
CHECK(!descriptors.add(Descriptor::NONE));
CHECK(!descriptors.add(Descriptor::UNKNOWN));
CHECK(!descriptors.add(Descriptor::ns));
}
SECTION("IgnoreConstructionPseudo") {
CHECK(!descriptors.add(Descriptor::r));
CHECK(!descriptors.add(Descriptor::s));
CHECK(descriptors.add(Descriptor::R));
CHECK(descriptors.add(Descriptor::S));
}
SECTION("Pairing") {
REQUIRE(descriptors.getPairing() == 0);
CHECK("0000000000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
descriptors.add(Descriptor::R);
CHECK("0000000000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// like
descriptors.add(Descriptor::R);
CHECK("0100000000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// like
descriptors.add(Descriptor::R);
CHECK("0110000000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// unlike
descriptors.add(Descriptor::S);
CHECK("0110000000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// like
descriptors.add(Descriptor::R);
CHECK("0110100000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// like
descriptors.add(Descriptor::R);
CHECK("0110110000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// like
descriptors.add(Descriptor::R);
CHECK("0110111000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// unlike
descriptors.add(Descriptor::S);
CHECK("0110111000000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
// like
descriptors.add(Descriptor::R);
CHECK("0110111010000000000000000000000000000000000000000000000000000000" ==
toBinaryString(descriptors.getPairing()));
}
SECTION("pairRM") {
PairList list1 = PairList();
PairList list2 = PairList();
list1.add(Descriptor::R);
list1.add(Descriptor::M);
list1.add(Descriptor::R);
list1.add(Descriptor::S);
list2.add(Descriptor::R);
list2.add(Descriptor::P);
list2.add(Descriptor::S);
list2.add(Descriptor::M);
CHECK(list1.toString() == "R:llu");
CHECK(list2.toString() == "R:uul");
}
}
void check_incoming_edge_count(Node *root) {
auto queue = std::list<Node *>({root});
for (const auto &node : queue) {
int incoming_edges = 0;
for (const auto &e : node->getEdges()) {
if (!e->isBeg(node)) {
REQUIRE(e->isEnd(node));
++incoming_edges;
} else if (!e->getEnd()->isTerminal()) {
queue.push_back(e->getEnd());
}
}
// Only the current root should have no incoming nodes.
// All other nodes should have exactly one incoming edge.
if (node == root) {
CHECK(incoming_edges == 0);
} else {
CHECK(incoming_edges == 1);
}
}
}
void expandAll(Digraph &g) {
auto queue = std::list<Node *>({g.getOriginalRoot()});
for (const auto &node : queue) {
for (const auto &e : node->getEdges()) {
if (!e->isBeg(node)) {
continue;
}
if (!e->getEnd()->isTerminal()) {
queue.push_back(e->getEnd());
}
}
}
}
TEST_CASE("Digraph", "[accurateCIP]") {
auto mol =
R"(CC1(OC2=C(C=3NC[C@@]4(C3C=C2)C([C@@H]5C[C@@]67C(N([C@]5(C4)CN6CC[C@@]7(C)O)C)=O)(C)C)OC=C1)C)"_smiles; // VS040
CIPLabeler::CIPMol cipmol(*mol);
auto initial_root_idx = 1u;
auto initial_root_atom = cipmol.getAtom(initial_root_idx);
Digraph g(cipmol, initial_root_atom);
expandAll(g);
REQUIRE(g.getNumNodes() == 3819);
auto current_root = g.getCurrentRoot();
REQUIRE(current_root->getAtom()->getIdx() == initial_root_idx);
check_incoming_edge_count(current_root);
auto new_root_idx = 24u;
auto new_root_atom = cipmol.getAtom(new_root_idx);
auto new_root_nodes = g.getNodes(new_root_atom);
CHECK(new_root_nodes.size() == 104);
Node *new_root_node = *new_root_nodes.begin();
for (const auto &node : new_root_nodes) {
if (!node->isDuplicate() &&
node->getDistance() > new_root_node->getDistance()) {
new_root_node = node;
}
}
REQUIRE(new_root_node->getDistance() == 25);
g.changeRoot(new_root_node);
REQUIRE(g.getNumNodes() == 3819);
current_root = g.getCurrentRoot();
REQUIRE(current_root->getAtom()->getIdx() == new_root_idx);
check_incoming_edge_count(current_root);
}
TEST_CASE("Rule1a", "[accurateCIP]") {
SECTION("Compare equal") {
auto mol = "COC"_smiles;
CIPLabeler::CIPMol cipmol(*mol);
Digraph g(cipmol, cipmol.getAtom(1));
auto origin = g.getOriginalRoot();
auto frac = origin->getAtomicNumFraction();
REQUIRE(frac.numerator() == 8);
REQUIRE(frac.denominator() == 1);
Rule1a rule;
auto edges = origin->getEdges();
REQUIRE(edges.size() == 2);
REQUIRE(edges[0] != edges[1]);
CHECK(0 == rule.compare(edges[0], edges[1]));
CHECK(!rule.getSorter()->prioritize(origin, edges).isUnique());
}
SECTION("Compare different") {
auto mol = "CON"_smiles;
CIPLabeler::CIPMol cipmol(*mol);
Digraph g(cipmol, cipmol.getAtom(1));
auto origin = g.getOriginalRoot();
auto frac = origin->getAtomicNumFraction();
REQUIRE(frac.numerator() == 8);
REQUIRE(frac.denominator() == 1);
Rule1a rule;
auto edges = origin->getEdges();
REQUIRE(edges.size() == 2);
REQUIRE(edges[0] != edges[1]);
auto frac0 = edges[0]->getEnd()->getAtomicNumFraction();
REQUIRE(frac0.numerator() == 6);
REQUIRE(frac0.denominator() == 1);
auto frac1 = edges[1]->getEnd()->getAtomicNumFraction();
REQUIRE(frac1.numerator() == 7);
REQUIRE(frac1.denominator() == 1);
CHECK(rule.compare(edges[0], edges[1]) < 0);
CHECK(rule.compare(edges[1], edges[0]) > 0);
CHECK(rule.getSorter()->prioritize(origin, edges).isUnique());
}
}
TEST_CASE("Rule2", "[accurateCIP]") {
SECTION("Compare equal") {
auto mol = "COC"_smiles;
CIPLabeler::CIPMol cipmol(*mol);
Digraph g(cipmol, cipmol.getAtom(1));
auto origin = g.getOriginalRoot();
auto frac = origin->getAtomicNumFraction();
REQUIRE(frac.numerator() == 8);
REQUIRE(frac.denominator() == 1);
Rule2 rule;
auto edges = origin->getEdges();
REQUIRE(edges.size() == 2);
REQUIRE(edges[0] != edges[1]);
CHECK(0 == rule.compare(edges[0], edges[1]));
CHECK(!rule.getSorter()->prioritize(origin, edges).isUnique());
}
SECTION("Compare different: Zero Mass Num") {
auto mol = "CO[13C]"_smiles;
CIPLabeler::CIPMol cipmol(*mol);
Digraph g(cipmol, cipmol.getAtom(1));
auto origin = g.getOriginalRoot();
auto frac = origin->getAtomicNumFraction();
REQUIRE(frac.numerator() == 8);
REQUIRE(frac.denominator() == 1);
Rule2 rule;
auto edges = origin->getEdges();
REQUIRE(edges.size() == 2);
REQUIRE(edges[0] != edges[1]);
REQUIRE(edges[0]->getEnd()->getMassNum() == 0);
REQUIRE(edges[1]->getEnd()->getMassNum() == 13);
CHECK(rule.compare(edges[0], edges[1]) < 0);
CHECK(rule.compare(edges[1], edges[0]) > 0);
CHECK(rule.getSorter()->prioritize(origin, edges).isUnique());
}
SECTION("Compare different: Non-Zero Mass Num") {
auto mol = "[13C]O[14C]"_smiles;
CIPLabeler::CIPMol cipmol(*mol);
Digraph g(cipmol, cipmol.getAtom(1));
auto origin = g.getOriginalRoot();
auto frac = origin->getAtomicNumFraction();
REQUIRE(frac.numerator() == 8);
REQUIRE(frac.denominator() == 1);
Rule2 rule;
auto edges = origin->getEdges();
REQUIRE(edges.size() == 2);
REQUIRE(edges[0] != edges[1]);
REQUIRE(edges[0]->getEnd()->getMassNum() == 13);
REQUIRE(edges[1]->getEnd()->getMassNum() == 14);
CHECK(rule.compare(edges[0], edges[1]) < 0);
CHECK(rule.compare(edges[1], edges[0]) > 0);
CHECK(rule.getSorter()->prioritize(origin, edges).isUnique());
}
}
TEST_CASE("Tetrahedral assignment", "[accurateCIP]") {
auto mol = "Br[C@H](Cl)F"_smiles;
REQUIRE(mol->getNumAtoms() == 4);
auto chiral_atom = mol->getAtomWithIdx(1);
chiral_atom->clearProp(common_properties::_CIPCode);
REQUIRE(chiral_atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW);
CHECK(!mol->hasProp(common_properties::_CIPComputed));
CIPLabeler::assignCIPLabels(*mol);
CHECK(mol->hasProp(common_properties::_CIPComputed));
std::string chirality;
CHECK(chiral_atom->getPropIfPresent(common_properties::_CIPCode, chirality));
CHECK(chirality == "S");
}
TEST_CASE("Double bond stereo assignment", "[accurateCIP]") {
auto useLegacy = GENERATE(true, false);
UseLegacyStereoPerceptionFixture fx(useLegacy);
CAPTURE(useLegacy);
auto mol = R"(CC\C(\C(\C)=N\O)=N\O)"_smiles; // VS013
REQUIRE(mol->getNumAtoms() == 9);
auto bond_1 = mol->getBondWithIdx(4);
auto bond_2 = mol->getBondWithIdx(6);
REQUIRE(bond_1->getBondType() == Bond::DOUBLE);
REQUIRE(bond_2->getBondType() == Bond::DOUBLE);
if (useLegacy) {
CHECK(bond_1->getStereo() == Bond::STEREOE);
CHECK(bond_2->getStereo() == Bond::STEREOZ);
} else {
CHECK(bond_1->getStereo() == Bond::STEREOTRANS);
CHECK(bond_1->getStereoAtoms() == std::vector<int>({2, 6}));
CHECK(bond_2->getStereo() == Bond::STEREOTRANS);
CHECK(bond_2->getStereoAtoms() == std::vector<int>({1, 8}));
}
CIPLabeler::assignCIPLabels(*mol);
std::string chirality;
CHECK(bond_1->getPropIfPresent(common_properties::_CIPCode, chirality));
CHECK(chirality == "E");
CHECK(bond_2->getPropIfPresent(common_properties::_CIPCode, chirality));
CHECK(chirality == "Z");
}
TEST_CASE("phosphine and arsine chirality", "[accurateCIP]") {
const std::vector<std::pair<std::string, std::string>> mols{
{"C[P@](C1CCCC1)C1=CC=CC=C1", "R"},
{"C[As@@](C1CCCC1)C1=CC=CC=C1", "S"},
{"C[P@H]C1CCCCC1", "R"},
{"C[P@@H]C1CCCCC1", "S"}};
for (const auto &ref : mols) {
INFO(ref.first);
std::unique_ptr<RWMol> mol{SmilesToMol(ref.first)};
REQUIRE(mol);
CIPLabeler::assignCIPLabels(*mol);
std::string chirality;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == ref.second);
}
}
TEST_CASE("assign specific atoms and bonds", "[accurateCIP]") {
SECTION("Assign atoms") {
auto mol = "C[C@H](Cl)CC[C@H](Cl)C"_smiles;
REQUIRE(mol);
auto atom1 = mol->getAtomWithIdx(1);
auto atom5 = mol->getAtomWithIdx(5);
REQUIRE(atom1->hasProp(common_properties::_CIPCode));
REQUIRE(atom5->hasProp(common_properties::_CIPCode));
atom1->clearProp(common_properties::_CIPCode);
atom5->clearProp(common_properties::_CIPCode);
boost::dynamic_bitset<> atoms(mol->getNumAtoms());
boost::dynamic_bitset<> bonds;
atoms.set(1);
CIPLabeler::assignCIPLabels(*mol, atoms, bonds);
std::string chirality;
CHECK(atom1->getPropIfPresent(common_properties::_CIPCode, chirality));
CHECK(chirality == "S");
CHECK(!atom5->hasProp(common_properties::_CIPCode));
}
SECTION("Assign bonds") {
auto mol = R"(C\C=C\C=C/C)"_smiles;
REQUIRE(mol);
auto bond1 = mol->getBondWithIdx(1);
auto bond3 = mol->getBondWithIdx(3);
REQUIRE(bond1->getBondType() == Bond::DOUBLE);
REQUIRE(bond3->getBondType() == Bond::DOUBLE);
REQUIRE(!bond1->hasProp(common_properties::_CIPCode));
REQUIRE(!bond3->hasProp(common_properties::_CIPCode));
boost::dynamic_bitset<> atoms;
boost::dynamic_bitset<> bonds(mol->getNumBonds());
bonds.set(3);
CIPLabeler::assignCIPLabels(*mol, atoms, bonds);
std::string stereo;
CHECK(!bond1->hasProp(common_properties::_CIPCode));
CHECK(bond3->getPropIfPresent(common_properties::_CIPCode, stereo));
CHECK(stereo == "Z");
}
}
TEST_CASE("para-stereochemistry", "[accurateCIP]") {
SECTION("example 1") {
// slightly simplified complex example from Salome Rieder
auto mol = "C\\C=C/[C@@H](\\C=C\\O)[C@H](C)[C@H](\\C=C/C)\\C=C\\O"_smiles;
REQUIRE(mol);
CIPLabeler::assignCIPLabels(*mol);
std::string chirality;
CHECK(mol->getAtomWithIdx(3)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "R");
CHECK(mol->getAtomWithIdx(7)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "r");
CHECK(mol->getAtomWithIdx(9)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "S");
}
SECTION("example 2") {
// lovely complex example from Salome Rieder
auto mol = "C\\C=C/[C@@H](\\C=C\\C)[C@H](C)[C@H](\\C=C/C)\\C=C\\C"_smiles;
REQUIRE(mol);
CIPLabeler::assignCIPLabels(*mol);
std::string chirality;
CHECK(mol->getAtomWithIdx(3)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "R");
CHECK(mol->getAtomWithIdx(7)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "r");
CHECK(mol->getAtomWithIdx(9)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "S");
}
}
TEST_CASE("para-stereochemistry2", "[accurateCIP]") {
SECTION("example 1") {
// example with one pseudo symmetry
UseLegacyStereoPerceptionFixture useLegacy(false);
auto mol = "OC(=O)[C@H]1CC[C@@H](CC1)O[C@@H](F)Cl"_smiles;
REQUIRE(mol);
CIPLabeler::assignCIPLabels(*mol);
std::string chirality;
CHECK(mol->getAtomWithIdx(3)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "S");
CHECK(mol->getAtomWithIdx(6)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "r");
CHECK(mol->getAtomWithIdx(10)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "S");
}
SECTION("example 2") {
// example with one pseudo symmetry
UseLegacyStereoPerceptionFixture useLegacy(false);
auto mol = "OC(=O)[C@H]1CC[C@@H](CC1)O[CH](Cl)Cl"_smiles;
REQUIRE(mol);
CIPLabeler::assignCIPLabels(*mol);
std::string chirality;
CHECK(mol->getAtomWithIdx(3)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "r");
CHECK(mol->getAtomWithIdx(6)->getPropIfPresent(common_properties::_CIPCode,
chirality));
CHECK(chirality == "r");
CHECK(!mol->getAtomWithIdx(10)->getPropIfPresent(
common_properties::_CIPCode, chirality));
// CHECK(chirality == "S");
}
}
TEST_CASE(
"Github #4996: Bad handling of dummy atoms in the CIP assignment code",
"[accurateCIP]") {
SECTION("case 1") {
auto m = "*[C@](F)(Cl)Br"_smiles;
REQUIRE(m);
bool cleanit = true;
bool force = true;
// original assignment:
MolOps::assignStereochemistry(*m, cleanit, force);
std::string cip;
CHECK(m->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
m->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
CIPLabeler::assignCIPLabels(*m);
CHECK(m->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
}
SECTION("dummies can match dummies") {
auto m = "*[C@](*)(Cl)Br"_smiles;
REQUIRE(m);
bool cleanit = true;
bool force = true;
// original assignment:
MolOps::assignStereochemistry(*m, cleanit, force);
CHECK(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
CIPLabeler::assignCIPLabels(*m);
CHECK(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
}
SECTION("case 2") {
auto m = "C1CC[C@](*)2CCCC[C@H]2C1"_smiles;
REQUIRE(m);
bool cleanit = true;
bool force = true;
// original assignment doesn't work for these:
MolOps::assignStereochemistry(*m, cleanit, force);
CHECK(!m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
CHECK(!m->getAtomWithIdx(9)->hasProp(common_properties::_CIPCode));
CIPLabeler::assignCIPLabels(*m);
std::string cip;
CHECK(m->getAtomWithIdx(3)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "s");
cip = "";
CHECK(m->getAtomWithIdx(9)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "s");
}
}
TEST_CASE("CIP code errors on fragments which cannot be kekulized",
"[accurateCIP]") {
SECTION("fragment not affecting the stereochem") {
auto m = "F[C@H](CNC)CCc(:c):c"_smarts;
m->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
m->updatePropertyCache();
CIPLabeler::assignCIPLabels(*m);
std::string cip;
CHECK(m->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
}
SECTION("fragment, unique bits") {
auto m = "F[C@H](C(N)C)c(:c):c"_smarts;
m->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
m->updatePropertyCache();
CIPLabeler::assignCIPLabels(*m);
std::string cip;
CHECK(m->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
}
SECTION("fragment, non-unique bits") {
auto m = "F[C@H]([C]([NH])[CH2])c(:n):c"_smarts;
m->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
m->updatePropertyCache();
CIPLabeler::assignCIPLabels(*m);
std::string cip;
CHECK(!m->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
}
}
TEST_CASE("GitHub Issue #5142", "[bug][accurateCIP]") {
auto mol = "*C1C[C@H](CCC)[C@@H](C)[C@H](C)C1"_smiles;
REQUIRE(mol);
CIPLabeler::assignCIPLabels(*mol);
}
TEST_CASE("Test early termination of CIP calculation", "[accurateCIP]") {
constexpr const char *molBlock = R"(
Mrv2117 11112217353D
40 50 0 0 0 0 999 V2000
7.5483 -7.7451 -3.3419 H 0 0 0 0 0 0 0 0 0 0 0 0
9.3984 -5.8792 -3.4318 H 0 0 0 0 0 0 0 0 0 0 0 0
9.3399 -6.5425 -1.9898 C 0 0 2 0 0 0 0 0 0 0 0 0
8.6820 -3.9425 -1.6474 H 0 0 0 0 0 0 0 0 0 0 0 0
5.8163 -7.1034 -1.6635 H 0 0 0 0 0 0 0 0 0 0 0 0
6.5722 -4.7343 -0.6304 H 0 0 0 0 0 0 0 0 0 0 0 0
7.1701 -7.2380 -0.8890 C 0 0 1 0 0 0 0 0 0 0 0 0
11.8300 -6.9765 -2.5544 H 0 0 0 0 0 0 0 0 0 0 0 0
10.6631 -7.1690 -1.5375 C 0 0 1 0 0 0 0 0 0 0 0 0
11.4077 -9.5239 -2.1472 H 0 0 0 0 0 0 0 0 0 0 0 0
11.9006 -10.0139 0.4722 H 0 0 0 0 0 0 0 0 0 0 0 0
10.6600 -8.8749 0.2914 C 0 0 2 0 0 0 0 0 0 0 0 0
12.5136 -5.9115 -0.4190 H 0 0 0 0 0 0 0 0 0 0 0 0
12.5338 -7.8406 1.4379 H 0 0 0 0 0 0 0 0 0 0 0 0
8.6981 -8.8654 3.4177 H 0 0 0 0 0 0 0 0 0 0 0 0
9.4046 -10.6907 1.7143 H 0 0 0 0 0 0 0 0 0 0 0 0
9.3185 -9.3106 0.9700 C 0 0 1 0 0 0 0 0 0 0 0 0
7.4958 -10.8075 -0.1783 H 0 0 0 0 0 0 0 0 0 0 0 0
6.5552 -7.8780 2.6983 H 0 0 0 0 0 0 0 0 0 0 0 0
5.8522 -9.1147 0.4514 H 0 0 0 0 0 0 0 0 0 0 0 0
7.1601 -8.2997 0.2353 C 0 0 2 0 0 0 0 0 0 0 0 0
7.5774 -7.5989 1.5700 C 0 0 1 0 0 0 0 0 0 0 0 0
10.6577 -4.0099 0.1683 H 0 0 0 0 0 0 0 0 0 0 0 0
11.0808 -6.4894 -0.1982 C 0 0 2 0 0 0 0 0 0 0 0 0
8.9123 -5.4699 -0.9424 C 0 0 1 0 0 0 0 0 0 0 0 0
8.9155 -8.2329 2.0184 C 0 0 2 0 0 0 0 0 0 0 0 0
11.0766 -7.5513 0.9147 C 0 0 1 0 0 0 0 0 0 0 0 0
10.6780 -6.9857 3.3021 H 0 0 0 0 0 0 0 0 0 0 0 0
7.5861 -5.8939 -0.2667 C 0 0 2 0 0 0 0 0 0 0 0 0
6.9973 -5.0597 1.9875 H 0 0 0 0 0 0 0 0 0 0 0 0
9.3193 -5.8429 1.5048 C 0 0 2 0 0 0 0 0 0 0 0 0
9.4740 -4.7173 2.5743 H 0 0 0 0 0 0 0 0 0 0 0 0
9.9809 -7.1457 1.9811 C 0 0 1 0 0 0 0 0 0 0 0 0
7.8270 -6.1245 1.2483 C 0 0 2 0 0 0 0 0 0 0 0 0
10.0023 -5.4308 0.1366 C 0 0 1 0 0 0 0 0 0 0 0 0
8.9125 -8.9385 -1.4737 C 0 0 2 0 0 0 0 0 0 0 0 0
8.2374 -9.3522 -0.1173 C 0 0 1 0 0 0 0 0 0 0 0 0
10.4116 -8.6461 -1.2148 C 0 0 1 0 0 0 0 0 0 0 0 0
8.7726 -9.9758 -2.5047 H 0 0 0 0 0 0 0 0 0 0 0 0
8.2577 -7.6250 -1.9478 C 0 0 2 0 0 0 0 0 0 0 0 0
1 40 1 0 0 0 0
2 3 1 0 0 0 0
3 9 1 0 0 0 0
3 25 1 0 0 0 0
3 40 1 0 0 0 0
4 25 1 0 0 0 0
5 7 1 0 0 0 0
6 29 1 0 0 0 0
7 21 1 0 0 0 0
7 29 1 0 0 0 0
7 40 1 0 0 0 0
8 9 1 0 0 0 0
9 24 1 0 0 0 0
9 38 1 0 0 0 0
10 38 1 0 0 0 0
11 12 1 0 0 0 0
12 17 1 0 0 0 0
12 27 1 0 0 0 0
12 38 1 0 0 0 0
13 24 1 0 0 0 0
14 27 1 0 0 0 0
15 26 1 0 0 0 0
16 17 1 0 0 0 0
17 26 1 0 0 0 0
17 37 1 0 0 0 0
18 37 1 0 0 0 0
19 22 1 0 0 0 0
20 21 1 0 0 0 0
21 22 1 0 0 0 0
21 37 1 0 0 0 0
22 26 1 0 0 0 0
22 34 1 0 0 0 0
23 35 1 0 0 0 0
24 27 1 0 0 0 0
24 35 1 0 0 0 0
25 29 1 0 0 0 0
25 35 1 0 0 0 0
26 33 1 0 0 0 0
27 33 1 0 0 0 0
28 33 1 0 0 0 0
29 34 1 0 0 0 0
30 34 1 0 0 0 0
31 32 1 0 0 0 0
31 33 1 0 0 0 0
31 35 1 0 0 0 0
31 34 1 0 0 0 0
36 37 1 0 0 0 0
36 38 1 0 0 0 0
36 39 1 0 0 0 0
36 40 1 0 0 0 0
M END
)";
v2::FileParsers::MolFileParserParams params{.sanitize = false};
auto mol = v2::FileParsers::MolFromMolBlock(molBlock, params);
REQUIRE(mol);
SECTION("Exceeds max iterations") {
CHECK_THROWS_AS(CIPLabeler::assignCIPLabels(*mol, 100000),
CIPLabeler::MaxIterationsExceeded);
// try a second call to test that the timer is reset
CHECK_THROWS_AS(CIPLabeler::assignCIPLabels(*mol, 100000),
CIPLabeler::MaxIterationsExceeded);
}
#ifdef RDK_TEST_MULTITHREADED
SECTION("Ctrl+c interruption") {
using namespace std::chrono_literals;
// create one thread for assignCIPLabels...
std::thread cgThread([&mol]() {
// give the calculation a while to run (~15 seconds on my laptop)
// but still make sure it won't run forever
constexpr size_t maxIterations = 8000000;
CIPLabeler::assignCIPLabels(*mol, maxIterations);
});
// ... then another one to raise SIGINT
std::thread interruptThread([]() {
// sleep for a bit to allow for a few iterations, but not enough to
// hit maxIterations and trigger the exception
std::this_thread::sleep_for(100ms);
std::raise(SIGINT);
});
cgThread.join();
interruptThread.join();
}
#endif
}
void testOneAtropIsomerMandP(std::string inputText, const std::string &expected,
bool isSmiles = true) {
std::unique_ptr<RWMol> mol;
if (isSmiles) {
SmilesParserParams smilesParserParams;
smilesParserParams.sanitize = true;
smilesParserParams.removeHs = false;
mol.reset(SmilesToMol(inputText, smilesParserParams));
} else {
mol.reset(MrvBlockToMol(inputText));
}
REQUIRE(mol);
CIPLabeler::assignCIPLabels(*mol, 100000);
std::ostrstream out;
bool foundOne = false;
for (auto bond : mol->bonds()) {
if (bond->hasProp(common_properties::_CIPCode)) {
out << bond->getBeginAtomIdx() << "-" << bond->getEndAtomIdx() << "="
<< bond->getProp<std::string>(common_properties::_CIPCode) << ":";
foundOne = true;
}
}
if (!foundOne) {
out << "none ";
}
out << std::ends;
CHECK(out.str() == expected);
}
TEST_CASE("AssignMandP", "[accurateCIP]") {
SECTION("Suzzana") {
testOneAtropIsomerMandP(
"<cml xmlns=\"http://www.chemaxon.com\" version=\"ChemAxon file format v20.20.0, generated by vunknown\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd\"><MDocument><MChemicalStruct><molecule molID=\"m1\" absStereo=\"true\"><atomArray><atom id=\"a1\" elementType=\"C\" x2=\"4.070453300769707\" y2=\"-1.47671998818624\"/><atom id=\"a2\" elementType=\"C\" x2=\"4.372853298350507\" y2=\"0.03322666640085333\"/><atom id=\"a3\" elementType=\"C\" x2=\"5.8316532866801065\" y2=\"0.5265866624539733\"/><atom id=\"a4\" elementType=\"C\" x2=\"6.134053284260906\" y2=\"2.0365333170410667\"/><atom id=\"a5\" elementType=\"C\" x2=\"4.977466626846933\" y2=\"3.053306642240213\"/><atom id=\"a6\" elementType=\"O\" x2=\"5.27967995776256\" y2=\"4.56343996349248\" lonePair=\"2\"/><atom id=\"a7\" elementType=\"C\" x2=\"3.51847997185216\" y2=\"2.5601333128522668\"/><atom id=\"a8\" elementType=\"C\" x2=\"2.361893314438187\" y2=\"3.576906638051413\"/><atom id=\"a9\" elementType=\"C\" x2=\"3.2162666409365337\" y2=\"1.0501866582651733\"/><atom id=\"a10\" elementType=\"N\" x2=\"-1.0962933245629867\" y2=\"-0.40786666340373334\" lonePair=\"1\"/><atom id=\"a11\" elementType=\"C\" x2=\"-2.3527466478446932\" y2=\"0.48253332947306665\"/><atom id=\"a12\" elementType=\"N\" x2=\"-2.37103998103168\" y2=\"2.022346650487893\" lonePair=\"1\"/><atom id=\"a13\" elementType=\"C\" x2=\"-3.58791997129664\" y2=\"-0.43735999650112\"/><atom id=\"a14\" elementType=\"C\" x2=\"-3.09455997524352\" y2=\"-1.89615998483072\"/><atom id=\"a15\" elementType=\"C\" x2=\"-1.5547466542286932\" y2=\"-1.8780533183089065\"/></atomArray><bondArray><bond id=\"b1\" atomRefs2=\"a1 a2\" order=\"1\"/><bond id=\"b2\" atomRefs2=\"a2 a3\" order=\"2\"/><bond id=\"b3\" atomRefs2=\"a3 a4\" order=\"1\"/><bond id=\"b4\" atomRefs2=\"a4 a5\" order=\"2\"/><bond id=\"b5\" atomRefs2=\"a5 a6\" order=\"1\"/><bond id=\"b6\" atomRefs2=\"a5 a7\" order=\"1\"/><bond id=\"b7\" atomRefs2=\"a7 a8\" order=\"1\"/><bond id=\"b8\" atomRefs2=\"a7 a9\" order=\"2\"/><bond id=\"b9\" atomRefs2=\"a9 a2\" order=\"1\"><bondStereo>W</bondStereo></bond><bond id=\"b10\" atomRefs2=\"a9 a10\" order=\"1\"/><bond id=\"b11\" atomRefs2=\"a10 a11\" order=\"1\"/><bond id=\"b12\" atomRefs2=\"a11 a12\" order=\"1\"/><bond id=\"b13\" atomRefs2=\"a11 a13\" order=\"2\"/><bond id=\"b14\" atomRefs2=\"a13 a14\" order=\"1\"/><bond id=\"b15\" atomRefs2=\"a14 a15\" order=\"2\"/><bond id=\"b16\" atomRefs2=\"a10 a15\" order=\"1\"/></bondArray></molecule></MChemicalStruct></MDocument></cml>",
"8-9=M:", false);
}
SECTION("Suzzana2") {
testOneAtropIsomerMandP(
"<cml xmlns=\"http://www.chemaxon.com\" version=\"ChemAxon file format v20.20.0, generated by vunknown\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.chemaxon.com http://www.chemaxon.com/marvin/schema/mrvSchema_20_20_0.xsd\"><MDocument><MChemicalStruct><molecule molID=\"m1\" absStereo=\"true\"><atomArray><atom id=\"a1\" elementType=\"C\" x2=\"4.070453300769707\" y2=\"-1.47671998818624\"/><atom id=\"a2\" elementType=\"C\" x2=\"4.372853298350507\" y2=\"0.03322666640085333\"/><atom id=\"a3\" elementType=\"C\" x2=\"5.8316532866801065\" y2=\"0.5265866624539733\"/><atom id=\"a4\" elementType=\"C\" x2=\"6.134053284260906\" y2=\"2.0365333170410667\"/><atom id=\"a5\" elementType=\"C\" x2=\"4.977466626846933\" y2=\"3.053306642240213\"/><atom id=\"a6\" elementType=\"O\" x2=\"5.27967995776256\" y2=\"4.56343996349248\" lonePair=\"2\"/><atom id=\"a7\" elementType=\"C\" x2=\"3.51847997185216\" y2=\"2.5601333128522668\"/><atom id=\"a8\" elementType=\"C\" x2=\"2.361893314438187\" y2=\"3.576906638051413\"/><atom id=\"a9\" elementType=\"C\" x2=\"3.2162666409365337\" y2=\"1.0501866582651733\"/><atom id=\"a10\" elementType=\"N\" x2=\"-1.0962933245629867\" y2=\"-0.40786666340373334\" lonePair=\"1\"/><atom id=\"a11\" elementType=\"C\" x2=\"-2.3527466478446932\" y2=\"0.48253332947306665\"/><atom id=\"a12\" elementType=\"N\" x2=\"-2.37103998103168\" y2=\"2.022346650487893\" lonePair=\"1\"/><atom id=\"a13\" elementType=\"C\" x2=\"-3.58791997129664\" y2=\"-0.43735999650112\"/><atom id=\"a14\" elementType=\"C\" x2=\"-3.09455997524352\" y2=\"-1.89615998483072\"/><atom id=\"a15\" elementType=\"C\" x2=\"-1.5547466542286932\" y2=\"-1.8780533183089065\"/></atomArray><bondArray><bond id=\"b1\" atomRefs2=\"a1 a2\" order=\"1\"/><bond id=\"b2\" atomRefs2=\"a2 a3\" order=\"2\"/><bond id=\"b3\" atomRefs2=\"a3 a4\" order=\"1\"/><bond id=\"b4\" atomRefs2=\"a4 a5\" order=\"2\"/><bond id=\"b5\" atomRefs2=\"a5 a6\" order=\"1\"/><bond id=\"b6\" atomRefs2=\"a5 a7\" order=\"1\"/><bond id=\"b7\" atomRefs2=\"a7 a8\" order=\"1\"/><bond id=\"b8\" atomRefs2=\"a7 a9\" order=\"2\"/><bond id=\"b9\" atomRefs2=\"a9 a2\" order=\"1\"><bondStereo>H</bondStereo></bond><bond id=\"b10\" atomRefs2=\"a9 a10\" order=\"1\"/><bond id=\"b11\" atomRefs2=\"a10 a11\" order=\"1\"/><bond id=\"b12\" atomRefs2=\"a11 a12\" order=\"1\"/><bond id=\"b13\" atomRefs2=\"a11 a13\" order=\"2\"/><bond id=\"b14\" atomRefs2=\"a13 a14\" order=\"1\"/><bond id=\"b15\" atomRefs2=\"a14 a15\" order=\"2\"/><bond id=\"b16\" atomRefs2=\"a10 a15\" order=\"1\"/></bondArray></molecule></MChemicalStruct></MDocument></cml>",
"8-9=P:", false);
}
SECTION("BMS-986142") {
testOneAtropIsomerMandP(
"FC1=C(C2=C(C)C(N3C(=O)C4=C(N(C)C3=O)C(F)=CC=C4)=CC=C2)C2=C(NC3=C2CC[C@H](C(O)(C)C)C3)C(C(=O)N)=C1 |(2.1158,0.5489,;1.4029,0.9642,;0.6554,0.5402,;0.6459,-0.2846,;1.3556,-0.7053,;2.0747,-0.3011,;1.346,-1.5302,;2.3682,-1.8618,;2.9748,-1.3027,;2.794,-0.4978,;3.7623,-1.5486,;3.9431,-2.3535,;3.3364,-2.9126,;3.5173,-3.7175,;2.549,-2.6667,;1.9423,-3.2258,;4.7594,-2.6222,;4.9309,-3.4292,;5.3958,-2.0448,;5.2074,-1.2063,;4.3851,-0.9565,;0.6268,-1.9345,;-0.0827,-1.5137,;-0.0732,-0.6889,;-0.0819,0.9813,;-0.0819,1.8063,;-0.8665,2.0612,;-1.3515,1.3938,;-0.8665,0.7264,;-1.2039,-0.0639,;-2.0578,-0.1602,;-2.5629,0.5349,;-3.3837,0.4518,;-4.2045,0.3687,;-3.4668,1.2725,;-3.3006,-0.369,;-2.2074,1.3172,;0.6555,2.2474,;0.6459,3.0723,;-0.0731,3.4765,;1.3556,3.4931,;1.403,1.8235,),wU:7.14wD:31.35|",
"6-7=P:");
}
SECTION("AtropManyChirals") {
testOneAtropIsomerMandP(
"O=C1C=CNC(=O)N1C(=C)[C@]([C@H](C)Br)([C@@H](F)C)[C@H](Cl)C |(1.6038,0.5917,;1.2842,-0.2899,;1.9435,-0.5613,;2.0181,-1.3829,;1.344,-1.8584,;0.5951,-1.5123,;0.0595,-2.2018,;0.5204,-0.6907,;-0.3117,-0.3431,;-0.861,-1.0085,;-0.5013,0.5405,;-0.4918,1.4387,;-0.0783,2.2018,;-1.0961,2.0398,;0.3347,0.736,;0.6313,-0.0436,;1.118,1.0786,;-1.3746,0.4021,;-2.0181,0.9732,;-1.9327,-0.2608,),wU:7.7,11.13,10.14,17.18wD:14.15|",
"7-8=M:");
}
SECTION("BMS-986142_3d") {
testOneAtropIsomerMandP(
"FC1=C(C2=C(C([H])([H])[H])C(N3C(=O)C4=C(N(C([H])([H])[H])C3=O)C(F)=C([H])C([H])=C4[H])=C([H])C([H])=C2[H])C2=C(N([H])C3=C2C([H])([H])C([H])([H])C(C(O[H])(C([H])([H])[H])C([H])([H])[H])([H])C3([H])[H])C(C(=O)N([H])[H])=C1[H] |(-1.4248,-1.9619,-2.2208;-1.8741,-1.6494,-1.6034;-1.6332,-0.9186,-1.2186;-0.9031,-0.4893,-1.4844;-0.138,-0.6553,-1.1342;-0.0582,-1.2887,-0.4699;-0.2862,-1.8851,-0.6843;0.5723,-1.396,-0.2643;-0.4068,-1.1014,0.0747;0.5573,-0.2316,-1.4028;1.3588,-0.3932,-1.0482;1.5905,0.0773,-0.3585;1.2002,0.6554,-0.0665;2.3933,-0.1194,0.0095;2.9068,-0.6967,-0.3594;2.6425,-1.1179,-1.0794;3.1982,-1.7169,-1.457;3.3106,-2.2227,-1.0278;3.7704,-1.4129,-1.6385;2.9318,-1.9829,-2.0144;1.8575,-1.0047,-1.4246;1.6168,-1.4364,-2.0026;3.6768,-0.8489,0.0041;4.2097,-1.3952,-0.3066;3.9217,-0.4363,0.7167;4.5184,-0.5645,0.9877;3.4017,0.1354,1.0788;3.5896,0.457,1.6328;2.6386,0.2956,0.7262;2.2428,0.7475,1.0192;0.4878,0.3584,-2.0214;1.0254,0.6927,-2.2354;-0.2773,0.5242,-2.3716;-0.3315,0.9837,-2.8531;-0.9727,0.1003,-2.1031;-1.5642,0.2383,-2.3831;-2.1142,-0.6018,-0.5711;-2.8218,-1.0304,-0.3345;-3.1799,-0.5981,0.3004;-3.7005,-0.7644,0.5964;-2.7239,0.0857,0.4696;-2.0583,0.1027,-0.0552;-1.4396,0.7778,-0.0395;-0.8137,0.538,-0.0869;-1.5466,1.1855,-0.5657;-1.4992,1.2797,0.7621;-1.2099,0.9291,1.2614;-1.1302,1.8345,0.67;-2.4007,1.4836,0.9934;-2.4335,2.0277,1.7578;-2.112,1.5747,2.4382;-2.128,1.9287,2.9199;-1.9128,2.8014,1.6418;-2.0588,3.1185,1.0662;-1.2527,2.6718,1.666;-2.0211,3.2354,2.1466;-3.3209,2.2556,1.9643;-3.6328,2.5429,1.4415;-3.3403,2.6896,2.48;-3.6795,1.7235,2.1686;-2.6689,1.821,0.4719;-2.9136,0.6925,1.1267;-2.7776,0.4065,1.7216;-3.5722,0.834,1.1115;-3.069,-1.7619,-0.7143;-3.8054,-2.1982,-0.4602;-4.2532,-1.9338,0.1012;-4.0043,-2.9212,-0.8738;-3.6777,-3.1773,-1.3373;-4.5184,-3.2354,-0.7104;-2.581,-2.0639,-1.3539;-2.7202,-2.6244,-1.6865),wD:10.20|", "9-10=P:");
}
SECTION("JDQ443_atrop2") {
testOneAtropIsomerMandP(
"ClC1=C(C2=C(C)N(C3CC4(C3)CN(C(=O)C=C)C4)N=C2C2=CC3=C(N(C)N=C3)C=C2)C2=C(NN=C2)C=C1C |(-2.3128,3.1804,;-2.4843,2.3736,;-1.8712,1.8214,;-1.0865,2.0764,;-0.8316,2.861,;-1.3166,3.5284,;-0.0066,2.861,;0.478,3.5284,;0.3491,4.3433,;1.164,4.4723,;1.2929,3.6576,;1.0348,5.2872,;1.8497,5.4162,;2.3346,6.0837,;1.9992,6.8374,;3.1551,5.9974,;3.6401,6.6649,;1.9788,4.6014,;0.2482,2.0765,;-0.4191,1.5915,;-0.0067,0.8771,;0.8182,0.877,;1.2308,0.1626,;0.8182,-0.5518,;1.3686,-1.1598,;1.1985,-1.9672,;2.1174,-0.8258,;2.0325,-0.01,;-0.0067,-0.5518,;-0.4193,0.1625,;-2.0427,1.0145,;-2.8273,0.7596,;-2.8254,-0.0605,;-2.0451,-0.3132,;-1.5624,0.3498,;-3.4405,1.3115,;-3.2689,2.1186,;-3.882,2.6705,),wD:3.21|",
"2-3=M:");
}
SECTION("Mrtx1719") {
testOneAtropIsomerMandP(
"ClC1=C(F)C(C2=C(C3=CC4=C(C=C3)C(=O)NN=C4CN)C=NN2C)=C(C#N)C(OC2CC2)=C1 |(0.9486,-2.0481,;0.2357,-1.6329,;0.2388,-0.808,;0.955,-0.3981,;-0.474,-0.3926,;-0.4707,0.4321,;0.1985,0.9146,;0.9821,0.6566,;1.254,1.4719,;2.0972,1.6376,;2.6493,1.0245,;2.3964,0.2031,;1.5571,0.0181,;3.4562,1.196,;4.0082,0.5829,;3.7112,1.9806,;3.1591,2.5937,;2.3522,2.4222,;1.8001,3.0353,;2.0551,3.8199,;-0.0533,1.7003,;-0.8784,1.7034,;-1.1363,0.9197,;-1.9219,0.6678,;-1.1899,-0.8024,;-1.9029,-0.3871,;-2.6157,0.0279,;-1.1932,-1.6273,;-1.9093,-2.0371,;-1.9124,-2.8622,;-2.3276,-3.5751,;-1.5026,-3.5781,;-0.4803,-2.0427,),wU:4.3|",
"4-5=M:");
}
SECTION("RP-6306") {
testOneAtropIsomerMandP(
"OC1=C(C)C(N2C3=C(C(C(=O)N)=C2N)C=C(C)C(C)=N3)=C(C)C=C1 |(2.0992,3.5589,;2.2694,2.7517,;1.6554,2.2008,;0.8712,2.4571,;1.8255,1.3935,;1.0637,0.4452,;0.8122,-0.3353,;-0.0126,-0.3353,;-0.264,0.4452,;-1.0482,0.7015,;-1.6621,0.1505,;-1.2182,1.5087,;0.3998,0.9266,;0.3998,1.7516,;-0.425,-1.0498,;-0.0126,-1.7642,;-0.425,-2.4786,;0.8122,-1.7642,;1.2247,-2.4786,;1.2247,-1.0498,;2.6096,1.1372,;2.7797,0.33,;3.2236,1.6882,;3.0535,2.4954,),wD:4.3|",
"4-5=P:");
}
SECTION("Sotorasib") {
testOneAtropIsomerMandP(
"FC1=C(C2=C(O)C=CC=C2F)N=C2N(C3=C(C)C=CN=C3C(C)C)C(=O)N=C(N3[C@H](C)CN(C(=O)C=C)CC3)C2=C1 |(1.4145,2.306,;1.4178,1.4809,;2.1619,1.0513,;2.8781,1.461,;2.8811,2.2859,;2.1683,2.7012,;3.5973,2.6956,;4.3101,2.2805,;4.3069,1.4555,;3.5908,1.0457,;3.5877,0.2207,;2.1553,0.1919,;1.4045,-0.226,;1.4045,-1.0512,;2.1191,-1.4637,;2.1191,-2.2887,;1.4045,-2.7012,;2.8335,-2.7012,;3.5479,-2.2887,;3.5479,-1.4637,;2.8336,-1.0512,;3.3638,-0.4191,;4.1763,-0.5623,;3.0816,0.3561,;0.6902,-1.4637,;0.6902,-2.2887,;-0.0243,-1.0512,;-0.0243,-0.2262,;-0.7388,0.1862,;-1.4531,-0.2262,;-1.4531,-1.0512,;-2.1677,0.1862,;-2.1677,1.0112,;-2.8821,1.4236,;-2.8821,2.2487,;-3.5966,1.0112,;-4.3112,1.4236,;-1.4531,1.4237,;-0.7386,1.0114,;0.6902,0.1864,;0.6768,1.0455,),wU:14.21wD:29.31|",
"13-14=M:");
}
SECTION("ZM374979") {
testOneAtropIsomerMandP(
"C(N(C[C@H](CCN1CCC(C2=C(S(C)=O)C=CC=C2)CC1)C1=CC(Cl)=C(Cl)C=C1)C)(=O)C1=C(CC)C(C#N)=CC2=C1C=CC=C2 |(2.5006,0.2061,;1.7861,-0.2061,;1.0716,0.2061,;0.3572,-0.2061,;-0.3572,0.2061,;-1.0716,-0.2061,;-1.7861,0.2061,;-1.7861,1.0313,;-2.5006,1.4438,;-3.215,1.0313,;-3.9296,1.4438,;-3.9296,2.2686,;-3.215,2.6811,;-2.5006,2.2686,;-3.215,3.5063,;-4.6441,2.6811,;-5.3584,2.2686,;-5.3584,1.4438,;-4.6441,1.0313,;-3.215,0.2061,;-2.5006,-0.2061,;0.3572,-1.0313,;-0.3572,-1.4438,;-0.3572,-2.2686,;-1.0716,-2.6811,;0.3572,-2.6811,;0.3572,-3.5063,;1.0716,-2.2686,;1.0716,-1.4438,;1.7861,-1.0313,;2.5006,1.0313,;3.215,-0.2061,;3.215,-1.0313,;2.5006,-1.4438,;2.5006,-2.2686,;3.9296,-1.4438,;3.9296,-2.2686,;3.9296,-3.0938,;4.6441,-1.0313,;4.6441,-0.2061,;3.9296,0.2061,;3.9296,1.0313,;4.6441,1.4438,;5.3584,1.0313,;5.3584,0.2061,),wU:3.22wD:0.0|",
"0-31=M:");
}
SECTION("two atropisomers") {
UseLegacyStereoPerceptionFixture(false);
// auto m = MolFileToMol(
testOneAtropIsomerMandP(
"C1(N2C(C)=CC=C2Br)=C(C)C(C)=C(N2C(C)=CC=C2Br)C(C)=C1C |(-0.0002,1.5403,;-0.0002,3.0805,;-1.334,3.8508,;-2.6678,3.0807,;-1.334,5.391,;1.3338,5.391,;1.3338,3.8508,;2.6676,3.0807,;-1.3338,0.7702,;-2.6678,1.5403,;-1.3338,-0.7702,;-2.6678,-1.5401,;-0.0002,-1.5403,;-0.0002,-3.0805,;1.3338,-3.8508,;2.6676,-3.0805,;1.3338,-5.391,;-1.334,-5.391,;-1.334,-3.8508,;-2.6678,-3.0805,;1.3338,-0.7702,;2.6678,-1.5403,;1.3338,0.7702,;2.6678,1.5404,),wU:1.6,13.14|",
"0-1=m:12-13=m:");
}
SECTION("pseudo") {
testOneAtropIsomerMandP(
"N1(n2c(C)ccc2Br)C(=O)[C@H](C)[C@H](C)C1=O |(-11.1517,1.8306,;-11.1517,3.3708,;-12.4855,4.1411,;-13.8193,3.371,;-12.4855,5.6813,;-9.8177,5.6813,;-9.8177,4.1411,;-8.4839,3.371,;-12.3975,0.9252,;-13.8622,1.4011,;-11.9217,-0.5394,;-12.8269,-1.7852,;-10.3817,-0.5394,;-9.4765,-1.7852,;-9.9059,0.9252,;-8.4413,1.4011,),wU:0.8,10.11,12.13|",
"0-1=p:");
}
}
TEST_CASE("upsertTest", "[basic]") {
SECTION("upsertTest1") {
auto ps = v2::SmilesParse::SmilesParserParams();
ps.allowCXSMILES = true;
ps.sanitize = true;
ps.removeHs = false;
auto m = v2::SmilesParse::MolFromSmiles(
"CC1=C(C2=C(F)C=C(C(N)=O)C3=C2C2=C(C[C@@H](C(C)(C)O)CC2)N3)C=CC=C1N1C(=O)C2=C(C(F)=CC=C2)N(C)C1=O |(-0.0582,-1.2887,-0.4699;-0.138,-0.6553,-1.1342;-0.9031,-0.4893,-1.4844;-1.6332,-0.9186,-1.2186;-1.8741,-1.6494,-1.6034;-1.4248,-1.9619,-2.2208;-2.581,-2.0639,-1.3539;-3.069,-1.7619,-0.7143;-3.8054,-2.1982,-0.4602;-4.0043,-2.9212,-0.8738;-4.2532,-1.9338,0.1012;-2.8218,-1.0304,-0.3345;-2.1142,-0.6018,-0.5711;-2.0583,0.1027,-0.0552;-2.7239,0.0857,0.4696;-2.9136,0.6925,1.1267;-2.4007,1.4836,0.9934;-2.4335,2.0277,1.7578;-1.9128,2.8014,1.6418;-3.3209,2.2556,1.9643;-2.112,1.5747,2.4382;-1.4992,1.2797,0.7621;-1.4396,0.7778,-0.0395;-3.1799,-0.5981,0.3004;-0.9727,0.1003,-2.1031;-0.2773,0.5242,-2.3716;0.4878,0.3584,-2.0214;0.5573,-0.2316,-1.4028;1.3588,-0.3932,-1.0482;1.5905,0.0773,-0.3585;1.2002,0.6554,-0.0665;2.3933,-0.1194,0.0095;2.9068,-0.6967,-0.3594;3.6768,-0.8489,0.0041;4.2097,-1.3952,-0.3066;3.9217,-0.4363,0.7167;3.4017,0.1354,1.0788;2.6386,0.2956,0.7262;2.6425,-1.1179,-1.0794;3.1982,-1.7169,-1.457;1.8575,-1.0047,-1.4246;1.6168,-1.4364,-2.0026),wU:27.30|",
ps);
unsigned int flags = RDKit::SmilesWrite::CXSmilesFields::CX_COORDS |
RDKit::SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
RDKit::SmilesWrite::CXSmilesFields::CX_ATOM_PROPS |
RDKit::SmilesWrite::CXSmilesFields::CX_BOND_CFG |
RDKit::SmilesWrite::CXSmilesFields::CX_ENHANCEDSTEREO;
auto smilesWriteParams = SmilesWriteParams();
smilesWriteParams.canonical = true;
auto smilesOut =
MolToCXSmiles(*m, smilesWriteParams, flags, RestoreBondDirOptionClear);
CHECK(smilesOut != "");
}
}
TEST_CASE("atropisomers", "[basic]") {
SECTION("atropisomers1") {
UseLegacyStereoPerceptionFixture useLegacy(false);
std::string rdbase = getenv("RDBASE");
std::vector<std::string> files = {
"BMS-986142_atrop5.sdf", "BMS-986142_atrop1.sdf",
"BMS-986142_atrop2.sdf", "JDQ443_atrop1.sdf",
"JDQ443_atrop2.sdf", "Mrtx1719_atrop1.sdf",
"Mrtx1719_atrop2.sdf", "RP-6306_atrop1.sdf",
"RP-6306_atrop2.sdf", "Sotorasib_atrop1.sdf",
"Sotorasib_atrop2.sdf", "ZM374979_atrop1.sdf",
"ZM374979_atrop2.sdf"};
for (auto file : files) {
auto fName =
rdbase + "/Code/GraphMol/FileParsers/test_data/atropisomers/" + file;
std::unique_ptr<RWMol> molsdf(MolFileToMol(fName, true, true, true));
REQUIRE(molsdf);
CIPLabeler::assignCIPLabels(*molsdf, 100000);
std::map<std::pair<unsigned int, unsigned int>, std::string> CIPVals;
for (auto bond : molsdf->bonds()) {
auto a1 = bond->getBeginAtomIdx();
auto a2 = bond->getEndAtomIdx();
if (a1 > a2) {
std::swap(a1, a2);
}
if (bond->hasProp(common_properties::_CIPCode)) {
CIPVals[std::make_pair(a1, a2)] =
bond->getProp<std::string>(common_properties::_CIPCode);
} else {
CIPVals[std::make_pair(a1, a2)] = "N/A";
}
}
molsdf->clearConformers();
SmilesWriteParams wp;
wp.canonical = false;
wp.doKekule = false;
unsigned int flags =
RDKit::SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
RDKit::SmilesWrite::CXSmilesFields::CX_ATOM_PROPS |
RDKit::SmilesWrite::CXSmilesFields::CX_BOND_CFG |
RDKit::SmilesWrite::CXSmilesFields::CX_BOND_ATROPISOMER;
v2::SmilesParse::SmilesParserParams pp;
pp.allowCXSMILES = true;
pp.sanitize = true;
auto smi = MolToCXSmiles(*molsdf, wp, flags);
auto newMol = v2::SmilesParse::MolFromSmiles(smi, pp);
CIPLabeler::assignCIPLabels(*newMol, 100000);
std::map<std::pair<unsigned int, unsigned int>, std::string> newCIPVals;
for (auto bond : newMol->bonds()) {
auto a1 = bond->getBeginAtomIdx();
auto a2 = bond->getEndAtomIdx();
if (a1 > a2) {
std::swap(a1, a2);
}
if (bond->hasProp(common_properties::_CIPCode)) {
newCIPVals[std::make_pair(a1, a2)] =
bond->getProp<std::string>(common_properties::_CIPCode);
} else {
newCIPVals[std::make_pair(a1, a2)] = "N/A";
}
}
RDKit::SubstructMatchParameters params;
auto match = RDKit::SubstructMatch(*molsdf, *newMol, params);
for (auto thisBond : newMol->bonds()) {
unsigned int a1 = thisBond->getBeginAtomIdx();
unsigned int a2 = thisBond->getEndAtomIdx();
if (a1 > a2) {
std::swap(a1, a2);
}
unsigned int a1match = match[0][a1].second;
unsigned int a2match = match[0][a2].second;
if (a1match > a2match) {
std::swap(a1match, a2match);
}
CHECK(CIPVals[std::make_pair(a1match, a2match)] ==
newCIPVals[std::make_pair(a1, a2)]);
}
}
}
}
TEST_CASE("CipLabelAtropsOnRing", "[basic]") {
SECTION("atropisomers1") {
std::string molBlock = R"(
Mrv2304 04172300142D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 24 26 0 0 1
M V30 BEGIN ATOM
M V30 1 C -0.0002 1.5403 0 0
M V30 2 N -0.0002 3.0805 0 0 CFG=1
M V30 3 C -1.334 3.8508 0 0
M V30 4 C -2.6678 3.0807 0 0
M V30 5 C -1.334 5.391 0 0
M V30 6 C 1.3338 5.391 0 0
M V30 7 C 1.3338 3.8508 0 0
M V30 8 Br 2.6676 3.0807 0 0
M V30 9 C -1.3338 0.7702 0 0
M V30 10 C -2.6678 1.5403 0 0
M V30 11 C -1.3338 -0.7702 0 0
M V30 12 C -2.6678 -1.5401 0 0
M V30 13 C -0.0002 -1.5403 0 0
M V30 14 N -0.0002 -3.0805 0 0 CFG=1
M V30 15 C 1.3338 -3.8508 0 0
M V30 16 C 2.6676 -3.0805 0 0
M V30 17 C 1.3338 -5.391 0 0
M V30 18 C -1.334 -5.391 0 0
M V30 19 C -1.334 -3.8508 0 0
M V30 20 Br -2.6678 -3.0805 0 0
M V30 21 C 1.3338 -0.7702 0 0
M V30 22 C 2.6678 -1.5403 0 0
M V30 23 C 1.3338 0.7702 0 0
M V30 24 C 2.6678 1.5404 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 2 3 5
M V30 5 1 5 6
M V30 6 2 6 7
M V30 7 1 2 7 CFG=1
M V30 8 1 7 8
M V30 9 2 1 9
M V30 10 1 9 10
M V30 11 1 9 11
M V30 12 1 11 12
M V30 13 2 11 13
M V30 14 1 13 14
M V30 15 1 14 15 CFG=1
M V30 16 1 15 16
M V30 17 2 15 17
M V30 18 1 17 18
M V30 19 2 18 19
M V30 20 1 14 19
M V30 21 1 19 20
M V30 22 1 13 21
M V30 23 1 21 22
M V30 24 2 21 23
M V30 25 1 1 23
M V30 26 1 23 24
M V30 END BOND
M V30 END CTAB
M END
)";
UseLegacyStereoPerceptionFixture useLegacy(false);
auto mol = std::unique_ptr<RWMol>(MolBlockToMol(molBlock, true, false));
RDKit::CIPLabeler::assignCIPLabels(*mol);
auto atom = mol->getBondWithIdx(0);
std::string thisVal;
if (atom->hasProp(common_properties::_CIPCode)) {
thisVal = atom->getProp<std::string>(common_properties::_CIPCode);
}
CHECK(thisVal == "m");
atom = mol->getBondWithIdx(13);
if (atom->hasProp(common_properties::_CIPCode)) {
thisVal = atom->getProp<std::string>(common_properties::_CIPCode);
}
CHECK(thisVal == "m");
}
}
TEST_CASE("CipLabelAromAtrop", "[basic]") {
SECTION("basic") {
std::string molBlock = R"(
Generated by WebMolKit
16 17 0 0 1 0 0 0 0 0999 V2000
14.7682 -11.2032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7682 -12.7032 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
16.0673 -13.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.3663 -12.7032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.3663 -11.2032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.0673 -10.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4693 -10.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4693 -8.9532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1702 -8.2032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8712 -8.9532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8712 -10.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1702 -11.2030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7682 -8.2030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1702 -12.7030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8711 -13.4530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4692 -13.4530 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
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
1 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
7 12 1 1 0 0 0
8 13 1 0 0 0 0
12 14 1 0 0 0 0
14 15 1 0 0 0 0
14 16 1 0 0 0 0
M END
)";
std::string molBlockInvertWedge = R"(
Generated by WebMolKit
16 17 0 0 1 0 0 0 0 0999 V2000
14.7682 -11.2032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7682 -12.7032 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
16.0673 -13.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.3663 -12.7032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.3663 -11.2032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.0673 -10.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4693 -10.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4693 -8.9532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1702 -8.2032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8712 -8.9532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8712 -10.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1702 -11.2030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7682 -8.2030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1702 -12.7030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8711 -13.4530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4692 -13.4530 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
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
1 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
7 12 1 6 0 0 0
8 13 1 0 0 0 0
12 14 1 0 0 0 0
14 15 1 0 0 0 0
14 16 1 0 0 0 0
M END
)";
std::string molBlock2 = R"(
Generated by WebMolKit
16 17 0 0 1 0 0 0 0 0999 V2000
11.5862 -13.1456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1816 -13.1449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8863 -12.3955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1816 -14.6463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.5862 -14.6530 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.8896 -15.3956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2872 -12.3954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6918 -12.3979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9876 -13.1465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6908 -10.8965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2862 -10.8880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9823 -10.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9876 -14.6465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6886 -15.3965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2867 -15.3964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.5826 -10.1334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
4 2 2 0 0 0 0
2 3 1 0 0 0 0
1 7 1 0 0 0 0
7 11 2 0 0 0 0
11 12 1 0 0 0 0
12 10 2 0 0 0 0
10 8 1 0 0 0 0
8 9 2 0 0 0 0
9 13 1 0 0 0 0
13 14 1 0 0 0 0
13 15 1 0 0 0 0
11 16 1 0 0 0 0
7 9 1 1 0 0 0
M END
)";
std::string molBlock2InvertWedge = R"(
Generated by WebMolKit
16 17 0 0 1 0 0 0 0 0999 V2000
11.5862 -13.1456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1816 -13.1449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8863 -12.3955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1816 -14.6463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.5862 -14.6530 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.8896 -15.3956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2872 -12.3954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6918 -12.3979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9876 -13.1465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6908 -10.8965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2862 -10.8880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9823 -10.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9876 -14.6465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6886 -15.3965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2867 -15.3964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.5826 -10.1334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
4 2 2 0 0 0 0
2 3 1 0 0 0 0
1 7 1 0 0 0 0
7 11 2 0 0 0 0
11 12 1 0 0 0 0
12 10 2 0 0 0 0
10 8 1 0 0 0 0
8 9 2 0 0 0 0
9 13 1 0 0 0 0
13 14 1 0 0 0 0
13 15 1 0 0 0 0
11 16 1 0 0 0 0
7 9 1 6 0 0 0
M END
)";
UseLegacyStereoPerceptionFixture useLegacy(false);
auto mol = std::unique_ptr<RWMol>(MolBlockToMol(molBlock, true, false));
RDKit::CIPLabeler::assignCIPLabels(*mol);
auto atom = mol->getBondWithIdx(6);
std::string thisVal;
if (atom->hasProp(common_properties::_CIPCode)) {
thisVal = atom->getProp<std::string>(common_properties::_CIPCode);
}
CHECK(thisVal == "P");
mol.reset(MolBlockToMol(molBlockInvertWedge, true, false));
RDKit::CIPLabeler::assignCIPLabels(*mol);
atom = mol->getBondWithIdx(6);
if (atom->hasProp(common_properties::_CIPCode)) {
thisVal = atom->getProp<std::string>(common_properties::_CIPCode);
}
CHECK(thisVal == "M");
auto mol2 = std::unique_ptr<RWMol>(MolBlockToMol(molBlock2, true, false));
RDKit::CIPLabeler::assignCIPLabels(*mol2);
auto atom2 = mol2->getBondWithIdx(6);
if (atom2->hasProp(common_properties::_CIPCode)) {
thisVal = atom2->getProp<std::string>(common_properties::_CIPCode);
}
CHECK(thisVal == "P");
mol.reset(MolBlockToMol(molBlock2InvertWedge, true, false));
RDKit::CIPLabeler::assignCIPLabels(*mol);
atom = mol->getBondWithIdx(6);
if (atom->hasProp(common_properties::_CIPCode)) {
thisVal = atom->getProp<std::string>(common_properties::_CIPCode);
}
CHECK(thisVal == "M");
}
}
TEST_CASE("Resolve easy CIP labels first", "[accurateCIP]") {
constexpr const char *molBlock = R"(
RDKit 3D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 44 54 0 0 1
M V30 BEGIN ATOM
M V30 1 H 7.548300 -7.745100 -3.341900 0
M V30 2 H 9.398400 -5.879200 -3.431800 0
M V30 3 C 9.339900 -6.542500 -1.989800 0 CFG=2
M V30 4 H 8.682000 -3.942500 -1.647400 0
M V30 5 H 5.816300 -7.103400 -1.663500 0
M V30 6 H 6.572200 -4.734300 -0.630400 0
M V30 7 C 7.170100 -7.238000 -0.889000 0 CFG=1
M V30 8 H 11.830000 -6.976500 -2.554400 0
M V30 9 C 10.663100 -7.169000 -1.537500 0 CFG=1
M V30 10 H 11.407700 -9.523900 -2.147200 0
M V30 11 H 11.900600 -10.013900 0.472200 0
M V30 12 C 10.660000 -8.874900 0.291400 0 CFG=2
M V30 13 H 12.513600 -5.911500 -0.419000 0
M V30 14 H 12.533800 -7.840600 1.437900 0
M V30 15 H 8.698100 -8.865400 3.417700 0
M V30 16 H 9.404600 -10.690700 1.714300 0
M V30 17 C 9.318500 -9.310600 0.970000 0 CFG=1
M V30 18 H 7.495800 -10.807500 -0.178300 0
M V30 19 H 6.555200 -7.878000 2.698300 0
M V30 20 H 5.852200 -9.114700 0.451400 0
M V30 21 C 7.160100 -8.299700 0.235300 0 CFG=2
M V30 22 C 7.577400 -7.598900 1.570000 0 CFG=1
M V30 23 C 10.647193 -4.032680 0.167792 0 CFG=1
M V30 24 C 11.080800 -6.489400 -0.198200 0 CFG=2
M V30 25 C 8.912300 -5.469900 -0.942400 0 CFG=1
M V30 26 C 8.915500 -8.232900 2.018400 0 CFG=2
M V30 27 C 11.076600 -7.551300 0.914700 0 CFG=1
M V30 28 H 10.678000 -6.985700 3.302100 0
M V30 29 C 7.586100 -5.893900 -0.266700 0 CFG=2
M V30 30 H 6.997300 -5.059700 1.987500 0
M V30 31 C 9.319300 -5.842900 1.504800 0 CFG=2
M V30 32 H 9.474000 -4.717300 2.574300 0
M V30 33 C 9.980900 -7.145700 1.981100 0 CFG=1
M V30 34 C 7.827000 -6.124500 1.248300 0 CFG=2
M V30 35 C 10.002300 -5.430800 0.136600 0
M V30 36 C 8.912500 -8.938500 -1.473700 0 CFG=2
M V30 37 C 8.237400 -9.352200 -0.117300 0
M V30 38 C 10.411600 -8.646100 -1.214800 0 CFG=1
M V30 39 H 8.772600 -9.975800 -2.504700 0
M V30 40 C 8.257700 -7.625000 -1.947800 0 CFG=2
M V30 41 O 9.665066 -3.068040 0.472747 0
M V30 42 Cl 11.932408 -3.993449 1.420272 0
M V30 43 H 11.083087 -3.811232 -0.806404 0
M V30 44 H 10.067077 -2.196484 0.492191 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 3 2 CFG=3
M V30 2 1 7 5 CFG=3
M V30 3 1 9 3
M V30 4 1 9 8 CFG=3
M V30 5 1 12 11 CFG=3
M V30 6 1 17 12
M V30 7 1 17 16 CFG=1
M V30 8 1 21 7
M V30 9 1 21 20 CFG=1
M V30 10 1 22 19 CFG=1
M V30 11 1 22 21
M V30 12 1 24 9
M V30 13 1 24 13 CFG=3
M V30 14 1 25 3
M V30 15 1 25 4 CFG=3
M V30 16 1 26 15 CFG=1
M V30 17 1 26 17
M V30 18 1 26 22
M V30 19 1 27 12
M V30 20 1 27 14 CFG=1
M V30 21 1 27 24
M V30 22 1 29 6 CFG=1
M V30 23 1 29 7
M V30 24 1 29 25
M V30 25 1 31 32 CFG=1
M V30 26 1 33 26
M V30 27 1 33 27
M V30 28 1 33 28 CFG=1
M V30 29 1 33 31
M V30 30 1 34 22
M V30 31 1 34 29
M V30 32 1 34 30 CFG=1
M V30 33 1 34 31
M V30 34 1 35 23
M V30 35 1 35 24
M V30 36 1 35 25
M V30 37 1 35 31
M V30 38 1 37 17
M V30 39 1 37 18
M V30 40 1 37 21
M V30 41 1 37 36
M V30 42 1 38 9
M V30 43 1 38 10 CFG=3
M V30 44 1 38 12
M V30 45 1 38 36
M V30 46 1 36 39 CFG=3
M V30 47 1 40 1 CFG=3
M V30 48 1 40 3
M V30 49 1 40 7
M V30 50 1 40 36
M V30 51 1 41 23
M V30 52 1 42 23
M V30 53 1 23 43 CFG=3
M V30 54 1 44 41
M V30 END BOND
M V30 END CTAB
M END
$$$$
)";
// The mol is a modification of the one in the above test
// "CIP max iterations test"
v2::FileParsers::MolFileParserParams params{.sanitize = false};
auto mol = v2::FileParsers::MolFromMolBlock(molBlock, params);
REQUIRE(mol);
REQUIRE_THROWS_AS(CIPLabeler::assignCIPLabels(*mol, 1000),
CIPLabeler::MaxIterationsExceeded);
auto at = mol->getAtomWithIdx(22);
REQUIRE(at->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW);
// This will fail if this chiral center is not resolved first (which
// depends on the order of the atoms in the molBlock).
CHECK(at->getProp<std::string>(common_properties::_CIPCode) == "S");
}
// Do we annotate/label the molecule with the ranks of their neighbors?
TEST_CASE("neighbor_annotations", "[basic]") {
SECTION("chirality") {
auto mol = R"(C1C[C@H](C)C(=O)C[C@H]1O)"_smiles;
REQUIRE(mol);
auto a = mol->getAtomWithIdx(2);
REQUIRE(a->getChiralTag() != Atom::CHI_UNSPECIFIED);
CIPLabeler::assignCIPLabels(*mol, 100);
std::vector<unsigned int> ranked_anchors;
REQUIRE(a->getPropIfPresent(common_properties::_CIPNeighborOrder,
ranked_anchors) == true);
CHECK(ranked_anchors == std::vector<unsigned int>{4, 1, 3});
}
SECTION("bond_stereo") {
auto mol = R"(C/C=C(C)/N)"_smiles;
REQUIRE(mol);
auto b = mol->getBondWithIdx(1);
REQUIRE(b->getBondType() == Bond::DOUBLE);
b->setStereoAtoms(0, 3);
auto &stereo_atoms1 = mol->getBondWithIdx(1)->getStereoAtoms();
CHECK(stereo_atoms1[0] == 0);
CHECK(stereo_atoms1[1] == 3);
CIPLabeler::assignCIPLabels(*mol, 100);
std::vector<unsigned int> ranked_anchors;
REQUIRE(b->getPropIfPresent(common_properties::_CIPNeighborOrder,
ranked_anchors) == true);
CHECK(ranked_anchors == std::vector<unsigned int>{0, 4});
}
SECTION("atropisomer") {
auto mol = R"(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 13 14 0 0 0
M V30 BEGIN ATOM
M V30 1 C -2.488395 0.189263 0.000000 0
M V30 2 C -1.189356 0.939262 0.000000 0
M V30 3 C -1.189356 2.439262 0.000000 0
M V30 4 C -2.488395 3.189262 0.000000 0
M V30 5 C -3.787433 2.439262 0.000000 0
M V30 6 N -3.787433 0.939262 0.000000 0
M V30 7 C -2.488395 -1.310738 0.000000 0
M V30 8 N -3.701920 -2.192416 0.000000 0
M V30 9 N -3.238394 -3.619001 0.000000 0
M V30 10 C -1.738395 -3.619001 0.000000 0
M V30 11 C -1.274869 -2.192416 0.000000 0
M V30 12 C 0.109682 0.189263 0.000000 0
M V30 13 C -5.128505 -1.728890 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 6 1
M V30 7 1 1 7
M V30 8 1 8 9
M V30 9 2 9 10
M V30 10 1 10 11
M V30 11 2 11 7
M V30 12 1 7 8 CFG=1
M V30 13 1 2 12
M V30 14 1 8 13
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STERAC1 ATOMS=(1 7)
M V30 END COLLECTION
M V30 END CTAB
M END
$$$$
)"_ctab;
REQUIRE(mol);
auto b = mol->getBondWithIdx(6);
REQUIRE(b->getStereo() == Bond::STEREOATROPCW);
// Check that reference atoms for the atropisomer bond
// are atoms 1 and 7
Atropisomers::AtropAtomAndBondVec atomAndBondVecs[2];
REQUIRE(
Atropisomers::getAtropisomerAtomsAndBonds(b, atomAndBondVecs, *mol));
REQUIRE(atomAndBondVecs[0].second[0]->getOtherAtomIdx(
atomAndBondVecs[0].first->getIdx()) == 1);
REQUIRE(atomAndBondVecs[1].second[0]->getOtherAtomIdx(
atomAndBondVecs[1].first->getIdx()) == 7);
CIPLabeler::assignCIPLabels(*mol, 100);
// ... but the highest ranked anchors are 5 and 7
std::vector<unsigned int> ranked_anchors;
REQUIRE(b->getPropIfPresent(common_properties::_CIPNeighborOrder,
ranked_anchors) == true);
CHECK(ranked_anchors == std::vector<unsigned int>{5, 7});
}
SECTION("_CIPNeighborOrder includes NOATOM") {
// This is VS185 in https://cipvalidationsuite.github.io/ValidationSuite/
auto mol = R"([2H]/C(=C(/[1H])\[H])/[H])"_smiles;
REQUIRE(mol);
auto b = mol->getBondWithIdx(1);
REQUIRE(b->getBondType() == Bond::DOUBLE);
b->setStereoAtoms(0, 3);
auto &stereo_atoms1 = mol->getBondWithIdx(1)->getStereoAtoms();
CHECK(stereo_atoms1[0] == 0);
CHECK(stereo_atoms1[1] == 3);
CIPLabeler::assignCIPLabels(*mol, 100);
std::vector<unsigned int> ranked_anchors;
REQUIRE(b->getPropIfPresent(common_properties::_CIPNeighborOrder,
ranked_anchors) == true);
CHECK(ranked_anchors == std::vector<unsigned int>{0, Atom::NOATOM});
}
}
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