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rdkit/Code/GraphMol/CIPLabeler/catch_tests.cpp
Dan Nealschneider 1a57191a8c CIP labeller performance: Don't calculate auxiliary descriptors unnecessarily (#9171) 
* CIP labeller: Don't calculate auxiliary descriptors unnecessarily

The first 3 rules (the constitutional rules) are pretty easy
to understand. After rule 3, we need to calculate auxiliary
stereo descriptors to break ties.

However, we _were actually_ calculating auxiliary stereodescriptors
for all centers! We should only need to calculate auxiliary
stereocenters for sites that are needed to break ties.

This cost time - it also caused errors if the auxiliary descriptors
needed a graph expansion, because bonds in the digraph might be
pointed in the wrong direction.

Example case PDB ID 4AXM
Before this commit, errored with "Could not calculate parity! Carrier mismatch"
after 14s. After this commit, completes successfully in 0.036s.
Labelled centers all match (for the centers that had labels in
the failure case).

Includes a test that I can imagine breaking with this optimization.
The reference labels are from before this change

* Ensure all "arms" of stereo bonds and atropisomer bonds are expanded

For tetrahedral centers, ranking using the constitutional rules
always expands as far as is needed (but no further). For SP2bond
and atropisomers, if the first side is not resolvable, the
second side is never visited.

If the constitutional rules don't resolve a side, we need to
label the auxiliary centers. It's important to label all
auxiliary centers that _will_ be visited, so we need to know
what centers will be visited.

This commit updates the label() call in SP2 and Atropisomer
bonds to always attempt to label both sides if using the
constitutional rule set.

The constitutional rules are cheap, and if they fail, we
always go on to the full rule set. It is not a savings to skip
the search on the second side if we're going to keep going
anyway!

Includes a test that reproduces Ricardo's example.

This has no measurable effect on performance relative to the
original solution

* If any parts of the center have been seen, label it.

I couldn't make an example hit this, but Ric is totally
theoretically right

* Greg's ranges suggestion #2

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* any_of for container search

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2026-05-29 05:45:28 +02:00

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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");
}
SECTION("auxiliary stereochem beyond initial expansion") {
// The label on atom 12 depends on the chirality at
// atom 2. The label on atom 9 depends on the label of
// atom 12. Atom 2 is not reached in the initial
// expansion to score atom 9
auto mol = "CC[C@H](C)CCCCC[C@H]1CC[C@@H](C)CC1"_smiles;
CIPLabeler::assignCIPLabels(*mol);
std::string chirality;
CHECK(mol->getAtomWithIdx(2)->getProp<std::string>(
common_properties::_CIPCode) == "S");
CHECK(mol->getAtomWithIdx(9)->getProp<std::string>(
common_properties::_CIPCode) == "s");
CHECK(mol->getAtomWithIdx(12)->getProp<std::string>(
common_properties::_CIPCode) == "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);
}
auto view_labels(const ROMol &mol) {
std::stringstream msg;
std::string label;
for (auto a : mol.atoms()) {
if (a->getPropIfPresent(common_properties::_CIPCode, label)) {
msg << a->getIdx() << label << ' ';
}
}
for (auto b : mol.bonds()) {
if (b->getPropIfPresent(common_properties::_CIPCode, label)) {
msg << b->getBeginAtomIdx() << '=' << b->getEndAtomIdx() << label << ' ';
}
}
return msg.str();
}
TEST_CASE("Bad skip side", "[accurateCIP]") {
auto m1 = "C1CC[C@H]2C/C(=C3\\C[C@H]4CCCC[C@H]4C3)C[C@H]2C1"_smiles;
CIPLabeler::assignCIPLabels(*m1);
CHECK("3S 8R 13S 16R 5=6E " == view_labels(*m1));
auto m2 = "C1/C(=C2\\C[C@H]3CCCC[C@H]3C2)C[C@H]2CCCC[C@@H]12"_smiles;
CIPLabeler::assignCIPLabels(*m2);
CHECK("4R 9S 12R 17S 1=2E " == view_labels(*m2));
}
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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