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8dd2ce446c726637aebcbe61e4db918d563f6fb4
rdkit/Code/GraphMol/catch_graphmol.cpp
Ric 8dd2ce446c Address issue #2890 (#3015) 
* add fix

* add tests
2020-03-21 14:01:54 +01:00

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//
//
// Copyright (C) 2018-2020 Greg Landrum and T5 Informatics GmbH
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/new_canon.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
using namespace RDKit;
#if 1
TEST_CASE("SMILES Parsing works", "[molops]") {
std::unique_ptr<RWMol> mol(SmilesToMol("C1CC1"));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 3);
}
TEST_CASE("Sanitization tests", "[molops]") {
std::unique_ptr<RWMol> mol(SmilesToMol("C1=CC=CC=C1Cc2ccccc2", false, false));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 13);
SECTION("properties") {
mol->updatePropertyCache();
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 1);
CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
CHECK(mol->getAtomWithIdx(10)->getIsAromatic());
SECTION("aromaticity") {
unsigned int opThatFailed;
MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_SETAROMATICITY);
// mol->debugMol(std::cerr);
CHECK(mol->getAtomWithIdx(10)->getIsAromatic());
// blocked by #1730
// CHECK(mol->getAtomWithIdx(0)->getIsAromatic());
}
SECTION("kekulize") {
unsigned int opThatFailed;
MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_KEKULIZE);
CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
CHECK(!mol->getAtomWithIdx(10)->getIsAromatic());
}
}
}
TEST_CASE("Github #2062", "[bug, molops]") {
SmilesParserParams ps;
ps.removeHs = false;
ps.sanitize = true;
std::unique_ptr<RWMol> mol(SmilesToMol("[C:1][C:2]([H:3])([H])[O:4][H]", ps));
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 6);
mol->getAtomWithIdx(1)->setProp("intProp", 42);
MolOps::mergeQueryHs(*mol);
CHECK(mol->getNumAtoms() == 3);
SECTION("basics") { CHECK(mol->getAtomWithIdx(1)->getAtomMapNum() == 2); }
SECTION("other props") {
REQUIRE(mol->getAtomWithIdx(1)->hasProp("intProp"));
CHECK(mol->getAtomWithIdx(1)->getProp<int>("intProp") == 42);
}
}
TEST_CASE("Github #2086", "[bug, molops]") {
SECTION("reported version") {
auto mol = "C1CCCC1"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
REQUIRE(mol->getNumAtoms() == 15);
mol->removeBond(4, 13);
MolOps::removeHs(*mol);
REQUIRE(mol->getNumAtoms() == 6);
}
}
TEST_CASE("github #299", "[bug, molops, SSSR]") {
SECTION("simplified") {
auto mol =
"C13%13%14.C124%18.C25%13%15.C368%17.C4679.C75%10%17.C8%11%14%16.C9%11%12%18.C%10%12%15%16"_smiles;
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 9);
}
SECTION("old example from molopstest") {
auto mol = "C123C45C11C44C55C22C33C14C523"_smiles;
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 9);
}
SECTION("carborane") {
std::unique_ptr<RWMol> mol(
SmilesToMol("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822["
"C]933[B]%1045[C]6123",
0, false));
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 12);
mol->updatePropertyCache(false);
MolOps::findSSSR(*mol);
REQUIRE(mol->getRingInfo()->isInitialized());
}
SECTION("original report from ChEbI") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> mol(
MolFileToMol(pathName + "ChEBI_50252.mol", false));
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 80);
mol->updatePropertyCache(false);
MolOps::findSSSR(*mol);
REQUIRE(mol->getRingInfo()->isInitialized());
}
}
TEST_CASE("github #2224", "[bug, molops, removeHs, query]") {
SECTION("the original report") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> mol(MolFileToMol(pathName + "github2224_1.mol"));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 7);
}
SECTION("basics") {
SmilesParserParams ps;
ps.removeHs = false;
ps.sanitize = true;
std::unique_ptr<ROMol> mol(SmilesToMol("C[H]", ps));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 2);
{ // The H without a query is removed
std::unique_ptr<ROMol> m2(MolOps::removeHs(*mol));
CHECK(m2->getNumAtoms() == 1);
}
{ // but if we add a query feature it's not removed
RWMol m2(*mol);
auto *qa = new QueryAtom(1);
m2.replaceAtom(1, qa);
m2.getAtomWithIdx(1)->setAtomicNum(1);
MolOps::removeHs(m2);
CHECK(m2.getNumAtoms() == 2);
delete qa;
}
}
}
TEST_CASE(
"github #2268: Recognize N in three-membered rings as potentially chiral",
"[bug,stereo]") {
SECTION("basics: N in a 3 ring") {
const auto mol = "C[N@]1CC1C"_smiles;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("basics: N in a 4 ring") {
const auto mol = "C[N@]1CCC1C"_smiles;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
}
SECTION("the original molecule") {
std::string mb = R"CTAB(
Mrv1810 02131915062D
18 20 0 0 1 0 999 V2000
-0.7207 -1.3415 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0
-0.0583 -0.8416 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.0083 -1.7540 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.3956 -0.8666 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.3250 -0.0667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1955 -0.6499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1499 -0.0792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6541 -0.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7830 -1.2291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.6081 -1.6623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4080 0.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3665 -0.8374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6416 0.3958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1996 0.3708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4121 1.1624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3498 0.8207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0790 -0.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0665 0.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
1 3 1 1 0 0 0
4 1 1 0 0 0 0
5 2 1 0 0 0 0
4 6 1 0 0 0 0
7 4 1 0 0 0 0
2 8 1 6 0 0 0
9 6 2 0 0 0 0
4 10 1 1 0 0 0
11 6 1 0 0 0 0
12 8 2 0 0 0 0
13 8 1 0 0 0 0
14 11 1 0 0 0 0
15 14 1 0 0 0 0
16 13 2 0 0 0 0
17 12 1 0 0 0 0
18 16 1 0 0 0 0
2 3 1 0 0 0 0
5 7 1 0 0 0 0
17 18 2 0 0 0 0
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
}
TEST_CASE("github #2244", "[bug, molops, stereo]") {
SECTION("the original report") {
auto mol = "CC=CC=CC"_smiles;
REQUIRE(mol);
MolOps::findPotentialStereoBonds(*mol, true);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY);
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
mol->getBondWithIdx(3)->setStereo(Bond::STEREONONE);
MolOps::findPotentialStereoBonds(*mol, true);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY);
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
}
}
TEST_CASE(
"github #2258: heterocycles with exocyclic bonds not failing valence check",
"[bug, molops]") {
SECTION("the original report") {
std::vector<std::string> smiles = {"C=n1ccnc1", "C#n1ccnc1"};
for (auto smi : smiles) {
CHECK_THROWS_AS(SmilesToMol(smi), MolSanitizeException);
}
}
}
TEST_CASE("github #908: AddHs() using 3D coordinates with 2D conformations",
"[bug, molops]") {
SECTION("basics: single atom mols") {
std::vector<std::string> smiles = {"Cl", "O", "N", "C"};
for (auto smi : smiles) {
// std::cerr << smi << std::endl;
std::unique_ptr<RWMol> mol(SmilesToMol(smi));
REQUIRE(mol);
auto conf = new Conformer(1);
conf->set3D(false);
conf->setAtomPos(0, RDGeom::Point3D(0, 0, 0));
mol->addConformer(conf, true);
bool explicitOnly = false;
bool addCoords = true;
MolOps::addHs(*mol, explicitOnly, addCoords);
for (size_t i = 0; i < mol->getNumAtoms(); ++i) {
// std::cerr << " " << i << " " << conf->getAtomPos(i) << std::endl;
CHECK(conf->getAtomPos(i).z == 0.0);
}
}
}
}
TEST_CASE(
"github #2437: Canon::rankMolAtoms results in crossed double bonds in "
"rings",
"[bug, molops]") {
SECTION("underlying problem") {
std::string molb = R"CTAB(testmol
Mrv1824 05081910082D
4 4 0 0 0 0 999 V2000
6.9312 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
2 4 2 0 0 0 0
M END
)CTAB";
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<RWMol> mol(MolBlockToMol(molb, sanitize, removeHs));
REQUIRE(mol);
mol->updatePropertyCache();
CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE);
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE);
std::vector<unsigned int> ranks;
CHECK(!mol->getRingInfo()->isInitialized());
Canon::rankMolAtoms(*mol, ranks);
CHECK(!mol->getRingInfo()->isInitialized());
}
SECTION("as discovered") {
std::string molb = R"CTAB(testmol
Mrv1824 05081910082D
4 4 0 0 0 0 999 V2000
6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7562 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9312 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
2 4 2 0 0 0 0
M END
)CTAB";
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<RWMol> mol(MolBlockToMol(molb, sanitize, removeHs));
REQUIRE(mol);
mol->updatePropertyCache();
CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE);
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE);
auto nmb = MolToMolBlock(*mol);
CHECK(nmb.find("2 4 2 3") == std::string::npos);
CHECK(nmb.find("2 4 2 0") != std::string::npos);
std::vector<unsigned int> ranks;
Canon::rankMolAtoms(*mol, ranks);
nmb = MolToMolBlock(*mol);
CHECK(nmb.find("2 4 2 3") == std::string::npos);
CHECK(nmb.find("2 4 2 0") != std::string::npos);
}
}
TEST_CASE(
"github #2423: Incorrect assignment of explicit Hs to Al+3 read from mol "
"block",
"[bug, molops]") {
SECTION("basics: single atom mols") {
std::string mb = R"CTAB(2300
-OEChem-01301907122D
1 0 0 0 0 0 0 0 0999 V2000
-66.7000 999.0000 0.0000 Al 0 1 0 0 0 0 0 0 0 0 0 0
M CHG 1 1 3
M END)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 3);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
}
TEST_CASE("Specialized exceptions for sanitization errors", "[molops]") {
SECTION("AtomValenceException") {
std::vector<std::pair<std::string, unsigned int>> smiles = {
{"C=n1ccnc1", 1}, {"CCO(C)C", 2}};
for (auto pr : smiles) {
CHECK_THROWS_AS(SmilesToMol(pr.first), AtomValenceException);
try {
auto m = SmilesToMol(pr.first);
} catch (const AtomValenceException &e) {
CHECK(e.getType() == "AtomValenceException");
CHECK(e.getAtomIdx() == pr.second);
}
}
}
SECTION("AtomKekulizeException") {
std::vector<std::pair<std::string, unsigned int>> smiles = {
{"CCcc", 2}, {"C1:c:CC1", 0}};
for (auto pr : smiles) {
CHECK_THROWS_AS(SmilesToMol(pr.first), AtomKekulizeException);
try {
auto m = SmilesToMol(pr.first);
} catch (const AtomKekulizeException &e) {
CHECK(e.getType() == "AtomKekulizeException");
CHECK(e.getAtomIdx() == pr.second);
}
}
}
SECTION("KekulizeException") {
std::vector<std::pair<std::string, std::vector<unsigned int>>> smiles = {
{"c1cccc1", {0, 1, 2, 3, 4}}, {"Cc1cc1", {1, 2, 3}}};
for (auto pr : smiles) {
CHECK_THROWS_AS(SmilesToMol(pr.first), KekulizeException);
try {
auto m = SmilesToMol(pr.first);
} catch (const KekulizeException &e) {
CHECK(e.getType() == "KekulizeException");
CHECK(e.getAtomIndices() == pr.second);
}
}
}
}
TEST_CASE("detectChemistryProblems", "[molops]") {
SECTION("Basics") {
SmilesParserParams ps;
ps.sanitize = false;
auto m = std::unique_ptr<ROMol>(SmilesToMol("CO(C)CFCc1cc1", ps));
REQUIRE(m);
auto res = MolOps::detectChemistryProblems(*m);
REQUIRE(res.size() == 3);
CHECK(res[0]->getType() == "AtomValenceException");
REQUIRE(dynamic_cast<AtomValenceException *>(res[0].get()));
CHECK(dynamic_cast<AtomSanitizeException *>(res[0].get())->getAtomIdx() ==
1);
CHECK(res[1]->getType() == "AtomValenceException");
REQUIRE(dynamic_cast<AtomSanitizeException *>(res[1].get()));
CHECK(dynamic_cast<AtomSanitizeException *>(res[1].get())->getAtomIdx() ==
4);
CHECK(res[2]->getType() == "KekulizeException");
REQUIRE(dynamic_cast<KekulizeException *>(res[2].get()));
CHECK(dynamic_cast<KekulizeException *>(res[2].get())->getAtomIndices() ==
std::vector<unsigned int>({6, 7, 8}));
}
SECTION("No problems") {
SmilesParserParams ps;
ps.sanitize = false;
auto m = std::unique_ptr<ROMol>(SmilesToMol("c1ccccc1", ps));
REQUIRE(m);
auto res = MolOps::detectChemistryProblems(*m);
REQUIRE(res.size() == 0);
}
}
TEST_CASE(
"github #2606: Bad valence corrections on Pb, Sn"
"[bug, molops]") {
SECTION("basics-Pb") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
5 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Pb 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
SECTION("basics-Sn") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
5 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Sn 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
SECTION("basics-Ge") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
5 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Ge 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
}
TEST_CASE(
"github #2607: Pb, Sn should support valence 2"
"[bug, molops]") {
SECTION("basics-Pb") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
3 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Pb 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 3 1 2 2 -1 3 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 2);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
SECTION("basics-Sn") {
std::string mb = R"CTAB(
Mrv1810 08141905562D
3 0 0 0 0 0 999 V2000
-3.6316 -0.4737 0.0000 Sn 0 0 0 0 0 0 0 0 0 0 0 0
-3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 3 1 2 2 -1 3 -1
M END
)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 2);
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
}
}
TEST_CASE(
"github #2649: Allenes read from mol blocks have crossed bonds assigned"
"[bug, stereochemistry]") {
SECTION("basics") {
std::string mb = R"CTAB(mol
Mrv1824 09191901002D
6 5 0 0 0 0 999 V2000
-1.6986 -7.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2522 -6.8245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1438 -8.0357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8095 -6.2156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3374 -7.8470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6162 -6.3886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 3 2 0 0 0 0
2 1 2 0 0 0 0
3 5 1 0 0 0 0
4 2 2 0 0 0 0
6 4 1 0 0 0 0
M END)CTAB";
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
REQUIRE(mol);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE);
auto outmolb = MolToMolBlock(*mol);
// std::cerr<<outmolb<<std::endl;
CHECK(outmolb.find("1 3 2 0") != std::string::npos);
CHECK(outmolb.find("2 1 2 0") != std::string::npos);
CHECK(outmolb.find("4 2 2 0") != std::string::npos);
}
}
TEST_CASE(
"GitHub 2712: setBondStereoFromDirections() returning incorrect results"
"[stereochemistry]") {
SECTION("basics 1a") {
std::string mb = R"CTAB(
Mrv1810 10141909562D
4 3 0 0 0 0 999 V2000
3.3412 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5162 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1037 -3.7112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7537 -2.2823 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
1 4 1 0 0 0 0
M END
)CTAB";
bool sanitize = false;
std::unique_ptr<ROMol> mol(MolBlockToMol(mb, sanitize));
REQUIRE(mol);
CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
MolOps::setBondStereoFromDirections(*mol);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOTRANS);
}
SECTION("basics 1b") {
std::string mb = R"CTAB(
Mrv1810 10141909562D
4 3 0 0 0 0 999 V2000
3.3412 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5162 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1037 -3.7112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7537 -2.2823 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
4 1 1 0 0 0 0
M END
)CTAB";
bool sanitize = false;
std::unique_ptr<ROMol> mol(MolBlockToMol(mb, sanitize));
REQUIRE(mol);
CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
MolOps::setBondStereoFromDirections(*mol);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOTRANS);
}
SECTION("basics 2a") {
std::string mb = R"CTAB(
Mrv1810 10141909582D
4 3 0 0 0 0 999 V2000
3.4745 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6495 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2370 -5.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8870 -5.9569 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
1 4 1 0 0 0 0
M END
)CTAB";
bool sanitize = false;
std::unique_ptr<ROMol> mol(MolBlockToMol(mb, sanitize));
REQUIRE(mol);
CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
MolOps::setBondStereoFromDirections(*mol);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOCIS);
}
SECTION("basics 2b") {
std::string mb = R"CTAB(
Mrv1810 10141909582D
4 3 0 0 0 0 999 V2000
3.4745 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6495 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2370 -5.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8870 -5.9569 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
4 1 1 0 0 0 0
M END
)CTAB";
bool sanitize = false;
std::unique_ptr<ROMol> mol(MolBlockToMol(mb, sanitize));
REQUIRE(mol);
CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
MolOps::setBondStereoFromDirections(*mol);
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOCIS);
}
}
TEST_CASE("removeHs screwing up double bond stereo", "[bug,removeHs]") {
SECTION("example1") {
std::string molblock = R"CTAB(molblock = """
SciTegic12221702182D
47 51 0 0 0 0 999 V2000
0.2962 6.2611 0.0000 C 0 0
-3.9004 4.4820 0.0000 C 0 0
1.4195 5.2670 0.0000 C 0 0
-3.8201 -7.4431 0.0000 C 0 0
-4.9433 -6.4490 0.0000 C 0 0
-2.3975 -6.9674 0.0000 C 0 0
3.5921 -3.5947 0.0000 C 0 0
-3.1475 2.3700 0.0000 C 0 0
2.1695 -4.0705 0.0000 C 0 0
-2.0242 1.3759 0.0000 C 0 0
-4.6440 -4.9792 0.0000 C 0 0
2.7681 -1.1308 0.0000 C 0 0
-5.8626 1.1332 0.0000 C 0 0
3.0674 0.3391 0.0000 C 0 0
3.6660 3.2787 0.0000 C 0 0
8.1591 -0.6978 0.0000 C 0 0
7.3351 1.7662 0.0000 C 0 0
-6.3876 3.5028 0.0000 C 0 0
-0.6756 -5.0219 0.0000 C 0 0
7.0358 0.2964 0.0000 C 0 0
3.8914 -2.1249 0.0000 C 0 0
-2.0982 -5.4976 0.0000 C 0 0
-4.5701 1.8943 0.0000 C 0 0 1 0 0 0
-6.9859 2.1273 0.0000 C 0 0 1 0 0 0
4.4900 0.8148 0.0000 C 0 0
1.3455 -1.6065 0.0000 C 0 0
4.7893 2.2846 0.0000 C 0 0
1.9442 1.3332 0.0000 C 0 0
1.0462 -3.0763 0.0000 C 0 0
2.2435 2.8030 0.0000 C 0 0
-0.6017 1.8516 0.0000 C 0 0
5.6132 -0.1794 0.0000 C 0 0
0.2223 -0.6124 0.0000 Cl 0 0
9.2823 -1.6919 0.0000 N 0 0
-3.2215 -4.5035 0.0000 N 0 0
6.2119 2.7603 0.0000 N 0 0
5.3139 -1.6492 0.0000 N 0 0
0.5216 0.8575 0.0000 N 0 0
-4.8945 3.3588 0.0000 N 0 0
-8.2913 2.8662 0.0000 O 0 0
-0.3024 3.3214 0.0000 O 0 0
1.1202 3.7971 0.0000 O 0 0
-0.3763 -3.5520 0.0000 O 0 0
-2.8482 3.8398 0.0000 H 0 0
-2.3235 -0.0940 0.0000 H 0 0
-3.9483 0.5292 0.0000 H 0 0
-7.8572 0.9063 0.0000 H 0 0
1 3 1 0
2 39 1 0
3 42 1 0
4 5 2 0
4 6 1 0
5 11 1 0
6 22 2 0
7 9 2 0
7 21 1 0
8 44 1 0
8 10 2 0
8 23 1 0
9 29 1 0
10 45 1 0
10 31 1 0
11 35 2 0
12 21 2 0
12 26 1 0
13 23 1 0
13 24 1 0
14 25 2 0
14 28 1 0
15 27 2 0
15 30 1 0
16 20 1 0
16 34 3 0
17 20 2 0
17 36 1 0
18 24 1 0
18 39 1 0
19 22 1 0
19 43 1 0
20 32 1 0
21 37 1 0
22 35 1 0
23 46 1 6
23 39 1 0
24 47 1 1
24 40 1 0
25 27 1 0
25 32 1 0
26 29 2 0
26 33 1 0
27 36 1 0
28 30 2 0
28 38 1 0
29 43 1 0
30 42 1 0
31 38 2 0
31 41 1 0
32 37 2 3
M END
"""
)CTAB";
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<RWMol> m(MolBlockToMol(molblock, sanitize, removeHs));
REQUIRE(m);
m->updatePropertyCache();
MolOps::setBondStereoFromDirections(*m);
CHECK(m->getBondWithIdx(10)->getBondType() == Bond::DOUBLE);
CHECK(m->getBondWithIdx(10)->getStereo() == Bond::STEREOTRANS);
REQUIRE(m->getBondWithIdx(10)->getStereoAtoms().size() == 2);
CHECK(m->getBondWithIdx(10)->getStereoAtoms()[0] == 43);
CHECK(m->getBondWithIdx(10)->getStereoAtoms()[1] == 44);
MolOps::removeHs(*m); // implicitOnly,updateExplicitCount,sanitize);
// m->debugMol(std::cerr);
CHECK(m->getBondWithIdx(9)->getBondType() == Bond::DOUBLE);
CHECK(m->getBondWithIdx(9)->getStereo() == Bond::STEREOTRANS);
REQUIRE(m->getBondWithIdx(9)->getStereoAtoms().size() == 2);
CHECK(m->getBondWithIdx(9)->getStereoAtoms()[0] == 22);
CHECK(m->getBondWithIdx(9)->getStereoAtoms()[1] == 30);
}
}
TEST_CASE("setDoubleBondNeighborDirections()", "[stereochemistry,bug]") {
SECTION("basics") {
auto m = "CC=CC"_smiles;
REQUIRE(m);
m->getBondWithIdx(1)->getStereoAtoms() = {0, 3};
m->getBondWithIdx(1)->setStereo(Bond::STEREOCIS);
MolOps::setDoubleBondNeighborDirections(*m);
CHECK(m->getBondWithIdx(0)->getBondDir() == Bond::ENDUPRIGHT);
CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::ENDDOWNRIGHT);
CHECK(MolToSmiles(*m) == "C/C=C\\C");
}
}
TEST_CASE("github #2782: addHs() fails on atoms with 'bad' valences", "[bug]") {
SECTION("basics") {
SmilesParserParams ps;
ps.sanitize = false;
std::unique_ptr<RWMol> m(
static_cast<RWMol *>(SmilesToMol("C=C1=CC=CC=C1", ps)));
REQUIRE(m);
bool strict = false;
m->updatePropertyCache(strict);
CHECK(m->getNumAtoms() == 7);
MolOps::addHs(*m);
CHECK(m->getNumAtoms() == 14);
// this doesn't change the fact that there's still a bad valence present:
CHECK_THROWS_AS(m->updatePropertyCache(), AtomValenceException);
}
}
TEST_CASE(
"Github #2784: Element symbol lookup for some transuranics returns "
"incorrect results",
"[transuranics,bug]") {
auto pt = PeriodicTable::getTable();
SECTION("number to symbol") {
std::vector<std::pair<unsigned int, std::string>> data = {
{113, "Nh"}, {114, "Fl"}, {115, "Mc"},
{116, "Lv"}, {117, "Ts"}, {118, "Og"}};
for (auto pr : data) {
CHECK(pt->getElementSymbol(pr.first) == pr.second);
}
}
SECTION("symbol to number") {
std::vector<std::pair<unsigned int, std::string>> data = {
{113, "Nh"}, {114, "Fl"}, {115, "Mc"}, {116, "Lv"},
{117, "Ts"}, {118, "Og"}, {113, "Uut"}, {115, "Uup"}};
for (auto pr : data) {
CHECK(pt->getAtomicNumber(pr.second) == pr.first);
}
}
}
TEST_CASE("github #2775", "[valence,bug]") {
SECTION("basics") {
std::string molblock = R"CTAB(bismuth citrate
Mrv1810 11111908592D
14 12 0 0 0 0 999 V2000
7.4050 -0.5957 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6906 -1.0082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9761 -0.5957 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.6906 -1.8332 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
7.4050 0.2293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5800 0.2293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1675 0.9438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5800 1.6583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.3425 0.9438 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
8.2300 0.2293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6425 -0.4851 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.6425 0.9438 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
7.4050 1.0543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.5175 0.9438 0.0000 Bi 0 1 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 4 1 0 0 0 0
1 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
7 9 1 0 0 0 0
5 10 1 0 0 0 0
10 11 2 0 0 0 0
10 12 1 0 0 0 0
5 13 1 0 0 0 0
M CHG 4 4 -1 9 -1 12 -1 14 3
M END
)CTAB";
std::unique_ptr<RWMol> m(MolBlockToMol(molblock));
REQUIRE(m);
CHECK(m->getAtomWithIdx(13)->getSymbol() == "Bi");
CHECK(m->getAtomWithIdx(13)->getNumImplicitHs() == 0);
}
}
TEST_CASE("RemoveHsParameters", "[molops]") {
SmilesParserParams smilesPs;
smilesPs.removeHs = false;
SECTION("H-H") {
std::unique_ptr<RWMol> m{SmilesToMol("[H][H].[H]O[H]", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 5);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 3);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 3);
}
{
MolOps::RemoveHsParameters ps;
ps.removeOnlyHNeighbors = true;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 1);
}
}
SECTION("dummies") {
std::unique_ptr<RWMol> m{SmilesToMol("[H][*]O[H]", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 4);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 3);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 3);
}
{
MolOps::RemoveHsParameters ps;
ps.removeDummyNeighbors = true;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 2);
}
}
SECTION("chiralHs") {
std::unique_ptr<RWMol> m{SmilesToMol("[C@]12([H])CCC1CO2", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 7);
// artificial wedging since we don't have a conformer
m->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BEGINWEDGE);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 6);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 6);
}
{
MolOps::RemoveHsParameters ps;
ps.removeWithWedgedBond = false;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 7);
}
}
SECTION("degree zero") {
std::unique_ptr<RWMol> m{SmilesToMol("[F-].[H+]", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 2);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 2);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 2);
}
{
MolOps::RemoveHsParameters ps;
ps.removeDegreeZero = true;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 1);
}
}
SECTION("isotopes") {
std::unique_ptr<RWMol> m{SmilesToMol("F[2H]", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 2);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 2);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 2);
}
{
MolOps::RemoveHsParameters ps;
ps.removeIsotopes = true;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 1);
}
}
SECTION("defining bond stereo") {
std::unique_ptr<RWMol> m{SmilesToMol("F/C=N/[H]", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 4);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 4);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 4);
}
{
MolOps::RemoveHsParameters ps;
ps.removeDefiningBondStereo = true;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 3);
}
}
SECTION("Query atoms") {
std::unique_ptr<RWMol> m{SmartsToMol("O[#1]")};
REQUIRE(m);
CHECK(m->getNumAtoms() == 2);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 2);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 2);
}
{
MolOps::RemoveHsParameters ps;
ps.removeWithQuery = true;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 1);
}
}
SECTION("higher degree") {
// this is a silly example
std::unique_ptr<RWMol> m{SmilesToMol("F[H-]F", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 3);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 3);
}
{
MolOps::RemoveHsParameters ps;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 3);
}
{
MolOps::RemoveHsParameters ps;
ps.removeHigherDegrees = true;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 2);
}
}
SECTION("mapped Hs") {
std::unique_ptr<RWMol> m{SmilesToMol("[H:1]O[H]", smilesPs)};
REQUIRE(m);
CHECK(m->getNumAtoms() == 3);
{
RWMol cp(*m);
MolOps::removeHs(cp);
CHECK(cp.getNumAtoms() == 1);
}
{
MolOps::RemoveHsParameters ps;
ps.removeMapped = false;
RWMol cp(*m);
MolOps::removeHs(cp, ps);
CHECK(cp.getNumAtoms() == 2);
}
}
SECTION("allHs") {
std::unique_ptr<RWMol> m{SmilesToMol(
"[C@]12([H])CCC1CO2.[H+].F[H-]F.[H][H].[H]*.F/C=C/[H]", smilesPs)};
REQUIRE(m);
// artificial wedging since we don't have a conformer
m->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BEGINWEDGE);
RWMol cp(*m);
MolOps::removeAllHs(cp);
for (auto atom : cp.atoms()) {
CHECK(atom->getAtomicNum() != 1);
}
}
SECTION("allHs2") {
std::unique_ptr<ROMol> m{SmilesToMol(
"[C@]12([H])CCC1CO2.[H+].F[H-]F.[H][H].[H]*.F/C=C/[H]", smilesPs)};
REQUIRE(m);
// artificial wedging since we don't have a conformer
m->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BEGINWEDGE);
std::unique_ptr<ROMol> cp{MolOps::removeAllHs(*m)};
for (auto atom : cp->atoms()) {
CHECK(atom->getAtomicNum() != 1);
}
}
}
#endif
TEST_CASE("github #2895: acepentalene aromaticity perception ",
"[molops,bug,aromaticity]") {
SECTION("acepentalene") {
std::unique_ptr<RWMol> m{SmilesToMol("C1=CC2=CC=C3C2=C1C=C3")};
REQUIRE(m);
auto smi = MolToSmiles(*m);
CHECK(smi == "C1=CC2=C3C1=CC=C3C=C2");
}
}
TEST_CASE("handling of bondStereoCare in updateQueryProperties") {
SECTION("fully specified") {
auto mol = R"CTAB(basic test
Mrv1810 01292006422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.0316 2.0632 0 0 STBOX=1
M V30 2 C -5.6979 2.8332 0 0 STBOX=1
M V30 3 O -4.3642 2.0632 0 0
M V30 4 F -8.3653 2.8332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 1 4
M V30 3 2 1 2 STBOX=1
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(0, 1));
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
MolOps::AdjustQueryParameters ps;
ps.useStereoCareForBonds = true;
MolOps::adjustQueryProperties(*mol, &ps);
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
}
SECTION("fully unspecified") {
auto mol = R"CTAB(basic test
Mrv1810 01292006422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.0316 2.0632 0 0
M V30 2 C -5.6979 2.8332 0 0
M V30 3 O -4.3642 2.0632 0 0
M V30 4 F -8.3653 2.8332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 1 4
M V30 3 2 1 2
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(0, 1));
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
MolOps::AdjustQueryParameters ps;
ps.useStereoCareForBonds = true;
MolOps::adjustQueryProperties(*mol, &ps);
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREONONE);
}
SECTION("partially unspecified") {
std::vector<std::string> mbs = {R"CTAB(keep
Mrv1810 01292006422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.0316 2.0632 0 0 STBOX=1
M V30 2 C -5.6979 2.8332 0 0 STBOX=1
M V30 3 O -4.3642 2.0632 0 0
M V30 4 F -8.3653 2.8332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 1 4
M V30 3 2 1 2
M V30 END BOND
M V30 END CTAB
M END
)CTAB",
R"CTAB(keep
Mrv1810 01292006422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.0316 2.0632 0 0
M V30 2 C -5.6979 2.8332 0 0
M V30 3 O -4.3642 2.0632 0 0
M V30 4 F -8.3653 2.8332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 1 4
M V30 3 2 1 2 STBOX=1
M V30 END BOND
M V30 END CTAB
M END
)CTAB",
R"CTAB(remove
Mrv1810 01292006422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.0316 2.0632 0 0
M V30 2 C -5.6979 2.8332 0 0
M V30 3 O -4.3642 2.0632 0 0
M V30 4 F -8.3653 2.8332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 1 4
M V30 3 2 1 2 STBOX=0
M V30 END BOND
M V30 END CTAB
M END
)CTAB",
R"CTAB(remove
Mrv1810 01292006422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.0316 2.0632 0 0
M V30 2 C -5.6979 2.8332 0 0 STBOX=1
M V30 3 O -4.3642 2.0632 0 0
M V30 4 F -8.3653 2.8332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 1 4
M V30 3 2 1 2
M V30 END BOND
M V30 END CTAB
M END
)CTAB",
R"CTAB(remove
Mrv1810 01292006422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.0316 2.0632 0 0 STBOX=1
M V30 2 C -5.6979 2.8332 0 0
M V30 3 O -4.3642 2.0632 0 0
M V30 4 F -8.3653 2.8332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 1 4
M V30 3 2 1 2
M V30 END BOND
M V30 END CTAB
M END
)CTAB"};
for (const auto &mb : mbs) {
std::unique_ptr<RWMol> mol{MolBlockToMol(mb)};
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(0, 1));
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
MolOps::AdjustQueryParameters ps;
ps.useStereoCareForBonds = true;
MolOps::adjustQueryProperties(*mol, &ps);
if (mol->getProp<std::string>(common_properties::_Name) == "keep") {
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
} else {
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREONONE);
}
}
}
SECTION("V2000") {
auto mol = R"CTAB(basic test
Mrv1810 01292015042D
4 3 0 0 0 0 999 V2000
-3.7669 1.1053 0.0000 C 0 0 0 0 1 0 0 0 0 0 0 0
-3.0524 1.5178 0.0000 C 0 0 0 0 1 0 0 0 0 0 0 0
-2.3380 1.1053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.4814 1.5178 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
1 4 1 0 0 0 0
1 2 2 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(0)->hasProp(common_properties::molStereoCare));
CHECK(mol->getAtomWithIdx(1)->hasProp(common_properties::molStereoCare));
REQUIRE(mol->getBondBetweenAtoms(0, 1));
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
// property added by the CTAB parser:
CHECK(mol->getBondBetweenAtoms(0, 1)->hasProp(
common_properties::molStereoCare));
MolOps::AdjustQueryParameters ps;
ps.useStereoCareForBonds = true;
MolOps::adjustQueryProperties(*mol, &ps);
CHECK(mol->getBondBetweenAtoms(0, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
}
SECTION("molecule from SMILES") {
auto mol = "C/C=C/C"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(2, 1));
CHECK(mol->getBondBetweenAtoms(2, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
MolOps::AdjustQueryParameters ps;
ps.useStereoCareForBonds = true;
// since stereoCare is not set on the bond from SMILES,
// stereochem will be removed:
{
RWMol molcp(*mol);
MolOps::adjustQueryProperties(molcp, &ps);
CHECK(molcp.getBondBetweenAtoms(2, 1)->getStereo() ==
Bond::BondStereo::STEREONONE);
}
// but we can preserve it by setting the property:
{
RWMol molcp(*mol);
molcp.getBondBetweenAtoms(2, 1)->setProp(common_properties::molStereoCare,
1);
MolOps::adjustQueryProperties(molcp, &ps);
CHECK(molcp.getBondBetweenAtoms(2, 1)->getStereo() ==
Bond::BondStereo::STEREOE);
}
}
}
TEST_CASE("updateQueryParameters from JSON") {
SECTION("basics") {
MolOps::AdjustQueryParameters ps;
CHECK(ps.makeAtomsGeneric == false);
CHECK(ps.makeBondsGeneric == false);
CHECK(ps.makeBondsGenericFlags == MolOps::ADJUST_IGNORENONE);
std::string json = R"JSON({"makeAtomsGeneric":true})JSON";
MolOps::parseAdjustQueryParametersFromJSON(ps, json);
CHECK(ps.makeAtomsGeneric == true);
CHECK(ps.makeBondsGeneric == false);
// the parsing updates the parameters, it doesn't replace them:
json = R"JSON({"makeBondsGeneric":true,
"makeBondsGenericFlags":"IGNOREDUMMIES|IGNORECHAINS"})JSON";
MolOps::parseAdjustQueryParametersFromJSON(ps, json);
CHECK(ps.makeAtomsGeneric == true);
CHECK(ps.makeBondsGeneric == true);
CHECK(ps.makeBondsGenericFlags ==
(MolOps::ADJUST_IGNOREDUMMIES | MolOps::ADJUST_IGNORECHAINS));
}
SECTION("useStereoCare") {
MolOps::AdjustQueryParameters ps;
CHECK(ps.useStereoCareForBonds == false);
std::string json = R"JSON({"useStereoCareForBonds":true})JSON";
MolOps::parseAdjustQueryParametersFromJSON(ps, json);
CHECK(ps.useStereoCareForBonds == true);
json = R"JSON({"useStereoCareForBonds":false})JSON";
MolOps::parseAdjustQueryParametersFromJSON(ps, json);
CHECK(ps.useStereoCareForBonds == false);
}
SECTION("bogus contents") {
MolOps::AdjustQueryParameters ps;
CHECK(ps.adjustDegree == true);
CHECK(ps.adjustDegreeFlags ==
(MolOps::ADJUST_IGNOREDUMMIES | MolOps::ADJUST_IGNORECHAINS));
std::string json = R"JSON({"bogosity":true})JSON";
MolOps::parseAdjustQueryParametersFromJSON(ps, json);
CHECK(ps.adjustDegree == true);
json = R"JSON({"adjustDegree":"foo"})JSON";
MolOps::parseAdjustQueryParametersFromJSON(ps, json);
CHECK(ps.adjustDegree == true);
json = R"JSON({"adjustDegreeFlags":"IGNORENONE|bogus"})JSON";
// clang-format off
CHECK_THROWS_AS(MolOps::parseAdjustQueryParametersFromJSON(ps, json),ValueErrorException);
}
}
TEST_CASE("phosphine and arsine chirality", "[Chirality]") {
SECTION("chiral center recognized"){
auto mol1 = "C[P@](C1CCCC1)C1=CC=CC=C1"_smiles;
auto mol2 = "C[As@](C1CCCC1)C1=CC=CC=C1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(mol2->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("chiral center selective"){
auto mol1 = "C[P@](C)C1CCCCC1"_smiles;
auto mol2 = "C[As@](C)C1CCCCC1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(mol2->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
}
SECTION("chiral center specific: P"){
auto mol1 = "C[P@](C1CCCC1)C1=CC=CC=C1"_smiles;
auto mol2 = "C[P@@](C1CCCC1)C1=CC=CC=C1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2));
}
SECTION("chiral center specific: As"){
auto mol1 = "C[As@](C1CCCC1)C1=CC=CC=C1"_smiles;
auto mol2 = "C[As@@](C1CCCC1)C1=CC=CC=C1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2));
}
SECTION("chiral center, implicit H: P"){
auto mol1 = "C[P@H]C1CCCCC1"_smiles;
auto mol2 = "C[P@@H]C1CCCCC1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("chiral center, implicit H: As"){
auto mol1 = "C[As@H]C1CCCCC1"_smiles;
auto mol2 = "C[As@@H]C1CCCCC1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("chiral center specific, implicit H: P"){
auto mol1 = "C[P@H]C1CCCCC1"_smiles;
auto mol2 = "C[P@@H]C1CCCCC1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2));
}
SECTION("chiral center specific, implicit H: As"){
auto mol1 = "C[As@H]C1CCCCC1"_smiles;
auto mol2 = "C[As@@H]C1CCCCC1"_smiles;
REQUIRE(mol1);
REQUIRE(mol2);
CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2));
}
}
TEST_CASE("github #2890", "[bug, molops, stereo]") {
auto mol = "CC=CC"_smiles;
REQUIRE(mol);
auto bond = mol->getBondWithIdx(1);
bond->setStereo(Bond::STEREOANY);
REQUIRE(bond->getStereoAtoms().empty());
MolOps::findPotentialStereoBonds(*mol);
CHECK(bond->getStereo() == Bond::STEREOANY);
CHECK(bond->getStereoAtoms().size() == 2);
}
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