mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
3095fccb53
* add test + fix * simplification Co-authored-by: Greg Landrum <greg.landrum@gmail.com> --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
277 lines
7.9 KiB
C++
277 lines
7.9 KiB
C++
//
|
|
// Copyright (C) 2024 Greg Landrum and other RDKit contributors
|
|
//
|
|
// @@ All Rights Reserved @@
|
|
// This file is part of the RDKit.
|
|
// The contents are covered by the terms of the BSD license
|
|
// which is included in the file license.txt, found at the root
|
|
// of the RDKit source tree.
|
|
//
|
|
|
|
#include <catch2/catch_all.hpp>
|
|
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <GraphMol/MolOps.h>
|
|
#include <GraphMol/test_fixtures.h>
|
|
|
|
#include <GraphMol/FileParsers/FileParsers.h>
|
|
#include <GraphMol/SmilesParse/SmilesParse.h>
|
|
#include <GraphMol/SmilesParse/SmilesWrite.h>
|
|
|
|
using namespace RDKit;
|
|
|
|
TEST_CASE("github #7556: chiral sulfur in conjugated rings") {
|
|
SECTION("as reported") {
|
|
auto m = "CC1=CC(Cl)=CC2=C1N=[S@](C)N=C2N"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(!m->getBondBetweenAtoms(8, 9)->getIsConjugated());
|
|
CHECK(!m->getBondBetweenAtoms(9, 11)->getIsConjugated());
|
|
REQUIRE(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("getAvgMolWt") {
|
|
SECTION("basics") {
|
|
auto mol = "C"_smiles;
|
|
REQUIRE(mol);
|
|
auto amw = MolOps::getAvgMolWt(*mol);
|
|
CHECK_THAT(amw, Catch::Matchers::WithinAbs(16.043, 0.001));
|
|
amw = MolOps::getAvgMolWt(*mol, true);
|
|
CHECK_THAT(amw, Catch::Matchers::WithinAbs(12.011, 0.001));
|
|
MolOps::addHs(*mol);
|
|
amw = MolOps::getAvgMolWt(*mol);
|
|
CHECK_THAT(amw, Catch::Matchers::WithinAbs(16.043, 0.001));
|
|
amw = MolOps::getAvgMolWt(*mol, true);
|
|
CHECK_THAT(amw, Catch::Matchers::WithinAbs(12.011, 0.001));
|
|
}
|
|
SECTION("Hs in SMILES") {
|
|
auto mol = "[CH4]"_smiles;
|
|
REQUIRE(mol);
|
|
auto amw = MolOps::getAvgMolWt(*mol);
|
|
CHECK_THAT(amw, Catch::Matchers::WithinAbs(16.043, 0.001));
|
|
amw = MolOps::getAvgMolWt(*mol, true);
|
|
CHECK_THAT(amw, Catch::Matchers::WithinAbs(12.011, 0.001));
|
|
}
|
|
SECTION("isotopes") {
|
|
auto mol = "C[2H]"_smiles;
|
|
REQUIRE(mol);
|
|
auto amw = MolOps::getAvgMolWt(*mol);
|
|
CHECK_THAT(amw, Catch::Matchers::WithinAbs(17.0, 0.1));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("getExactMolWt") {
|
|
SECTION("basics") {
|
|
auto mol = "C"_smiles;
|
|
REQUIRE(mol);
|
|
auto mw = MolOps::getExactMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(16.031, 0.001));
|
|
mw = MolOps::getExactMolWt(*mol, true);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
|
|
MolOps::addHs(*mol);
|
|
mw = MolOps::getExactMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(16.031, 0.001));
|
|
mw = MolOps::getExactMolWt(*mol, true);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
|
|
}
|
|
SECTION("Hs in SMILES") {
|
|
auto mol = "[CH4]"_smiles;
|
|
REQUIRE(mol);
|
|
auto mw = MolOps::getExactMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(16.031, 0.001));
|
|
mw = MolOps::getExactMolWt(*mol, true);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
|
|
}
|
|
SECTION("isotopes") {
|
|
auto mol = "C[2H]"_smiles;
|
|
REQUIRE(mol);
|
|
auto mw = MolOps::getExactMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(17.037, 0.001));
|
|
mw = MolOps::getExactMolWt(*mol, true);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
|
|
}
|
|
SECTION("Cl") {
|
|
auto mol = "Cl"_smiles;
|
|
REQUIRE(mol);
|
|
auto mw = MolOps::getExactMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(34.9688 + 1.0078, 0.001));
|
|
mw = MolOps::getAvgMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(35.453 + 1.008, 0.001));
|
|
|
|
mol = "[35ClH]"_smiles;
|
|
REQUIRE(mol);
|
|
mw = MolOps::getExactMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(34.9688 + 1.0078, 0.001));
|
|
mw = MolOps::getAvgMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(34.9688 + 1.008, 0.001));
|
|
|
|
mol = "[36ClH]"_smiles;
|
|
REQUIRE(mol);
|
|
mw = MolOps::getExactMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(35.9683 + 1.0078, 0.001));
|
|
mw = MolOps::getAvgMolWt(*mol);
|
|
CHECK_THAT(mw, Catch::Matchers::WithinAbs(35.9683 + 1.008, 0.001));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("getMolFormula") {
|
|
SECTION("basics") {
|
|
auto mol = "C"_smiles;
|
|
REQUIRE(mol);
|
|
auto formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH4");
|
|
MolOps::addHs(*mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH4");
|
|
|
|
mol = "[CH4]"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH4");
|
|
|
|
mol = "CO"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH4O");
|
|
MolOps::addHs(*mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH4O");
|
|
|
|
mol = "C(=O)N"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH3NO");
|
|
|
|
mol = "C(=O)=O"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CO2");
|
|
|
|
mol = "C(=O)[O-]"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CHO2-");
|
|
|
|
mol = "C([O-])[O-]"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH2O2-2");
|
|
|
|
mol = "C([NH3+])[O-]"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH5NO");
|
|
|
|
mol = "C([NH3+])O"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH6NO+");
|
|
|
|
mol = "C([NH3+])[NH3+]"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH8N2+2");
|
|
}
|
|
SECTION("H isotopes") {
|
|
auto mol = "[2H]C([3H])O"_smiles;
|
|
REQUIRE(mol);
|
|
auto formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "CH4O");
|
|
formula = MolOps::getMolFormula(*mol, true);
|
|
CHECK(formula == "CH2DTO");
|
|
formula = MolOps::getMolFormula(*mol, true, false);
|
|
CHECK(formula == "CH2[2H][3H]O");
|
|
}
|
|
|
|
SECTION("isotopes") {
|
|
auto mol = "[13CH3]C[13CH2]C"_smiles;
|
|
REQUIRE(mol);
|
|
auto formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "C4H10");
|
|
formula = MolOps::getMolFormula(*mol, true);
|
|
CHECK(formula == "C2[13C]2H10");
|
|
formula = MolOps::getMolFormula(*mol, true, false);
|
|
CHECK(formula == "C2[13C]2H10");
|
|
|
|
mol = "[13CH3]C([2H])O"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "C2H6O");
|
|
formula = MolOps::getMolFormula(*mol, true);
|
|
CHECK(formula == "C[13C]H5DO");
|
|
formula = MolOps::getMolFormula(*mol, true, false);
|
|
CHECK(formula == "C[13C]H5[2H]O");
|
|
|
|
mol = "[13CH3]C[13CH2]CB(O)O[2H]"_smiles;
|
|
REQUIRE(mol);
|
|
formula = MolOps::getMolFormula(*mol);
|
|
CHECK(formula == "C4H11BO2");
|
|
formula = MolOps::getMolFormula(*mol, true);
|
|
CHECK(formula == "C2[13C]2H10DBO2");
|
|
formula = MolOps::getMolFormula(*mol, true, false);
|
|
CHECK(formula == "C2[13C]2H10[2H]BO2");
|
|
}
|
|
}
|
|
|
|
TEST_CASE("check division by zero in setTerminalAtomCoords") {
|
|
SECTION("degree 4") {
|
|
auto m = R"CTAB(
|
|
Mrv2311 11162401483D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 0 0 0 0
|
|
M V30 2 F -0.7971 -0.9945 1.275 0
|
|
M V30 3 F 0.7971 0.9945 -1.275 0
|
|
M V30 4 F -1.2069 -0.1568 -0.8768 0
|
|
M V30 5 Cl 1.1223 1.1513 0.8154 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 1 3
|
|
M V30 3 1 1 4
|
|
M V30 4 1 1 5
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
|
|
CHECK_NOTHROW(MolOps::setTerminalAtomCoords(*m, 4, 0));
|
|
}
|
|
SECTION("degree 2, aligned 2nd neighbors") {
|
|
// This looks like a weird mol, but it's an intermediate
|
|
// state in AddHs.
|
|
auto mb = R"CTAB(
|
|
Mrv1908 06032010402D
|
|
|
|
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 -19.8317 16.5 0 1 CHG=-1
|
|
M V30 2 N -18.2917 16.5 0 2 CHG=1
|
|
M V30 3 N -16.7517 16.5 0 3
|
|
M V30 4 H 0 0 0 3
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 3 2 3
|
|
M V30 3 1 1 4
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB";
|
|
|
|
v2::FileParsers::MolFileParserParams p;
|
|
p.removeHs = false;
|
|
|
|
auto m = v2::FileParsers::MolFromMolBlock(mb, p);
|
|
REQUIRE(m);
|
|
REQUIRE(m->getNumAtoms() == 4);
|
|
|
|
CHECK_NOTHROW(MolOps::setTerminalAtomCoords(*m, 3, 0));
|
|
}
|
|
} |