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rdkit/Code/GraphMol/catch_adjustquery.cpp
Greg Landrum daf78eb62c add test for #3325 (#3331)
2020-08-10 13:17:41 -04:00

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//
//
// Copyright (C) 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/RDKitQueries.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
using namespace RDKit;
using matchCase = std::tuple<std::string, std::string, bool, bool>;
class _IsSubstructOf : public Catch::MatcherBase<const std::string &> {
ROMol const *m_query;
std::string m_description;
SubstructMatchParameters m_ps;
public:
_IsSubstructOf(const ROMol &m, const std::string &description)
: m_query(&m), m_description(description) {}
_IsSubstructOf(const ROMol &m, const std::string &description,
SubstructMatchParameters ps)
: m_query(&m), m_description(description), m_ps(ps) {}
virtual bool match(const std::string &smiles) const override {
std::unique_ptr<ROMol> mol(SmilesToMol(smiles));
return !SubstructMatch(*mol, *m_query, m_ps).empty();
}
virtual std::string describe() const override {
std::ostringstream ss;
ss << "is not a substructure of " << m_description;
return ss.str();
}
};
static _IsSubstructOf IsSubstructOf(const ROMol &m, const std::string &smarts,
const SubstructMatchParameters &ps) {
return _IsSubstructOf(m, smarts, ps);
}
static _IsSubstructOf IsSubstructOf(const ROMol &m, const std::string &smarts) {
return _IsSubstructOf(m, smarts);
}
TEST_CASE("handling of bondStereoCare in adjustQueryProperties") {
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("adjustQueryParameters 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("MDL five-rings") {
MolOps::AdjustQueryParameters ps = MolOps::AdjustQueryParameters::noAdjustments();
ps.setMDLFiveRingAromaticity = true;
SECTION("query details") {
using extuple=std::tuple<std::string,std::string,std::string>;
std::vector<extuple> examples = {
// no queries, no change
extuple{"adjustqueryprops_MDLfivering_1.mol","[#7H]1:[#6]:[#6]:[#6]:[#6]:1",""},
// Q atom, no change
extuple{"adjustqueryprops_MDLfivering_2.mol","[!#6&!#1]1:[#6]:[#6]:[#6]:[#6]:1",""},
// A atom, this one changes
extuple{"adjustqueryprops_MDLfivering_3.mol","[!#1]1:[#6]:[#6]:[#6]:[#6]:1","[!#1]1-,:[#6]=,:[#6]-,:[#6]=,:[#6]-,:1"},
// NOTE that this is not technically correct according to the documentation, but if we make the bridging bond
// aromatic then it won't match azulene in a normal RDKit molecule, which is certainly not the intent of this.
extuple{"adjustqueryprops_MDLfivering_4.mol","[#6]12:[#6]:[#6]:[#6]:[#6]-1:[#6]:[#6]:[#6]:[#6]:[#6]:2",""},
};
for( auto tpl : examples){
if(std::get<2>(tpl).empty()){
std::get<2>(tpl) = std::get<1>(tpl);
}
auto fname = std::get<0>(tpl);
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> qry(MolFileToMol(pathName + fname));
REQUIRE(qry);
CHECK(std::get<1>(tpl)==MolToSmarts(*qry));
MolOps::adjustQueryProperties(*qry,&ps);
CHECK(std::get<2>(tpl)==MolToSmarts(*qry));
}
}
}
TEST_CASE("conjugated five-rings") {
MolOps::AdjustQueryParameters ps = MolOps::AdjustQueryParameters::noAdjustments();
ps.adjustConjugatedFiveRings = true;
SECTION("matching") {
std::vector<matchCase> examples = {
// 1,3 cyclopentadiene
matchCase{"C1=CCC=C1","adjustqueryprops_fivering_1.mol",true,true},
matchCase{"C1=CCC=C1","adjustqueryprops_fivering_2.mol",false,true},
matchCase{"C1=CCC=C1","adjustqueryprops_fivering_3.mol",true,true},
matchCase{"C1=CCC=C1","adjustqueryprops_fivering_4.mol",false,false},
matchCase{"C1=CCC=C1","adjustqueryprops_fivering_5.mol",false,false},
matchCase{"C1=CCC=C1","adjustqueryprops_fivering_6.mol",false,false},
// pyrrole
matchCase{"C1=CNC=C1","adjustqueryprops_fivering_1.mol",false,true},
matchCase{"C1=CNC=C1","adjustqueryprops_fivering_2.mol",true,true},
matchCase{"C1=CNC=C1","adjustqueryprops_fivering_3.mol",false,false},
matchCase{"C1=CNC=C1","adjustqueryprops_fivering_4.mol",false,false},
matchCase{"C1=CNC=C1","adjustqueryprops_fivering_5.mol",false,false},
matchCase{"C1=CNC=C1","adjustqueryprops_fivering_6.mol",false,false},
// thiophene
matchCase{"C1=CSC=C1","adjustqueryprops_fivering_1.mol",false,false},
matchCase{"C1=CSC=C1","adjustqueryprops_fivering_2.mol",true,true},
matchCase{"C1=CSC=C1","adjustqueryprops_fivering_3.mol",false,false},
matchCase{"C1=CSC=C1","adjustqueryprops_fivering_4.mol",true,true},
matchCase{"C1=CSC=C1","adjustqueryprops_fivering_5.mol",false,false},
matchCase{"C1=CSC=C1","adjustqueryprops_fivering_6.mol",true,true},
// thiophene oxide
matchCase{"C1=CS(=O)C=C1","adjustqueryprops_fivering_1.mol",false,false},
matchCase{"C1=CS(=O)C=C1","adjustqueryprops_fivering_2.mol",false,true},
matchCase{"C1=CS(=O)C=C1","adjustqueryprops_fivering_3.mol",false,false},
matchCase{"C1=CS(=O)C=C1","adjustqueryprops_fivering_4.mol",false,true},
matchCase{"C1=CS(=O)C=C1","adjustqueryprops_fivering_5.mol",false,false},
matchCase{"C1=CS(=O)C=C1","adjustqueryprops_fivering_6.mol",true,true},
// furan
matchCase{"C1=COC=C1","adjustqueryprops_fivering_1.mol",false,true},
matchCase{"C1=COC=C1","adjustqueryprops_fivering_2.mol",true,true},
matchCase{"C1=COC=C1","adjustqueryprops_fivering_3.mol",false,false},
matchCase{"C1=COC=C1","adjustqueryprops_fivering_4.mol",false,false},
matchCase{"C1=COC=C1","adjustqueryprops_fivering_5.mol",false,false},
matchCase{"C1=COC=C1","adjustqueryprops_fivering_6.mol",false,false},
};
for( const auto tpl : examples){
auto fname = std::get<1>(tpl);
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> qry(MolFileToMol(pathName + fname));
REQUIRE(qry);
if(std::get<2>(tpl)){
CHECK_THAT(std::get<0>(tpl),IsSubstructOf(*qry,fname));
} else {
CHECK_THAT(std::get<0>(tpl),!IsSubstructOf(*qry,fname));
}
MolOps::adjustQueryProperties(*qry,&ps);
if(std::get<3>(tpl)){
CHECK_THAT(std::get<0>(tpl),IsSubstructOf(*qry,fname));
} else {
CHECK_THAT(std::get<0>(tpl),!IsSubstructOf(*qry,fname));
}
}
}
SECTION("query details") {
auto fname = "adjustqueryprops_fivering_2.mol";
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> qry(MolFileToMol(pathName + fname));
REQUIRE(qry);
auto smarts = MolToSmarts(*qry);
CHECK(smarts=="[!#1]1:[#6]:[#6]:[#6]:[#6]:1");
MolOps::adjustQueryProperties(*qry,&ps);
smarts = MolToSmarts(*qry);
CHECK(smarts=="[!#1]1-,=,:[#6]-,=,:[#6]-,=,:[#6]-,=,:[#6]-,=,:1");
}
SECTION("some edge cases") {
{
auto qry="C1=COCC1"_smiles;
auto smarts = MolToSmarts(*qry);
CHECK(smarts == "[#6]1=[#6]-[#8]-[#6]-[#6]-1");
MolOps::adjustQueryProperties(*qry,&ps);
CHECK(MolToSmarts(*qry) == smarts);
}
{
auto qry="C1=CCC=C1"_smiles;
auto smarts = MolToSmarts(*qry);
CHECK(smarts == "[#6]1=[#6]-[#6]-[#6]=[#6]-1");
MolOps::adjustQueryProperties(*qry,&ps);
CHECK(MolToSmarts(*qry) == "[#6]1-,=,:[#6]-,=,:[#6]-,=,:[#6]-,=,:[#6]-,=,:1");
}
{
// conjugation (not bond order)
auto qry="C1=COOO1"_smiles;
auto smarts = MolToSmarts(*qry);
CHECK(smarts == "[#6]1=[#6]-[#8]-[#8]-[#8]-1");
MolOps::adjustQueryProperties(*qry,&ps);
CHECK(MolToSmarts(*qry) == "[#6]1-,=,:[#6]-,=,:[#8]-,=,:[#8]-,=,:[#8]-,=,:1");
}
{
// conjugation (not bond order)
auto qry="O=C1C(=O)C(=O)C(=O)C1=O"_smiles;
auto smarts = MolToSmarts(*qry);
CHECK(smarts == "[#8]=[#6]1-[#6](=[#8])-[#6](=[#8])-[#6](=[#8])-[#6]-1=[#8]");
MolOps::adjustQueryProperties(*qry,&ps);
CHECK(MolToSmarts(*qry) == "[#8]=[#6]1-,=,:[#6](=[#8])-,=,:[#6](=[#8])-,=,:[#6](=[#8])-,=,:[#6]-,=,:1=[#8]");
}
}
}
TEST_CASE("single bonds to degree-one neighbors") {
MolOps::AdjustQueryParameters ps = MolOps::AdjustQueryParameters::noAdjustments();
ps.adjustSingleBondsToDegreeOneNeighbors = true;
SECTION("matching") {
std::vector<matchCase> examples = {
matchCase{"C2CCCc1c2nncc1","Cc1cnncc1",true,true},
matchCase{"C2CCCc1c2nncc1","CCc1cnncc1",true,true},
matchCase{"C2CCC(C)c1c2nncc1","CCc1cnncc1",true,true},
matchCase{"c2cccc1c2nncc1","Cc1cnncc1",false,true},
matchCase{"c2cccc1c2nncc1","CCc1cnncc1",false,false},
matchCase{"c2ccc(C)c1c2nncc1","CCc1cnncc1",false,false},
matchCase{"C2CCCc1[nH]ccc12","Cc1[nH]ccc1",true,true},
matchCase{"C2CCCc1[nH]ccc12","CCc1[nH]ccc1",true,true},
matchCase{"c2cccc1[nH]ccc12","Cc1[nH]ccc1",false,true},
matchCase{"c2cccc1[nH]ccc12","CCc1[nH]ccc1",false,false},
};
for( const auto tpl : examples){
auto smi = std::get<1>(tpl);
std::unique_ptr<RWMol> qry(SmilesToMol(smi));
REQUIRE(qry);
if(std::get<2>(tpl)){
CHECK_THAT(std::get<0>(tpl),IsSubstructOf(*qry,smi));
} else {
CHECK_THAT(std::get<0>(tpl),!IsSubstructOf(*qry,smi));
}
MolOps::adjustQueryProperties(*qry,&ps);
if(std::get<3>(tpl)){
CHECK_THAT(std::get<0>(tpl),IsSubstructOf(*qry,smi));
} else {
CHECK_THAT(std::get<0>(tpl),!IsSubstructOf(*qry,smi));
}
}
}
}
TEST_CASE("single bonds to aromatic neighbors") {
MolOps::AdjustQueryParameters ps = MolOps::AdjustQueryParameters::noAdjustments();
ps.adjustSingleBondsBetweenAromaticAtoms = true;
SECTION("matching") {
std::vector<matchCase> examples = {
matchCase{"c1ncccc1-c1cnncc1","c1ncccc1-c1cnncc1",true,true},
matchCase{"C1=CC2=C(C=CC3=C2C=NN=C3)N=C1","c1ncccc1-c1cnncc1",false,true},
matchCase{"C1CC2=C(C=CC=N2)C2=C1C=NN=C2","c1ncccc1-c1cnncc1",true,true},
matchCase{"C1CC2=NN=CC3=C2C2=C(C=C3)N=CC=C12","c1ncccc1-c1cnncc1",false,true},
// confirm that we don't modify ring bonds
matchCase{"C1=CC2=C(C=CC3=C2C=NN=C3)N=C1","C1CC2=C(C=CC=N2)C2=C1C=NN=C2",false,false},
matchCase{"C1CC2=C(C=CC=N2)C2=C1C=NN=C2","C1CC2=C(C=CC=N2)C2=C1C=NN=C2",true,true},
matchCase{"C1CC2=C3C(C=CC4=NN=CC1=C34)=CC=N2","C1CC2=C(C=CC=N2)C2=C1C=NN=C2",false,true}, // was github #3325
};
for( const auto tpl : examples){
auto smi = std::get<1>(tpl);
std::unique_ptr<RWMol> qry(SmilesToMol(smi));
REQUIRE(qry);
if(std::get<2>(tpl)){
CHECK_THAT(std::get<0>(tpl),IsSubstructOf(*qry,smi));
} else {
CHECK_THAT(std::get<0>(tpl),!IsSubstructOf(*qry,smi));
}
MolOps::adjustQueryProperties(*qry,&ps);
if(std::get<3>(tpl)){
CHECK_THAT(std::get<0>(tpl),IsSubstructOf(*qry,smi));
} else {
CHECK_THAT(std::get<0>(tpl),!IsSubstructOf(*qry,smi));
}
}
}
}
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