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//
// Copyright (C) 2021 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 "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolBundle.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SubstructLibrary/SubstructLibrary.h>
#include <GraphMol/SubstructLibrary/PatternFactory.h>
using namespace RDKit;
TEST_CASE("querying with a molbundle") {
std::vector<std::string> libSmiles = {"CCCC", "CCOC", "CCNC"};
SubstructLibrary ssslib;
for (const auto &smi : libSmiles) {
std::unique_ptr<RWMol> mol(SmilesToMol(smi));
REQUIRE(mol);
ssslib.addMol(*mol);
}
SubstructMatchParameters params;
SECTION("basics") {
std::vector<std::string> qSmiles = {"CCC", "COC", "CNC"};
MolBundle bundle;
for (const auto &smi : qSmiles) {
boost::shared_ptr<ROMol> mol(SmilesToMol(smi));
REQUIRE(mol);
bundle.addMol(mol);
}
for (auto numThreads : std::vector<int>{1, -1}) {
CHECK(ssslib.countMatches(bundle, params, numThreads) == 3);
CHECK(ssslib.hasMatch(bundle, params, numThreads));
auto libMatches = ssslib.getMatches(bundle, params, numThreads);
CHECK(libMatches.size() == 3);
std::sort(libMatches.begin(), libMatches.end());
CHECK(libMatches == std::vector<unsigned int>{0, 1, 2});
}
}
SECTION("some bundle members don't match") {
std::vector<std::string> qSmiles = {"CCC", "CSC", "CNC"};
MolBundle bundle;
for (const auto &smi : qSmiles) {
boost::shared_ptr<ROMol> mol(SmilesToMol(smi));
REQUIRE(mol);
bundle.addMol(mol);
}
for (auto numThreads : std::vector<int>{1, -1}) {
CHECK(ssslib.countMatches(bundle, params, numThreads) == 2);
CHECK(ssslib.hasMatch(bundle, params, numThreads));
auto libMatches = ssslib.getMatches(bundle, params, numThreads);
CHECK(libMatches.size() == 2);
std::sort(libMatches.begin(), libMatches.end());
CHECK(libMatches == std::vector<unsigned int>{0, 2});
}
}
SECTION("no dupes please") {
std::vector<std::string> qSmiles = {"CCC", "CNC", "CC"};
MolBundle bundle;
for (const auto &smi : qSmiles) {
boost::shared_ptr<ROMol> mol(SmilesToMol(smi));
REQUIRE(mol);
bundle.addMol(mol);
}
for (auto numThreads : std::vector<int>{1, -1}) {
CHECK(ssslib.countMatches(bundle, params, numThreads) == 3);
CHECK(ssslib.hasMatch(bundle, params, numThreads));
auto libMatches = ssslib.getMatches(bundle, params, numThreads);
CHECK(libMatches.size() == 3);
std::sort(libMatches.begin(), libMatches.end());
CHECK(libMatches == std::vector<unsigned int>{0, 1, 2});
}
}
}
TEST_CASE("using modified query parameters") {
std::vector<std::string> libSmiles = {"C[C@H](F)Cl", "C[C@@H](F)Cl",
"C[CH](F)Cl"};
SubstructLibrary ssslib;
for (const auto &smi : libSmiles) {
std::unique_ptr<RWMol> mol(SmilesToMol(smi));
REQUIRE(mol);
ssslib.addMol(*mol);
}
SECTION("basics") {
auto qm = "C[C@@H](F)Cl"_smiles;
{ // by default stereo is not used
SubstructMatchParameters params;
CHECK(ssslib.countMatches(*qm, params) == 3);
CHECK(ssslib.hasMatch(*qm, params));
auto libMatches = ssslib.getMatches(*qm, params);
CHECK(libMatches.size() == 3);
std::sort(libMatches.begin(), libMatches.end());
CHECK(libMatches == std::vector<unsigned int>{0, 1, 2});
}
{ // use stereo
SubstructMatchParameters params;
params.useChirality = true;
CHECK(ssslib.countMatches(*qm, params) == 1);
CHECK(ssslib.hasMatch(*qm, params));
auto libMatches = ssslib.getMatches(*qm, params);
CHECK(libMatches.size() == 1);
std::sort(libMatches.begin(), libMatches.end());
CHECK(libMatches == std::vector<unsigned int>{1});
}
}
}
TEST_CASE("searchOrder") {
std::vector<std::string> libSmiles = {"CCCOC", "CCCCOCC", "CCOC", "COC",
"CCCCCOC"};
boost::shared_ptr<MolHolder> mholder(new MolHolder());
boost::shared_ptr<PatternHolder> fpholder(new PatternHolder());
SubstructLibrary ssslib(mholder, fpholder);
for (const auto &smi : libSmiles) {
std::unique_ptr<RWMol> mol(SmilesToMol(smi));
REQUIRE(mol);
ssslib.addMol(*mol);
}
SECTION("basics") {
auto qm = "COC"_smiles;
for (auto numThreads : std::vector<int>{1, -1}) {
{ // default search order
ssslib.setSearchOrder(std::vector<unsigned int>());
unsigned int maxResults = 2;
SubstructMatchParameters params;
CHECK(ssslib.countMatches(*qm, params, numThreads) == 5);
CHECK(ssslib.hasMatch(*qm, params));
auto libMatches =
ssslib.getMatches(*qm, params, numThreads, maxResults);
CHECK(libMatches.size() == 2);
CHECK(libMatches == std::vector<unsigned int>{0, 1});
}
{ // specified search order
unsigned int maxResults = 2;
std::vector<unsigned int> searchOrder = {3, 2, 0, 1, 4};
ssslib.setSearchOrder(searchOrder);
SubstructMatchParameters params;
CHECK(ssslib.countMatches(*qm, params, numThreads) == 5);
CHECK(ssslib.hasMatch(*qm, params));
auto libMatches =
ssslib.getMatches(*qm, params, numThreads, maxResults);
CHECK(libMatches.size() == 2);
CHECK(libMatches == std::vector<unsigned int>{3, 2});
}
{ // search order not the full length
unsigned int maxResults = 2;
std::vector<unsigned int> searchOrder = {3, 2, 0};
ssslib.setSearchOrder(searchOrder);
SubstructMatchParameters params;
CHECK(ssslib.countMatches(*qm, params, numThreads) == 3);
CHECK(ssslib.hasMatch(*qm, params));
auto libMatches =
ssslib.getMatches(*qm, params, numThreads, maxResults);
CHECK(libMatches.size() == 2);
CHECK(libMatches == std::vector<unsigned int>{3, 2});
}
}
}
SECTION("overly long searchOrder") {
auto qm = "COC"_smiles;
unsigned int maxResults = 2;
int numThreads = -1;
std::vector<unsigned int> searchOrder = {3, 2, 0, 1, 4, 2, 1, 4, 0};
ssslib.setSearchOrder(searchOrder);
SubstructMatchParameters params;
CHECK(ssslib.countMatches(*qm, params, numThreads) == 5);
CHECK(ssslib.hasMatch(*qm, params));
auto libMatches = ssslib.getMatches(*qm, params, numThreads, maxResults);
CHECK(libMatches.size() == 2);
CHECK(libMatches == std::vector<unsigned int>{3, 2});
}
SECTION("bogus indices in searchOrder") {
auto qm = "COC"_smiles;
std::vector<unsigned int> searchOrder = {3, 12, 0};
CHECK_THROWS_AS(ssslib.setSearchOrder(searchOrder), IndexErrorException);
}
#ifdef RDK_USE_BOOST_SERIALIZATION
SECTION("serialization") {
std::vector<unsigned int> searchOrder = {3, 0, 1};
ssslib.setSearchOrder(searchOrder);
std::string pickle = ssslib.Serialize();
SubstructLibrary serialized;
serialized.initFromString(pickle);
CHECK(serialized.size() == ssslib.size());
CHECK(serialized.getSearchOrder() == ssslib.getSearchOrder());
}
#endif
}
void setSearchSmallestFirst(SubstructLibrary &ssslib) {
const auto holder = ssslib.getMolHolder();
std::vector<unsigned int> searchOrder(holder->size());
std::iota(searchOrder.begin(), searchOrder.end(), 0);
std::stable_sort(searchOrder.begin(), searchOrder.end(),
[holder](unsigned int i1, unsigned int i2) {
return holder->getMol(i1)->getNumAtoms() <
holder->getMol(i2)->getNumAtoms();
});
ssslib.setSearchOrder(searchOrder);
}
TEST_CASE("searchOrderFunctionDemo") {
std::vector<std::string> libSmiles = {"CCCOC", "CCCCOCC", "CCOC", "COC",
"CCCCCOC"};
boost::shared_ptr<MolHolder> mholder(new MolHolder());
boost::shared_ptr<PatternHolder> fpholder(new PatternHolder());
SubstructLibrary ssslib(mholder, fpholder);
for (const auto &smi : libSmiles) {
std::unique_ptr<RWMol> mol(SmilesToMol(smi));
REQUIRE(mol);
ssslib.addMol(*mol);
}
SECTION("basics") {
auto qm = "COC"_smiles;
setSearchSmallestFirst(ssslib);
auto libMatches = ssslib.getMatches(*qm);
CHECK(libMatches.size() == 5);
CHECK(libMatches == std::vector<unsigned int>{3, 2, 0, 1, 4});
}
}
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