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//
// Copyright (c) 2024 Greg Landrum
// 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 "RDGeneral/test.h"
#include <string>
#include <catch2/catch_all.hpp>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/FileParsers/MultithreadedMolSupplier.h>
#include <GraphMol/FileParsers/MultithreadedSDMolSupplier.h>
#include <GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h>
using namespace RDKit;
TEST_CASE("multithreaded supplier destruction without reading") {
v2::FileParsers::MultithreadedMolSupplier::Parameters params;
params.numWriterThreads = 4;
std::string rdbase = getenv("RDBASE");
std::string sdpath = rdbase + "/Data/NCI/first_200.props.sdf";
auto sdsuppl = v2::FileParsers::MultithreadedSDMolSupplier(sdpath, params);
}
TEST_CASE("callbacks SDF") {
v2::FileParsers::MultithreadedMolSupplier::Parameters params;
params.numWriterThreads = 4;
std::string rdbase = getenv("RDBASE");
std::string sdpath = rdbase + "/Data/NCI/first_200.props.sdf";
auto sdsuppl = v2::FileParsers::MultithreadedSDMolSupplier(sdpath, params);
// std::string smiPath = rdbase + "/Data/NCI/first_5K.smi";
// auto smisuppl =
// v2::FileParsers::MultithreadedSmilesMolSupplier(smiPath, params);
// {
// std::string smiPath = rdbase + "/Data/NCI/first_5K.smi";
// auto suppl =
// v2::FileParsers::MultithreadedSmilesMolSupplier(smiPath, params);
// }
SECTION("nextCallback") {
std::map<unsigned int, unsigned int> callbackNats;
auto callback =
[&](RWMol &mol,
const v2::FileParsers::MultithreadedMolSupplier &suppl) {
callbackNats[suppl.getLastRecordId()] = mol.getNumAtoms();
};
auto &suppl = sdsuppl;
suppl.setNextCallback(callback);
unsigned int nMols = 0;
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
auto nats = mol->getNumAtoms();
CHECK(callbackNats[suppl.getLastRecordId()] == nats);
++nMols;
}
CHECK(nMols == callbackNats.size());
}
SECTION("nextCallbackException") {
std::map<unsigned int, unsigned int> callbackNats;
auto callback =
[&](RWMol &,
const v2::FileParsers::MultithreadedMolSupplier &) {
throw std::runtime_error(
"This is not the callback you are looking for");
};
auto &suppl = sdsuppl;
suppl.setNextCallback(callback);
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
// Check some arbitrary property present in all molecules in test file
// just to make sure we got *something*.
CHECK(mol->hasProp("AMW"));
}
}
SECTION("writeCallback") {
auto callback = [](RWMol &mol, const std::string &, unsigned int recordId) {
MolOps::addHs(mol);
mol.setProp("recordId", recordId);
};
auto &suppl = sdsuppl;
suppl.setWriteCallback(callback);
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
CHECK(!MolOps::needsHs(*mol));
CHECK(mol->hasProp("recordId"));
CHECK(mol->getProp<unsigned int>("recordId") == suppl.getLastRecordId());
}
}
SECTION("writeCallbackException") {
auto callback = [](RWMol &, const std::string &, unsigned int) {
throw std::runtime_error("You cannot pass!");
};
auto &suppl = sdsuppl;
suppl.setWriteCallback(callback);
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
CHECK(mol->hasProp("AMW"));
}
}
SECTION("readCallback") {
auto callback = [](const std::string &sdf, unsigned int recordId) {
auto res = sdf;
auto pos = sdf.find("$$$$");
if (pos == std::string::npos) {
return res;
}
res.replace(pos, 4,
std::string("> <recordId>\n") + std::to_string(recordId) +
"\n\n$$$$");
return res;
};
auto &suppl = sdsuppl;
suppl.setReadCallback(callback);
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
CHECK(mol->hasProp("recordId"));
CHECK(mol->getProp<unsigned int>("recordId") == suppl.getLastRecordId());
}
}
SECTION("readCallbackException") {
auto callback = [](const std::string &, unsigned int) -> std::string {
throw std::runtime_error("I'm Sorry Dave. I'm afraid I can't do that.");
};
auto &suppl = sdsuppl;
suppl.setReadCallback(callback);
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
CHECK(mol->hasProp("AMW"));
}
}
}
TEST_CASE("callbacks smiles") {
v2::FileParsers::MultithreadedMolSupplier::Parameters params;
params.numWriterThreads = 4;
std::string rdbase = getenv("RDBASE");
std::string smiPath = rdbase + "/Data/NCI/first_5K.smi";
auto suppl = v2::FileParsers::MultithreadedSmilesMolSupplier(smiPath, params);
SECTION("nextCallback") {
std::map<unsigned int, unsigned int> callbackNats;
auto callback =
[&](RWMol &mol,
const v2::FileParsers::MultithreadedMolSupplier &suppl) {
callbackNats[suppl.getLastRecordId()] = mol.getNumAtoms();
};
suppl.setNextCallback(callback);
unsigned int nMols = 0;
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
auto nats = mol->getNumAtoms();
CHECK(callbackNats[suppl.getLastRecordId()] == nats);
++nMols;
}
CHECK(nMols == callbackNats.size());
}
SECTION("writeCallback") {
auto callback = [](RWMol &mol, const std::string &, unsigned int recordId) {
MolOps::addHs(mol);
mol.setProp("recordId", recordId);
};
suppl.setWriteCallback(callback);
while (!suppl.atEnd()) {
auto mol = suppl.next();
if (!mol) {
continue;
}
CHECK(!MolOps::needsHs(*mol));
CHECK(mol->hasProp("recordId"));
CHECK(mol->getProp<unsigned int>("recordId") == suppl.getLastRecordId());
}
}
}
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