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//
// 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 <algorithm>
#include <fstream>
#include <string>
#include <sstream>
#include "RDGeneral/test.h"
#include <catch2/catch_all.hpp>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <RDGeneral/FileParseException.h>
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
using namespace RDKit;
using namespace RDKit::v2;
TEST_CASE("ForwardSDMolSupplier") {
SECTION("basics") {
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.props.sdf";
{
std::ifstream inStream(fName);
FileParsers::ForwardSDMolSupplier sdsup(&inStream, false);
auto mol = sdsup.next();
REQUIRE(mol);
}
{ // v1
std::ifstream inStream(fName);
ForwardSDMolSupplier sdsup(&inStream, false);
std::unique_ptr<ROMol> mol{sdsup.next()};
REQUIRE(mol);
}
}
}
TEST_CASE("SDMolSupplier") {
SECTION("basics") {
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.props.sdf";
{
std::ifstream inStream(fName);
FileParsers::SDMolSupplier sdsup(&inStream, false);
auto mol = sdsup.next();
REQUIRE(mol);
auto mol2 = sdsup[10];
REQUIRE(mol2);
}
{ // v1
std::ifstream inStream(fName);
SDMolSupplier sdsup(&inStream, false);
std::unique_ptr<ROMol> mol{sdsup.next()};
REQUIRE(mol);
}
}
}
TEST_CASE("SmilesMolSupplier") {
SECTION("basics") {
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.tpsa.csv";
{
std::ifstream inStream(fName);
FileParsers::SmilesMolSupplierParams params;
params.delimiter = ',';
FileParsers::SmilesMolSupplier smsup(&inStream, false, params);
auto mol = smsup.next();
REQUIRE(mol);
auto mol2 = smsup[10];
REQUIRE(mol2);
}
{ // v1
std::ifstream inStream(fName);
SmilesMolSupplier smsup(&inStream, false, ",");
std::unique_ptr<ROMol> mol{smsup.next()};
REQUIRE(mol);
}
}
}
TEST_CASE("TDTMolSupplier") {
SECTION("basics") {
std::string fName = getenv("RDBASE");
fName += "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
{
std::ifstream inStream(fName);
FileParsers::TDTMolSupplier smsup(&inStream, false);
auto mol = smsup.next();
REQUIRE(mol);
CHECK(smsup.length() == 10);
auto mol2 = smsup[8];
REQUIRE(mol2);
}
{ // v1
std::ifstream inStream(fName);
TDTMolSupplier smsup(&inStream, false, ",");
std::unique_ptr<ROMol> mol{smsup.next()};
REQUIRE(mol);
}
}
}
#ifdef RDK_BUILD_MAEPARSER_SUPPORT
TEST_CASE("MaeMolSupplier") {
SECTION("basics") {
std::string fName = getenv("RDBASE");
fName += "/Code/GraphMol/FileParsers/test_data/props_test.mae";
MaeMolSupplier maesup(fName);
std::unique_ptr<ROMol> nmol(maesup.next());
TEST_ASSERT(nmol);
}
}
TEST_CASE("TestParsingInvalidChiralityLabelsWithMaeMolSupplier") {
constexpr const char *maeblock_template = R"DATA(f_m_ct {
i_m_ct_stereo_status
s_m_title
s_st_Chirality_1
:::
1
""
%s
m_atom[5] {
# First column is Index #
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_atomic_number
i_m_formal_charge
:::
1 -1.000000 -0.060606 0.000000 6 0
2 -1.000000 -1.560606 0.000000 6 0
3 -0.250000 -2.859644 0.000000 17 0
4 -2.500000 -1.560606 0.000000 9 0
5 0.299038 -0.810606 0.000000 35 0
:::
}
m_bond[4] {
# First column is Index #
i_m_from
i_m_order
i_m_to
:::
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
:::
}
}
)DATA";
auto invalid_chirality_label =
GENERATE("12_R_1_3_4_5", // missing chiral atom
"12_ANR_1_3_4_15", // missing substituent atom
"2_S_1_3_4", // incomplete substituent list
"2_ANS_1_3_4_5_2" // self bond and too many atoms
);
CAPTURE(invalid_chirality_label);
auto maeblock =
(boost::format(maeblock_template) % invalid_chirality_label).str();
auto iss = std::make_unique<std::istringstream>(maeblock);
constexpr bool sanitize = false;
constexpr bool takeOwnership = true;
MaeMolSupplier suppl(iss.release(), takeOwnership, sanitize);
auto mol = suppl.next();
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 5);
CHECK(mol->getNumBonds() == 4);
}
#endif
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