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72340e33c2
* Fixes #3648 Code now builds without either MAEParser or coordgen integration enabled. * add CI build with minimal dependencies * remove doctests from the new CI build they need the cairo support
299 lines
9.2 KiB
C++
299 lines
9.2 KiB
C++
//
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// Copyright (C) 2020 Shrey Aryan
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <GraphMol/MonomerInfo.h>
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#include <GraphMol/RDKitBase.h>
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#include <RDGeneral/FileParseException.h>
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#include <RDGeneral/RDLog.h>
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#include <RDGeneral/test.h>
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#include <boost/iostreams/device/file.hpp>
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#include <boost/iostreams/filtering_stream.hpp>
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#include <fstream>
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#include <iostream>
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#include <map>
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#include <memory>
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#include <string>
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#include "GeneralFileReader.h"
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namespace io = boost::iostreams;
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using namespace RDKit;
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using namespace GeneralMolSupplier;
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void testDetermineFormat() {
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std::string fname1 = "1kv1.maegz";
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std::string fname2 = "first_200.tpsa.csv";
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std::string fname3 = "esters.prop_name_trunc.sdf";
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std::string fname4 = "NCI_aids_few.sdf.gz";
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std::string fname5 = "t.o.o.m.a.n.y.dots.mae";
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std::string fname6 = "checkCaseSensitiveFormat.sDf.Gz";
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std::string fname7 = "something.sdfgz";
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std::string fileFormat, compressionFormat;
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determineFormat(fname1, fileFormat, compressionFormat);
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TEST_ASSERT(fileFormat == "mae");
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TEST_ASSERT(compressionFormat == "gz");
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determineFormat(fname2, fileFormat, compressionFormat);
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TEST_ASSERT(fileFormat == "csv");
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TEST_ASSERT(compressionFormat == "");
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determineFormat(fname3, fileFormat, compressionFormat);
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TEST_ASSERT(fileFormat == "sdf");
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TEST_ASSERT(compressionFormat == "");
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determineFormat(fname4, fileFormat, compressionFormat);
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TEST_ASSERT(fileFormat == "sdf");
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TEST_ASSERT(compressionFormat == "gz");
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determineFormat(fname5, fileFormat, compressionFormat);
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TEST_ASSERT(fileFormat == "mae");
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TEST_ASSERT(compressionFormat == "");
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determineFormat(fname6, fileFormat, compressionFormat);
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TEST_ASSERT(fileFormat == "sdf");
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TEST_ASSERT(compressionFormat == "gz");
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determineFormat(fname7, fileFormat, compressionFormat);
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TEST_ASSERT(fileFormat == "sdf");
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TEST_ASSERT(compressionFormat == "gz");
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}
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void testSdf() {
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//! Open uncompressed SDF file format
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
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struct SupplierOptions opt;
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auto sdsup = getSupplier(fname, opt);
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unsigned int i = 0;
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while (!sdsup->atEnd()) {
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ROMol* nmol = sdsup->next();
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TEST_ASSERT(nmol || sdsup->atEnd());
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if (nmol) {
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TEST_ASSERT(nmol->hasProp(common_properties::_Name));
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TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
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delete nmol;
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i++;
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}
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}
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TEST_ASSERT(i == 16);
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//! Use Multithreaded Supplier
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struct SupplierOptions optConcurrent;
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optConcurrent.sanitize = false;
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optConcurrent.numWriterThreads = 2;
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auto sdsupMulti = getSupplier(fname, optConcurrent);
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i = 0;
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while (!sdsupMulti->atEnd()) {
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ROMol* nmol = sdsupMulti->next();
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if (nmol) {
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TEST_ASSERT(nmol->hasProp(common_properties::_Name));
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TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
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delete nmol;
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i++;
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}
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}
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TEST_ASSERT(i == 16);
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//! Open compressed SDF file format
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fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf.gz";
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opt.takeOwnership = false;
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auto sdsup2 = getSupplier(fname, opt);
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i = 0;
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while (!sdsup2->atEnd()) {
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ROMol* nmol = sdsup2->next();
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if (nmol) {
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TEST_ASSERT(nmol->hasProp(common_properties::_Name));
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TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
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delete nmol;
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i++;
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}
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}
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TEST_ASSERT(i == 16);
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}
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void testSmi() {
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//! Open uncompressed SMI file format, try .csv formats
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std::string mname;
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.2.csv";
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struct SupplierOptions opt_smi;
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opt_smi.takeOwnership = false;
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opt_smi.delimiter = ",";
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opt_smi.smilesColumn = 1;
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opt_smi.nameColumn = 0;
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opt_smi.titleLine = true;
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auto sup = getSupplier(fname, opt_smi);
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unsigned int i = 0;
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while (!sup->atEnd()) {
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ROMol* mol = sup->next();
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if (i == 3) {
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mol->getProp(common_properties::_Name, mname);
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CHECK_INVARIANT(mname == "4", "");
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mol->getProp("TPSA", mname);
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CHECK_INVARIANT(mname == "82.78", "");
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}
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delete mol;
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i++;
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}
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TEST_ASSERT(i == 10);
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//! Use Multithreaded Supplier
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opt_smi.numWriterThreads = 2;
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auto supMulti = getSupplier(fname, opt_smi);
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i = 0;
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while (!supMulti->atEnd()) {
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ROMol* mol = supMulti->next();
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if (mol) {
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delete mol;
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i++;
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}
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}
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TEST_ASSERT(i == 10);
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}
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void testMae() {
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#ifdef RDK_BUILD_MAEPARSER_SUPPORT
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//! Open uncompressed MAE file format
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/props_test.mae";
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struct SupplierOptions opt;
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auto maesup = getSupplier(fname, opt);
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std::unique_ptr<ROMol> nmol(maesup->next());
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TEST_ASSERT(nmol);
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//! Test mol properties
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TEST_ASSERT(nmol->hasProp(common_properties::_Name));
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TEST_ASSERT(nmol->hasProp("b_sd_chiral_flag"));
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TEST_ASSERT(nmol->getProp<bool>("b_sd_chiral_flag") == false);
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TEST_ASSERT(nmol->hasProp("i_sd_NSC"));
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TEST_ASSERT(nmol->getProp<int>("i_sd_NSC") == 48);
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TEST_ASSERT(nmol->hasProp("s_m_entry_name"));
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TEST_ASSERT(nmol->getProp<std::string>("s_m_entry_name") == "NCI_aids_few.1");
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TEST_ASSERT(nmol->hasProp("r_f3d_dummy"));
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TEST_ASSERT(abs(nmol->getProp<double>("r_f3d_dummy") - 42.123) < 0.0001);
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//! Test atom properties
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TEST_ASSERT(nmol->getNumAtoms() == 19);
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for (int i = 0; i < 19; ++i) {
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const auto* atom = nmol->getAtomWithIdx(i);
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//! The integer property is present for all atoms
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TEST_ASSERT(atom->hasProp("i_m_minimize_atom_index"));
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TEST_ASSERT(atom->getProp<int>("i_m_minimize_atom_index") == 1 + i);
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//! The bool property is only defined for i < 10
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if (i < 10) {
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TEST_ASSERT(atom->hasProp("b_m_dummy"));
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TEST_ASSERT(atom->getProp<bool>("b_m_dummy") == static_cast<bool>(i % 2));
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} else {
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TEST_ASSERT(!atom->hasProp("b_m_dummy"));
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}
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//! The real property is only defined for i >= 10
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if (i >= 10) {
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TEST_ASSERT(atom->hasProp("r_f3d_dummy"));
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TEST_ASSERT(abs(atom->getProp<double>("r_f3d_dummy") - (19.1 - i)) <
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0.0001);
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} else {
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TEST_ASSERT(!atom->hasProp("r_f3d_dummy"));
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}
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//! All atoms have the string prop
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TEST_ASSERT(atom->hasProp("s_m_dummy"));
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TEST_ASSERT(atom->getProp<std::string>("s_m_dummy") ==
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std::to_string(19 - i));
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}
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TEST_ASSERT(maesup->atEnd());
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//! Open compressed MAE file, .maegz format
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fname = rdbase + "/Code/GraphMol/FileParsers/test_data/1kv1.maegz";
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auto cmaesup = getSupplier(fname, opt);
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std::shared_ptr<ROMol> nmol2;
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nmol2.reset(cmaesup->next());
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const Atom* atom = nmol2->getAtomWithIdx(0);
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auto* info = (AtomPDBResidueInfo*)(atom->getMonomerInfo());
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TEST_ASSERT(info->getResidueName() == "ARG ");
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TEST_ASSERT(info->getChainId() == "A");
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TEST_ASSERT(info->getResidueNumber() == 5);
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#endif
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}
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void testTdt() {
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//! Open uncompressed TDT file
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
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struct SupplierOptions opt;
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opt.nameRecord = "PN";
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auto suppl = getSupplier(fname, opt);
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unsigned int i = 0;
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while (!suppl->atEnd()) {
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ROMol* nmol = suppl->next();
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if (nmol) {
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std::string prop1, prop2;
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TEST_ASSERT(nmol->getNumAtoms() > 0);
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TEST_ASSERT(nmol->hasProp("PN"));
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TEST_ASSERT(nmol->hasProp(common_properties::_Name));
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TEST_ASSERT(nmol->hasProp("MFCD"));
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nmol->getProp("PN", prop1);
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nmol->getProp(common_properties::_Name, prop2);
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TEST_ASSERT(prop1 == prop2);
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//! we didn't ask for 2D conformers, so there should be a property 2D:
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TEST_ASSERT(nmol->hasProp(common_properties::TWOD));
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//! and no conformer:
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TEST_ASSERT(!nmol->getNumConformers());
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delete nmol;
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i++;
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}
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}
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TEST_ASSERT(i == 10);
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}
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int main() {
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RDLog::InitLogs();
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BOOST_LOG(rdErrorLog) << "\n-----------------------------------------\n";
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testDetermineFormat();
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BOOST_LOG(rdErrorLog) << "Finished: testDetermineFormat()\n";
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BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
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BOOST_LOG(rdErrorLog) << "\n-----------------------------------------\n";
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testSdf();
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BOOST_LOG(rdErrorLog) << "Finished: testSdf()\n";
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BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
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BOOST_LOG(rdErrorLog) << "\n-----------------------------------------\n";
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testSmi();
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BOOST_LOG(rdErrorLog) << "Finished: testSmi()\n";
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BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
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BOOST_LOG(rdErrorLog) << "\n-----------------------------------------\n";
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testMae();
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BOOST_LOG(rdErrorLog) << "Finished: testMae()\n";
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BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
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BOOST_LOG(rdErrorLog) << "\n-----------------------------------------\n";
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testTdt();
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BOOST_LOG(rdErrorLog) << "Finished: testTdt()\n";
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BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
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return 0;
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}
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