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// $Id$
//
// Created by Greg Landrum, July 2008
//
//
// Expected test results here correspond to v1.0 of the open-source
// avalontoolkit
//
#include <RDGeneral/test.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/Invariant.h>
#include <DataStructs/ExplicitBitVect.h>
#include <iostream>
#include <fstream>
#include <cstdio>
#include "AvalonTools.h"
#include <string>
using namespace RDKit;
void test1() {
BOOST_LOG(rdInfoLog) << "testing canonical smiles generation" << std::endl;
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccc1"));
TEST_ASSERT(m);
std::string smi = AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi == "c1ccccc1");
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1cccnc1"));
TEST_ASSERT(m);
std::string smi = AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi == "c1ccncc1");
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("n1ccccc1"));
TEST_ASSERT(m);
std::string smi = AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi == "c1ccncc1");
delete m;
}
{
std::string smi = AvalonTools::getCanonSmiles("n1ccccc1", true);
TEST_ASSERT(smi == "c1ccncc1");
}
{
std::string smi = AvalonTools::getCanonSmiles("c1cccnc1", true);
TEST_ASSERT(smi == "c1ccncc1");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test2() {
BOOST_LOG(rdInfoLog) << "testing coordinate generation" << std::endl;
#if 1
{
RWMol *m = SmilesToMol("c1cccnc1");
TEST_ASSERT(m);
unsigned int confId = AvalonTools::set2DCoords(*m);
TEST_ASSERT(m->getNumConformers() == 1);
TEST_ASSERT(confId == 0);
delete m;
}
#endif
{
std::string molb = AvalonTools::set2DCoords("c1cccnc1", true);
TEST_ASSERT(molb != "");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test3() {
BOOST_LOG(rdInfoLog) << "testing fingerprint generation" << std::endl;
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccn1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m, bv, 512, false, true, 0x00006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccn1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 18);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m, bv, 512, false, true, 0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccn1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 6);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1nnccc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m, bv, 512, false, true, 0x006FFF);
BOOST_LOG(rdInfoLog) << "c1nnccc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 28);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ncncc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m, bv, 512, false, true, 0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ncncc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 25);
delete m;
}
{
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP("c1cccnc1", true, bv, 512, false, true, 0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cccnc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 18);
}
{
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP("c1ccccc1", true, bv, 512, false, true, 0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 6);
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1cccnc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(1024);
AvalonTools::getAvalonFP(*m, bv, 1024, false, true, 0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cccnc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 19);
delete m;
}
{
ExplicitBitVect bv(2048);
AvalonTools::getAvalonFP("c1cocc1", true, bv, 2048, false, true, 0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cocc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 53);
}
{
ExplicitBitVect bv(2048);
AvalonTools::getAvalonFP("C1=COC=C1", true, bv, 2048, false, true,
0x006FFF);
BOOST_LOG(rdInfoLog) << "C1=COC=C1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits() == 53);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRDK151() {
BOOST_LOG(rdInfoLog) << "testing Jira issue RDK-151: pyAvalonTools not "
"generating chiral smiles from molecules"
<< std::endl;
{
std::string tSmi = "C[C@H](F)Cl";
ROMol *m = static_cast<ROMol *>(SmilesToMol(tSmi));
TEST_ASSERT(m);
std::string smi = AvalonTools::getCanonSmiles(tSmi, true);
CHECK_INVARIANT(smi == tSmi, smi + "!=" + tSmi);
smi = AvalonTools::getCanonSmiles(*m);
CHECK_INVARIANT(smi == tSmi, smi + "!=" + tSmi);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSmilesFailures() {
BOOST_LOG(rdInfoLog) << "testing handling of bad smiles strings" << std::endl;
{
std::string tSmi = "C1C";
std::string smi = AvalonTools::getCanonSmiles(tSmi, true);
CHECK_INVARIANT(smi == "", smi);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSubstructFps() {
BOOST_LOG(rdInfoLog) << "testing substructure fingerprints " << std::endl;
{
ExplicitBitVect bv1(512), bv2(512);
AvalonTools::getAvalonFP("c1ccccc1", true, bv1, 512, true, true,
AvalonTools::avalonSSSBits);
AvalonTools::getAvalonFP("c1ccccc1C(F)(F)F", true, bv2, 512);
TEST_ASSERT((bv1 & bv2) == bv1);
AvalonTools::getAvalonFP("c1ccccc1C(F)(F)F", true, bv1, 512);
TEST_ASSERT((bv1 & bv2) == bv1);
AvalonTools::getAvalonFP("c1cccc(C)c1C(F)(F)F", true, bv2, 512);
TEST_ASSERT((bv1 & bv2) == bv1);
}
{
ExplicitBitVect bv1(512), bv2(512);
AvalonTools::getAvalonFP("c1ccccc1O", true, bv1, 512, true, true,
AvalonTools::avalonSSSBits);
AvalonTools::getAvalonFP("c1ccccc1OC", true, bv2, 512);
TEST_ASSERT((bv1 & bv2) == bv1);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testStruChk() {
BOOST_LOG(rdInfoLog) << "testing structure checking " << std::endl;
{
int errs = 0;
RDKit::ROMOL_SPTR m = AvalonTools::checkMol(errs, "c1ccccc1", true);
TEST_ASSERT(errs == 0);
m = AvalonTools::checkMol(errs, "c1c(R)cccc1C1(CC-C(C)C1)C", true);
TEST_ASSERT(errs != 0);
}
{
int errs = 0;
std::string res;
boost::tie(res, errs) = AvalonTools::checkMolString("c1ccccc1", true);
TEST_ASSERT(errs == 0);
TEST_ASSERT(res != "");
boost::tie(res, errs) =
AvalonTools::checkMolString("c1c(R)cccc1C1(CC-C(C)C1)C", true);
TEST_ASSERT(errs == 1);
TEST_ASSERT(res == "");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBadMolfile() {
BOOST_LOG(rdInfoLog) << "testing handling bad molecules " << std::endl;
// some tests around dealing with bad mol blocks
{
std::string molb =
"SNAP007157A\n\
MACCS-II3194121345\n\
\n\
0 0 0 0 0";
std::string smi = AvalonTools::getCanonSmiles(molb, false);
CHECK_INVARIANT(smi == "", smi);
ExplicitBitVect bv(1024);
AvalonTools::getAvalonFP(molb, false, bv, 1024);
TEST_ASSERT(bv.getNumOnBits() == 0);
std::string oMolb;
AvalonTools::set2DCoords(molb, false);
CHECK_INVARIANT(oMolb == "", oMolb);
}
}
void testSmilesSegFault() {
BOOST_LOG(rdInfoLog)
<< "testing a canonical smiles case that led to seg faults " << std::endl;
// some tests around dealing with bad mol blocks
{
std::string inSmi(1024, 'C');
std::string smi = AvalonTools::getCanonSmiles(inSmi, true);
TEST_ASSERT(smi == inSmi);
}
{
std::string inSmi(1534, 'C');
std::string smi = AvalonTools::getCanonSmiles(inSmi, true);
TEST_ASSERT(smi == inSmi);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub336() {
BOOST_LOG(rdInfoLog) << "testing github issue 336: bad canonical smiles for "
"conjugated double bonds"
<< std::endl;
// some tests around dealing with bad mol blocks
{
std::string pathName = getenv("RDBASE");
pathName += "/External/AvalonTools/test_data/";
std::ifstream ins((pathName + "EZ_test.2.sdf").c_str());
std::string mb((std::istreambuf_iterator<char>(ins)),
std::istreambuf_iterator<char>());
ROMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 17);
std::string smi1 = AvalonTools::getCanonSmiles(mb, false);
std::string smi2 = AvalonTools::getCanonSmiles(*m);
std::cerr << "smi1: " << smi1 << std::endl;
std::cerr << "smi2: " << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
delete m;
}
{
std::string pathName = getenv("RDBASE");
pathName += "/External/AvalonTools/test_data/";
std::ifstream ins((pathName + "heterocycle.mol").c_str());
std::string mb((std::istreambuf_iterator<char>(ins)),
std::istreambuf_iterator<char>());
RWMol *m = MolBlockToMol(mb, false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 6);
m->updatePropertyCache();
MolOps::cleanUp(*m);
MolOps::setAromaticity(*m);
std::string smi1 = AvalonTools::getCanonSmiles(mb, false);
std::string smi2 = AvalonTools::getCanonSmiles(*m);
std::cerr << "smi1: " << smi1 << std::endl;
std::cerr << "smi2: " << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
TEST_ASSERT(smi1 == "CC1C=NNC=1");
delete m;
}
{
std::string pathName = getenv("RDBASE");
pathName += "/External/AvalonTools/test_data/";
std::ifstream ins((pathName + "heterocycle2.mol").c_str());
std::string mb((std::istreambuf_iterator<char>(ins)),
std::istreambuf_iterator<char>());
RWMol *m = MolBlockToMol(mb, false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 11);
m->updatePropertyCache();
MolOps::cleanUp(*m);
MolOps::setAromaticity(*m);
std::string smi1 = AvalonTools::getCanonSmiles(mb, false);
std::string smi2 = AvalonTools::getCanonSmiles(*m);
std::cerr << "smi1: " << smi1 << std::endl;
std::cerr << "smi2: " << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
TEST_ASSERT(smi1 == "CN2C=CC1=CC(=O)NC=C12");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testCountFps() {
BOOST_LOG(rdInfoLog) << "testing substructure fingerprints " << std::endl;
{
SparseIntVect<boost::uint32_t> cv1(5000), cv2(5000);
AvalonTools::getAvalonCountFP("c1ccccc1", true, cv1, 5000);
AvalonTools::getAvalonCountFP("c1ccccc1.c1ccccc1", true, cv2, 5000);
for (unsigned int i = 0; i < cv1.size(); ++i) {
if (cv1[i] && (cv2[i] != 2 * cv1[i])) {
std::cerr << " mismatch: " << i << " " << cv1[i] << " " << cv2[i]
<< std::endl;
}
}
for (unsigned int i = 0; i < cv1.size(); ++i) {
TEST_ASSERT(!cv1[i] || (cv2[i] == 2 * cv1[i]));
}
}
{
ROMol *m1 = static_cast<ROMol *>(SmilesToMol("c1ccccc1"));
TEST_ASSERT(m1);
ROMol *m2 = static_cast<ROMol *>(SmilesToMol("c1ccccc1.c1ccccc1"));
TEST_ASSERT(m2);
SparseIntVect<boost::uint32_t> cv1(5000), cv2(5000);
AvalonTools::getAvalonCountFP(*m1, cv1, 5000);
AvalonTools::getAvalonCountFP(*m2, cv2, 5000);
for (unsigned int i = 0; i < cv1.size(); ++i) {
if (cv1[i] && (cv2[i] != 2 * cv1[i])) {
std::cerr << " mismatch: " << i << " " << cv1[i] << " " << cv2[i]
<< std::endl;
}
}
for (unsigned int i = 0; i < cv1.size(); ++i) {
TEST_ASSERT(!cv1[i] || (cv2[i] == 2 * cv1[i]));
}
delete m1;
delete m2;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testInitStruChk() {
BOOST_LOG(rdInfoLog) << "testing init struchk " << std::endl;
{
std::string pathName = getenv("RDBASE");
pathName += "/Data/struchk/";
std::string struchk_init =
"-tm\n"
"-ta " +
pathName + std::string("checkfgs.trn\n") +
"-tm\n"
"-or\n"
"-ca " +
pathName + std::string("checkfgs.chk\n") +
"-cc\n"
"-cl 3\n"
"-cs\n"
"-cn 999\n"
"-l " +
#ifdef _WIN32
std::getenv("TEMP") +
#endif
std::string(std::tmpnam(nullptr)) + std::string("\n");
int errs = AvalonTools::initCheckMol(struchk_init);
TEST_ASSERT(!errs);
RDKit::ROMOL_SPTR m = AvalonTools::checkMol(errs, "c1ccccc1", true);
TEST_ASSERT(errs == 0);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main() {
RDLog::InitLogs();
#if 1
test1();
test2();
test3();
testRDK151();
testSmilesFailures();
testSubstructFps();
testStruChk();
testBadMolfile();
testSmilesSegFault();
testGithub336();
testCountFps();
#endif
testInitStruChk();
return 0;
}
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