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rdkit/Code/GraphMol/SmilesParse/cxsmiles_test.cpp
Ric 27f50e332d ignore HTML char codes (#2395)
2019-04-06 05:36:56 +02:00

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//
// Copyright (C) 2016 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 <GraphMol/RDKitBase.h>
#include "SmilesParse.h"
#include "SmilesWrite.h"
#include <RDGeneral/RDLog.h>
using namespace RDKit;
void testBase() {
BOOST_LOG(rdInfoLog) << "testing base functionality" << std::endl;
{ // it works when nothing is provided
std::string smiles = "CC";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testCoords2D() {
BOOST_LOG(rdInfoLog) << "testing reading 2D coordinates" << std::endl;
{
std::string smiles = "CC |(0,.75,;0,-.75,)|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
TEST_ASSERT(m->getNumConformers() == 1);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(0).x) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(0).y - 0.75) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(0).z) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(1).x) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(1).y + 0.75) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(1).z) < 1e-4);
delete m;
}
{
std::string smiles = "CC |(,,;,,-.75)|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
TEST_ASSERT(m->getNumConformers() == 1);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(0).x) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(0).y) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(0).z) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(1).x) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(1).y) < 1e-4);
TEST_ASSERT(fabs(m->getConformer().getAtomPos(1).z + 0.75) < 1e-4);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testAtomLabels() {
BOOST_LOG(rdInfoLog) << "testing reading Atom Labels" << std::endl;
{
std::string smiles = "CCC |$foo;;bar$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>(
common_properties::atomLabel) == "foo");
TEST_ASSERT(m->getAtomWithIdx(2)->getProp<std::string>(
common_properties::atomLabel) == "bar");
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::atomLabel));
delete m;
}
{ // attachment points, example from the docs
std::string smiles = "C[C@H](N*)C(*)=O |$;;;_AP1;;_AP2;$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 7);
TEST_ASSERT(m->getAtomWithIdx(3)->getAtomicNum() == 0);
TEST_ASSERT(m->getAtomWithIdx(3)->getProp<std::string>(
common_properties::atomLabel) == "_AP1");
TEST_ASSERT(m->getAtomWithIdx(3)->getAtomMapNum() == 1);
TEST_ASSERT(m->getAtomWithIdx(5)->getAtomicNum() == 0);
TEST_ASSERT(m->getAtomWithIdx(5)->getProp<std::string>(
common_properties::atomLabel) == "_AP2");
TEST_ASSERT(m->getAtomWithIdx(5)->getAtomMapNum() == 2);
delete m;
}
{ // query properties
std::string smiles = "**C |$Q_e;QH_p;;$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>(
common_properties::atomLabel) == "Q_e");
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::atomLabel) == "QH_p");
TEST_ASSERT(!m->getAtomWithIdx(2)->hasProp(common_properties::atomLabel));
TEST_ASSERT(m->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(!m->getAtomWithIdx(2)->hasQuery());
delete m;
}
{ // query properties2
std::string smiles = "** |$;AH_p;$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::atomLabel) == "AH_p");
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::atomLabel));
TEST_ASSERT(m->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(0)->getQuery()->getDescription() ==
"AtomAtomicNum");
TEST_ASSERT(m->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(1)->getQuery()->getDescription() ==
"AtomNull");
delete m;
}
{ // query properties3
std::string smiles = "** |$;XH_p;$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::atomLabel) == "XH_p");
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::atomLabel));
TEST_ASSERT(m->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(0)->getQuery()->getDescription() ==
"AtomAtomicNum");
TEST_ASSERT(m->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(1)->getQuery()->getDescription() == "AtomOr");
delete m;
}
{ // query properties3
std::string smiles = "** |$MH_p;M_p;$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>(
common_properties::atomLabel) == "MH_p");
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::atomLabel) == "M_p");
TEST_ASSERT(m->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(0)->getQuery()->getDescription() == "AtomOr");
TEST_ASSERT(m->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(1)->getQuery()->getDescription() == "AtomOr");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testCXSmilesAndName() {
BOOST_LOG(rdInfoLog) << "testing CSXMILES and mol name" << std::endl;
{
std::string smiles = "CCC |$foo;;bar$|";
SmilesParserParams params;
params.allowCXSMILES = true;
params.parseName = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>(
common_properties::atomLabel) == "foo");
TEST_ASSERT(m->getProp<std::string>("_CXSMILES_Data") == "|$foo;;bar$|");
TEST_ASSERT(!m->hasProp("_Name"));
delete m;
}
{
std::string smiles = "CCC |$foo;;bar$| ourname";
SmilesParserParams params;
params.allowCXSMILES = true;
params.parseName = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>(
common_properties::atomLabel) == "foo");
TEST_ASSERT(m->getProp<std::string>("_CXSMILES_Data") == "|$foo;;bar$|");
TEST_ASSERT(m->getProp<std::string>(common_properties::_Name) == "ourname");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testCoordinateBonds() {
BOOST_LOG(rdInfoLog) << "testing coordinate bonds" << std::endl;
{
std::string smiles = "[Fe]1C=C1 |C:1.0,2.2|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getBondBetweenAtoms(1, 2));
TEST_ASSERT(m->getBondBetweenAtoms(1, 2)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(0, 1));
TEST_ASSERT(m->getBondBetweenAtoms(0, 1)->getBondType() == Bond::DATIVE);
TEST_ASSERT(m->getBondBetweenAtoms(0, 1)->getBeginAtomIdx() == 1);
TEST_ASSERT(m->getBondBetweenAtoms(0, 2));
TEST_ASSERT(m->getBondBetweenAtoms(0, 2)->getBondType() == Bond::DATIVE);
TEST_ASSERT(m->getBondBetweenAtoms(0, 2)->getBeginAtomIdx() == 2);
delete m;
}
{
std::string smiles = "C1[Fe]C=1 |C:0.0,2.1|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getBondBetweenAtoms(0, 2));
TEST_ASSERT(m->getBondBetweenAtoms(0, 2)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(0, 1));
TEST_ASSERT(m->getBondBetweenAtoms(0, 1)->getBondType() == Bond::DATIVE);
TEST_ASSERT(m->getBondBetweenAtoms(0, 1)->getBeginAtomIdx() == 0);
TEST_ASSERT(m->getBondBetweenAtoms(1, 2));
TEST_ASSERT(m->getBondBetweenAtoms(1, 2)->getBondType() == Bond::DATIVE);
TEST_ASSERT(m->getBondBetweenAtoms(1, 2)->getBeginAtomIdx() == 2);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRadicals() {
BOOST_LOG(rdInfoLog) << "testing radicals" << std::endl;
{
std::string smiles = "[O]C[O] |^1:0,2|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 1);
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons() == 0);
TEST_ASSERT(m->getAtomWithIdx(2)->getNumRadicalElectrons() == 1);
delete m;
}
{
std::string smiles = "[O][C][O] |^1:0,2,^4:1|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 1);
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons() == 2);
TEST_ASSERT(m->getAtomWithIdx(2)->getNumRadicalElectrons() == 1);
delete m;
}
{ // radicals and coordinate bonds
std::string smiles = "[Fe]N([O])[O] |^1:2,3,C:1.0|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 4);
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons() == 0);
TEST_ASSERT(m->getAtomWithIdx(2)->getNumRadicalElectrons() == 1);
TEST_ASSERT(m->getAtomWithIdx(3)->getNumRadicalElectrons() == 1);
TEST_ASSERT(m->getBondBetweenAtoms(0, 1));
TEST_ASSERT(m->getBondBetweenAtoms(0, 1)->getBondType() == Bond::DATIVE);
TEST_ASSERT(m->getBondBetweenAtoms(0, 1)->getBeginAtomIdx() == 1);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testAtomValues() {
BOOST_LOG(rdInfoLog) << "testing atom values" << std::endl;
{ // testing atom values
std::string smiles =
"CCC1=CC=CC=C1 |$_AV:value 2;&#59;value1;value "
"5&#59;6;;;;;$,c:4,6,t:2|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 8);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::molFileValue));
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>(
common_properties::molFileValue) == "value 2");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::molFileValue));
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::molFileValue) == ";value1");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp(common_properties::molFileValue));
TEST_ASSERT(m->getAtomWithIdx(2)->getProp<std::string>(
common_properties::molFileValue) == "value 5;6");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testAtomProps() {
BOOST_LOG(rdInfoLog) << "testing atom properties" << std::endl;
{ // testing atom properties
std::string smiles =
"C1CN1 "
"|atomProp:0.prop2.val2:0.prop1.val1:1.prop2.v2&#38;4:1.prop1.v1;2;3|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("prop1"));
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>("prop1") == "val1");
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("prop2"));
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>("prop2") == "val2");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("prop2"));
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>("prop2") == "v2&4");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("prop1"));
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>("prop1") ==
"v1;2;3");
delete m;
}
{ // testing atom properties + values
std::string smiles =
"C1CN1 "
"|atomProp:0.prop2.val2:1.prop1.v1;2;3,$_AV:value 2;&#59;value1;$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("prop2"));
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>("prop2") == "val2");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("prop1"));
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>("prop1") ==
"v1;2;3");
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::molFileValue));
TEST_ASSERT(m->getAtomWithIdx(0)->getProp<std::string>(
common_properties::molFileValue) == "value 2");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::molFileValue));
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::molFileValue) == ";value1");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub1968() {
BOOST_LOG(rdInfoLog)
<< "testing Github1968: CXSMILES should be parsed before H removal"
<< std::endl;
{ // the original report
std::string smiles = "[H]C* |$;;X$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::atomLabel));
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::atomLabel) == "X");
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::atomLabel));
delete m;
}
{
std::string smiles = "C([H])* |$;Y;X$|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 2);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::atomLabel));
TEST_ASSERT(m->getAtomWithIdx(1)->getProp<std::string>(
common_properties::atomLabel) == "X");
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::atomLabel));
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testEnhancedStereo() {
BOOST_LOG(rdInfoLog) << "Testing CXSMILES Enhanced Stereo" << std::endl;
std::vector<unsigned int> atom_ref1({4, 5});
{
std::string smiles = "C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:4,5|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 8);
auto &stereo_groups = m->getStereoGroups();
TEST_ASSERT(stereo_groups.size() == 2);
auto stg = stereo_groups.begin();
TEST_ASSERT(stg->getGroupType() == StereoGroupType::STEREO_ABSOLUTE);
{
auto &atoms = stg->getAtoms();
TEST_ASSERT(atoms.size() == 1);
TEST_ASSERT(atoms[0]->getIdx() == 1);
}
++stg;
TEST_ASSERT(stg->getGroupType() == StereoGroupType::STEREO_OR);
{
auto &atoms = stg->getAtoms();
TEST_ASSERT(atoms.size() == 2);
TEST_ASSERT(atoms[0]->getIdx() == 4);
TEST_ASSERT(atoms[1]->getIdx() == 5);
}
delete m;
}
{
std::string smiles = "C[C@H](F)[C@H](C)[C@@H](C)Br |&1:4,5,a:1|";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 8);
auto &stereo_groups = m->getStereoGroups();
TEST_ASSERT(stereo_groups.size() == 2);
auto stg = stereo_groups.begin();
TEST_ASSERT(stg->getGroupType() == StereoGroupType::STEREO_AND);
{
auto &atoms = stg->getAtoms();
TEST_ASSERT(atoms.size() == 2);
TEST_ASSERT(atoms[0]->getIdx() == 4);
TEST_ASSERT(atoms[1]->getIdx() == 5);
}
++stg;
TEST_ASSERT(stg->getGroupType() == StereoGroupType::STEREO_ABSOLUTE);
{
auto &atoms = stg->getAtoms();
TEST_ASSERT(atoms.size() == 1);
TEST_ASSERT(atoms[0]->getIdx() == 1);
}
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testHTMLCharCodes() {
BOOST_LOG(rdInfoLog) << "Testing CXSMILES with HTML char codes" << std::endl;
{
std::string smiles = R"(CCCC* |$;;;;_AP1$,Sg:n:2:2&#44;6-7:ht|)";
SmilesParserParams params;
params.allowCXSMILES = true;
ROMol *m = SmilesToMol(smiles, params);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 5);
delete m;
}
}
int main(int argc, char *argv[]) {
(void)argc;
(void)argv;
RDLog::InitLogs();
#if 1
testBase();
testCoords2D();
testAtomLabels();
testCXSmilesAndName();
testCoordinateBonds();
testRadicals();
testAtomValues();
#endif
testAtomProps();
testGithub1968();
testEnhancedStereo();
testHTMLCharCodes();
}
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