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rdkit/Code/GraphMol/test1.cpp
Ricardo Rodriguez 2469263f8d Fix some mem errors in 2024.09.1 (#7867)
2024-10-25 05:05:36 +02:00

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//
// Copyright (C) 2001-2018 Greg Landrum and Rational Discovery LLC
//
// @@ 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 <GraphMol/RDKitBase.h>
#include <GraphMol/MonomerInfo.h>
#include <GraphMol/RDKitQueries.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <sstream>
#include <iostream>
#include <boost/format.hpp>
#include <boost/range/iterator_range.hpp>
using namespace std;
using namespace RDKit;
// -------------------------------------------------------------------
void testBookmarks(ROMol m) {
int i;
// ------------------------
// simple bookmark stuff
Atom *a1 = m.getAtomWithIdx(1);
m.setAtomBookmark(a1, 666);
Atom *a2 = m.getAtomWithBookmark(666);
TEST_ASSERT(a2->getIdx() == a1->getIdx());
bool ok;
m.clearAtomBookmark(666);
boost::logging::disable_logs("rdApp.error");
try {
a2 = m.getAtomWithBookmark(666);
ok = 0;
} catch (...) {
ok = 1;
}
boost::logging::enable_logs("rdApp.error");
CHECK_INVARIANT(ok, "atom bookmark not properly cleared");
// ------------------------
// repeat a bookmark
a1 = m.getAtomWithIdx(1);
CHECK_INVARIANT(a1->getIdx() == 1, "");
m.setAtomBookmark(a1, 666);
m.setAtomBookmark(m.getAtomWithIdx(0), 666);
a2 = m.getAtomWithBookmark(666);
CHECK_INVARIANT(a2->getIdx() == 1, "");
CHECK_INVARIANT(a2->getIdx() == a1->getIdx(), "");
m.clearAtomBookmark(666, a2);
a2 = m.getAtomWithBookmark(666);
i = a2->getIdx();
CHECK_INVARIANT(i == 0, "");
m.clearAtomBookmark(666, a2);
boost::logging::disable_logs("rdApp.error");
try {
a2 = m.getAtomWithBookmark(666);
ok = 0;
} catch (...) {
ok = 1;
}
boost::logging::enable_logs("rdApp.error");
CHECK_INVARIANT(ok, "atom bookmark not properly cleared");
// make sure clearAtomBookmark doesn't barf if there's no
// such bookmark:
m.clearAtomBookmark(777);
//----------------------------
// now do bond bookmarks
Bond *b1 = m.getBondWithIdx(0);
m.setBondBookmark(b1, 23);
Bond *b2 = m.getBondWithBookmark(23);
CHECK_INVARIANT(b2->getIdx() == b1->getIdx(), "");
m.clearBondBookmark(23);
boost::logging::disable_logs("rdApp.error");
try {
b2 = m.getBondWithBookmark(23);
ok = 0;
} catch (...) {
ok = 1;
}
boost::logging::enable_logs("rdApp.error");
CHECK_INVARIANT(ok, "bond bookmark not properly cleared");
m.setBondBookmark(b1, 23);
m.setBondBookmark(m.getBondWithIdx(1), 23);
b2 = m.getBondWithBookmark(23);
CHECK_INVARIANT(b2->getIdx() == b1->getIdx(), "");
m.clearBondBookmark(23, b2);
b2 = m.getBondWithBookmark(23);
CHECK_INVARIANT(b2->getIdx() == 1, "");
m.clearBondBookmark(23, b2);
boost::logging::disable_logs("rdApp.error");
try {
b2 = m.getBondWithBookmark(23);
ok = 0;
} catch (...) {
ok = 1;
}
boost::logging::enable_logs("rdApp.error");
CHECK_INVARIANT(ok, "bond bookmark not properly cleared");
// make sure clearAtomBookmark doesn't barf if there's no
// such bookmark:
m.clearBondBookmark(777);
}
void testMolProps() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Mol Property Caches" << std::endl;
RWMol m2;
STR_VECT propNames;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addBond(0, 1, Bond::TRIPLE);
CHECK_INVARIANT(!m2.hasProp("prop1"), "");
CHECK_INVARIANT(!m2.hasProp("prop2"), "");
m2.setProp("prop1", 2);
int tmpI;
std::string tmpS;
CHECK_INVARIANT(m2.hasProp("prop1"), "");
m2.getProp("prop1", tmpI);
CHECK_INVARIANT(tmpI == 2, "");
m2.getProp("prop1", tmpS);
CHECK_INVARIANT(tmpS == "2", "");
m2.setProp("prop1", std::string("2"));
CHECK_INVARIANT(m2.hasProp("prop1"), "");
m2.getProp("prop1", tmpS);
CHECK_INVARIANT(tmpS == "2", "");
std::string tmpString("2");
m2.setProp("prop1", tmpString.c_str());
CHECK_INVARIANT(m2.hasProp("prop1"), "");
m2.getProp("prop1", tmpS);
CHECK_INVARIANT(tmpS == "2", "");
tmpS = "name";
m2.setProp(common_properties::_Name, tmpS);
propNames = m2.getPropList(false, false);
TEST_ASSERT(propNames.size() == 1);
propNames = m2.getPropList(true, false);
TEST_ASSERT(propNames.size() == 2);
// check for computed properties
m2.setProp("cprop1", 1, true);
m2.setProp("cprop2", 2, true);
STR_VECT cplst;
m2.getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 2, "");
CHECK_INVARIANT(cplst[0] == "cprop1", "");
CHECK_INVARIANT(cplst[1] == "cprop2", "");
propNames = m2.getPropList(false, false);
TEST_ASSERT(propNames.size() == 1);
propNames = m2.getPropList(true, false);
TEST_ASSERT(propNames.size() == 2);
propNames = m2.getPropList(false, true);
TEST_ASSERT(propNames.size() == 3);
propNames = m2.getPropList(true, true);
TEST_ASSERT(propNames.size() == 5);
propNames = m2.getPropList();
TEST_ASSERT(propNames.size() == 5);
m2.clearProp("cprop1");
CHECK_INVARIANT(!m2.hasProp("cprop1"), "");
m2.getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
m2.clearComputedProps();
CHECK_INVARIANT(!m2.hasProp("cprop2"), "");
m2.getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 0, "");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testClearMol() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing RWMol.clear()"
<< std::endl;
RWMol m2;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addBond(0, 1, Bond::TRIPLE);
TEST_ASSERT(!m2.hasProp("prop1"));
m2.setProp("prop1", 2);
int tmpI;
TEST_ASSERT(m2.hasProp("prop1"));
m2.getProp("prop1", tmpI);
TEST_ASSERT(tmpI == 2);
TEST_ASSERT(m2.hasProp(RDKit::detail::computedPropName));
m2.clear();
TEST_ASSERT(!m2.hasProp("prop1"));
TEST_ASSERT(m2.getNumAtoms() == 0);
TEST_ASSERT(m2.getNumBonds() == 0);
TEST_ASSERT(m2.getAtomBookmarks()->empty());
TEST_ASSERT(m2.getBondBookmarks()->empty());
TEST_ASSERT(
m2.hasProp(RDKit::detail::computedPropName)); // <- github issue 176
TEST_ASSERT(m2.getPropList().size() == 1);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAtomProps() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Atom Property Caches" << std::endl;
RWMol m2;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addBond(0, 1, Bond::TRIPLE);
Atom *a1 = m2.getAtomWithIdx(0);
Atom *a2 = m2.getAtomWithIdx(0);
Atom *a3 = &(*a1);
CHECK_INVARIANT(!a1->hasProp("prop1"), "");
CHECK_INVARIANT(!a1->hasProp("prop2"), "");
CHECK_INVARIANT(!a2->hasProp("prop1"), "");
CHECK_INVARIANT(!a2->hasProp("prop2"), "");
CHECK_INVARIANT(!a3->hasProp("prop1"), "");
CHECK_INVARIANT(!a3->hasProp("prop2"), "");
a1->setProp("prop1", 3);
a1->setProp("prop2", 4);
CHECK_INVARIANT(a1->hasProp("prop1"), "");
CHECK_INVARIANT(a1->hasProp("prop2"), "");
CHECK_INVARIANT(a2->hasProp("prop1"), "");
CHECK_INVARIANT(a2->hasProp("prop2"), "");
CHECK_INVARIANT(a3->hasProp("prop1"), "");
CHECK_INVARIANT(a3->hasProp("prop2"), "");
CHECK_INVARIANT(!a1->hasProp("bogus"), "");
CHECK_INVARIANT(!a2->hasProp("bogus"), "");
CHECK_INVARIANT(!a3->hasProp("bogus"), "");
bool ok = false;
a1->setProp<double>("dprop", 4);
TEST_ASSERT(a1->hasProp("dprop"));
try {
a1->getProp<int>("dprop");
} catch (const std::bad_any_cast &) {
ok = true;
}
TEST_ASSERT(ok);
a1->setProp<int>("iprop", 4);
TEST_ASSERT(a1->hasProp("iprop"));
ok = false;
try {
a1->getProp<double>("iprop");
} catch (const std::bad_any_cast &) {
ok = true;
}
TEST_ASSERT(ok);
int tmp;
a1->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
a1->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
a2->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
a2->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
a3->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
a3->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
// check for computed properties
a1->setProp("cprop1", 1, true);
a1->setProp("cprop2", 2, true);
STR_VECT cplst;
a1->getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 2, "");
CHECK_INVARIANT(cplst[0] == "cprop1", "");
CHECK_INVARIANT(cplst[1] == "cprop2", "");
a1->clearProp("cprop1");
CHECK_INVARIANT(!a1->hasProp("cprop1"), "");
a1->getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
a1->clearComputedProps();
CHECK_INVARIANT(!a1->hasProp("cprop2"), "");
a1->getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 0, "");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testBondProps() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Bond Property Caches" << std::endl;
RWMol m2;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addBond(0, 1, Bond::TRIPLE);
Bond *b1 = m2.getBondWithIdx(0);
Bond *b2 = m2.getBondWithIdx(0);
CHECK_INVARIANT(!b1->hasProp("prop1"), "");
CHECK_INVARIANT(!b1->hasProp("prop2"), "");
CHECK_INVARIANT(!b2->hasProp("prop1"), "");
CHECK_INVARIANT(!b2->hasProp("prop2"), "");
b1->setProp("prop1", 3);
b1->setProp("prop2", 4);
CHECK_INVARIANT(b1->hasProp("prop1"), "");
CHECK_INVARIANT(b1->hasProp("prop2"), "");
CHECK_INVARIANT(b2->hasProp("prop1"), "");
CHECK_INVARIANT(b2->hasProp("prop2"), "");
CHECK_INVARIANT(!b1->hasProp("bogus"), "");
CHECK_INVARIANT(!b2->hasProp("bogus"), "");
int tmp;
b1->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
b1->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
b2->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
b2->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
// check for computed properties
b1->setProp("cprop1", 1, true);
b1->setProp("cprop2", 2, true);
STR_VECT cplst;
b1->getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 2, "");
CHECK_INVARIANT(cplst[0] == "cprop1", "");
CHECK_INVARIANT(cplst[1] == "cprop2", "");
b1->clearProp("cprop1");
CHECK_INVARIANT(!b1->hasProp("cprop1"), "");
b1->getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
b1->clearComputedProps();
CHECK_INVARIANT(!b1->hasProp("cprop2"), "");
b1->getProp(RDKit::detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 0, "");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
// this is here because there was at one time a problem with crashes when doing
// this stuff
void testPropLeak() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Atom and Bond Property Caches"
<< std::endl;
RWMol m2;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addBond(0, 1, Bond::TRIPLE);
Atom *a1 = m2.getAtomWithIdx(0);
Atom *a2 = m2.getAtomWithIdx(0);
CHECK_INVARIANT(!a1->hasProp("prop1"), "");
CHECK_INVARIANT(!a1->hasProp("prop2"), "");
CHECK_INVARIANT(!a2->hasProp("prop1"), "");
CHECK_INVARIANT(!a2->hasProp("prop2"), "");
a1->setProp("prop1", 3);
a1->setProp("prop2", 4);
CHECK_INVARIANT(a1->hasProp("prop1"), "");
CHECK_INVARIANT(a1->hasProp("prop2"), "");
CHECK_INVARIANT(a2->hasProp("prop1"), "");
CHECK_INVARIANT(a2->hasProp("prop2"), "");
CHECK_INVARIANT(!a1->hasProp("bogus"), "");
CHECK_INVARIANT(!a2->hasProp("bogus"), "");
int tmp;
a1->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
a1->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
a2->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
a2->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
Bond *b1 = m2.getBondWithIdx(0);
Bond *b2 = m2.getBondWithIdx(0);
CHECK_INVARIANT(!b1->hasProp("prop1"), "");
CHECK_INVARIANT(!b1->hasProp("prop2"), "");
CHECK_INVARIANT(!b2->hasProp("prop1"), "");
CHECK_INVARIANT(!b2->hasProp("prop2"), "");
b1->setProp("prop1", 3);
b1->setProp("prop2", 4);
CHECK_INVARIANT(b1->hasProp("prop1"), "");
CHECK_INVARIANT(b1->hasProp("prop2"), "");
CHECK_INVARIANT(b2->hasProp("prop1"), "");
CHECK_INVARIANT(b2->hasProp("prop2"), "");
CHECK_INVARIANT(!b1->hasProp("bogus"), "");
CHECK_INVARIANT(!b2->hasProp("bogus"), "");
b1->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
b1->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
b2->getProp("prop1", tmp);
CHECK_INVARIANT(tmp == 3, "");
b2->getProp("prop2", tmp);
CHECK_INVARIANT(tmp == 4, "");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testMisc() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Misc Properties"
<< std::endl;
RWMol m2;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addBond(0, 1, Bond::SINGLE);
m2.addBond(1, 2, Bond::SINGLE);
m2.addBond(0, 2, Bond::SINGLE);
m2.addBond(2, 3, Bond::SINGLE);
MolOps::sanitizeMol(m2);
Bond *bnd;
bnd = m2.getBondBetweenAtoms(0, 1);
CHECK_INVARIANT(bnd, "");
bnd = m2.getBondBetweenAtoms(1, 0);
CHECK_INVARIANT(bnd, "");
bnd = m2.getBondBetweenAtoms(3, 0);
CHECK_INVARIANT(!bnd, "");
bnd = m2.getBondBetweenAtoms(0, 3);
CHECK_INVARIANT(!bnd, "");
const Bond *cbnd;
cbnd = m2.getBondBetweenAtoms(0, 1);
CHECK_INVARIANT(cbnd, "");
cbnd = m2.getBondBetweenAtoms(1, 0);
CHECK_INVARIANT(cbnd, "");
cbnd = m2.getBondBetweenAtoms(0, 3);
CHECK_INVARIANT(!cbnd, "");
cbnd = m2.getBondBetweenAtoms(3, 0);
CHECK_INVARIANT(!cbnd, "");
CHECK_INVARIANT(m2.getAtomWithIdx(0)->getTotalNumHs() == 2, "");
// we'll check atom deletion and handling of bookmarks on deletion
// simultaneously:
// (The bookmark thing was the root of Issue 96)
m2.setAtomBookmark(m2.getAtomWithIdx(0), 2342);
m2.setBondBookmark(m2.getBondWithIdx(0), 2343);
m2.removeAtom(static_cast<unsigned int>(0));
CHECK_INVARIANT(!m2.hasAtomBookmark(2342), "");
CHECK_INVARIANT(!m2.hasBondBookmark(2343), "");
CHECK_INVARIANT(m2.getNumAtoms() == 3, "");
CHECK_INVARIANT(m2.getNumBonds() == 2, "");
MolOps::sanitizeMol(m2);
CHECK_INVARIANT(m2.getAtomWithIdx(0)->getTotalNumHs() == 3, "");
m2.addAtom(new Atom(1), true, true);
m2.addBond(2, 3, Bond::SINGLE);
MolOps::sanitizeMol(m2);
CHECK_INVARIANT(m2.getAtomWithIdx(0)->getTotalNumHs() == 3, "");
CHECK_INVARIANT(m2.getAtomWithIdx(0)->getTotalNumHs(true) == 3, "");
CHECK_INVARIANT(m2.getAtomWithIdx(2)->getTotalNumHs() == 2, "");
CHECK_INVARIANT(m2.getAtomWithIdx(2)->getTotalNumHs(true) == 3, "");
Atom *other = m2.getBondWithIdx(1)->getOtherAtom(m2.getAtomWithIdx(1));
CHECK_INVARIANT(other, "");
const Atom *at = m2.getAtomWithIdx(1);
ROMol::OEDGE_ITER begin, end;
boost::tie(begin, end) = m2.getAtomBonds(at);
while (begin != end) {
const Atom *at2 = m2[*begin]->getOtherAtom(at);
TEST_ASSERT(at2);
begin++;
}
ROMol::VERTEX_ITER atBegin, atEnd;
boost::tie(atBegin, atEnd) = m2.getVertices();
TEST_ASSERT(atBegin != atEnd);
while (atBegin != atEnd) {
const Atom *at2 = m2[*atBegin];
TEST_ASSERT(at2->getIdx() == *atBegin);
atBegin++;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testDegree() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing degree operations"
<< std::endl;
RWMol *m;
m = new RWMol();
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(2, 3, Bond::SINGLE);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getDegree() == 2);
TEST_ASSERT(m->getAtomWithIdx(0)->getTotalNumHs() == 2);
TEST_ASSERT(m->getAtomWithIdx(0)->getTotalDegree() == 4);
TEST_ASSERT(m->getAtomWithIdx(2)->getDegree() == 3);
TEST_ASSERT(m->getAtomWithIdx(2)->getTotalNumHs() == 1);
TEST_ASSERT(m->getAtomWithIdx(2)->getTotalDegree() == 4);
delete m;
m = new RWMol();
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(1), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(1, 2, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(2, 3, Bond::SINGLE);
m->addBond(0, 4, Bond::SINGLE);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getDegree() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getTotalNumHs() == 1);
TEST_ASSERT(m->getAtomWithIdx(0)->getTotalNumHs(true) == 2);
TEST_ASSERT(m->getAtomWithIdx(0)->getTotalDegree() == 4);
TEST_ASSERT(m->getAtomWithIdx(2)->getDegree() == 3);
TEST_ASSERT(m->getAtomWithIdx(2)->getTotalNumHs() == 1);
TEST_ASSERT(m->getAtomWithIdx(2)->getTotalDegree() == 4);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue1993296() {
auto *m = new RWMol();
bool ok;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 1993296" << std::endl;
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
ok = false;
try {
m->addBond(0, 1, Bond::SINGLE);
} catch (...) {
ok = true;
}
TEST_ASSERT(ok);
ok = false;
try {
m->addBond(1, 0, Bond::SINGLE);
} catch (...) {
ok = true;
}
TEST_ASSERT(ok);
// not technically part of 1993296, but related: we also throw
// on adding self bonds
ok = false;
try {
m->addBond(1, 1, Bond::SINGLE);
} catch (...) {
ok = true;
}
auto *newB = new Bond();
newB->setBeginAtomIdx(0);
newB->setEndAtomIdx(1);
newB->setBondType(Bond::SINGLE);
ok = false;
try {
m->addBond(newB);
} catch (...) {
ok = true;
}
TEST_ASSERT(ok);
// not technically part of 1993296, but related: we also throw
// on adding self bonds
newB->setBeginAtomIdx(0);
newB->setEndAtomIdx(0);
ok = false;
try {
m->addBond(newB);
} catch (...) {
ok = true;
}
TEST_ASSERT(ok);
delete newB;
delete m;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue2381580() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 2381580" << std::endl;
{
auto *m = new RWMol();
m->addAtom(new Atom(5), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(0, 3, Bond::SINGLE);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge() == 0);
TEST_ASSERT(m->getAtomWithIdx(0)->getExplicitValence() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumImplicitHs() == 0);
delete m;
}
{
auto *m = new RWMol();
m->addAtom(new Atom(5), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(0, 3, Bond::SINGLE);
m->addBond(0, 4, Bond::SINGLE);
m->getAtomWithIdx(0)->setFormalCharge(-1);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge() == -1);
TEST_ASSERT(m->getAtomWithIdx(0)->getExplicitValence() == 4);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumImplicitHs() == 0);
delete m;
}
{
auto *m = new RWMol();
m->addAtom(new Atom(5), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(0, 3, Bond::SINGLE);
m->addBond(0, 4, Bond::SINGLE);
bool ok = false;
try {
MolOps::sanitizeMol(*m);
} catch (MolSanitizeException &) {
ok = true;
}
TEST_ASSERT(ok);
delete m;
}
{
auto *m = new RWMol();
m->addAtom(new Atom(5), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(0, 3, Bond::SINGLE);
m->addBond(0, 4, Bond::SINGLE);
m->getAtomWithIdx(0)->setFormalCharge(+1);
bool ok = false;
try {
MolOps::sanitizeMol(*m);
} catch (MolSanitizeException &) {
ok = true;
}
TEST_ASSERT(ok);
delete m;
}
{
auto *m = new RWMol();
m->addAtom(new Atom(5), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->getAtomWithIdx(0)->setFormalCharge(+1);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge() == 1);
TEST_ASSERT(m->getAtomWithIdx(0)->getExplicitValence() == 2);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumImplicitHs() == 0);
delete m;
}
{
auto *m = new RWMol();
m->addAtom(new Atom(5), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addBond(0, 2, Bond::SINGLE);
m->addBond(0, 3, Bond::SINGLE);
m->getAtomWithIdx(0)->setFormalCharge(-1);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge() == -1);
TEST_ASSERT(m->getAtomWithIdx(0)->getExplicitValence() == 3);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumImplicitHs() == 1);
TEST_ASSERT(m->getAtomWithIdx(0)->getExplicitValence() +
m->getAtomWithIdx(0)->getImplicitValence() ==
rdcast<int>(m->getAtomWithIdx(0)->getTotalValence()));
TEST_ASSERT(m->getAtomWithIdx(1)->getExplicitValence() +
m->getAtomWithIdx(1)->getImplicitValence() ==
rdcast<int>(m->getAtomWithIdx(1)->getTotalValence()));
TEST_ASSERT(m->getAtomWithIdx(2)->getExplicitValence() +
m->getAtomWithIdx(2)->getImplicitValence() ==
rdcast<int>(m->getAtomWithIdx(2)->getTotalValence()));
TEST_ASSERT(m->getAtomWithIdx(3)->getExplicitValence() +
m->getAtomWithIdx(3)->getImplicitValence() ==
rdcast<int>(m->getAtomWithIdx(3)->getTotalValence()));
delete m;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue2840217() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 2840217" << std::endl;
{
auto *m = new RWMol();
for (unsigned int i = 0; i < 200; ++i) {
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
for (unsigned int j = 0; j < 5; ++j) {
m->addBond(i * 6 + j, i * 6 + j + 1, Bond::AROMATIC);
}
m->addBond(i * 6, i * 6 + 5, Bond::AROMATIC);
}
TEST_ASSERT(m->getNumBonds() == 1200);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getNumAtoms() == 1200);
delete m;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test1() {
{
RWMol m;
auto *newAtom = new Atom(8);
m.addAtom(newAtom, true, true);
CHECK_INVARIANT(m.getAtomWithIdx(0)->getIdx() == 0, "");
newAtom = new Atom(6);
m.addAtom(newAtom, true, true);
CHECK_INVARIANT(m.getAtomWithIdx(0)->getIdx() == 0, "");
CHECK_INVARIANT(m.getAtomWithIdx(1)->getIdx() == 1, "");
newAtom = new Atom(7);
m.addAtom(newAtom, true, true);
CHECK_INVARIANT(m.getAtomWithIdx(0)->getIdx() == 0, "");
CHECK_INVARIANT(m.getAtomWithIdx(1)->getIdx() == 1, "");
CHECK_INVARIANT(m.getAtomWithIdx(2)->getIdx() == 2, "");
CHECK_INVARIANT(
m.getAtomWithIdx(1)->getOwningMol().getAtomWithIdx(1)->getIdx() == 1,
"");
m.addBond(0, 1, Bond::SINGLE);
m.addBond(1, 2, Bond::DOUBLE);
CHECK_INVARIANT(m.getBondWithIdx(0)->getIdx() == 0, "");
CHECK_INVARIANT(m.getBondWithIdx(1)->getIdx() == 1, "");
CHECK_INVARIANT(m.getBondWithIdx(0)->getBondType() == Bond::SINGLE, "");
CHECK_INVARIANT(m.getBondWithIdx(1)->getBondType() == Bond::DOUBLE, "");
CHECK_INVARIANT(m.getBondWithIdx(0)->getBeginAtom()->getIdx() == 0, "");
CHECK_INVARIANT(m.getBondWithIdx(0)->getEndAtom()->getIdx() == 1, "");
CHECK_INVARIANT(m.getBondWithIdx(1)->getBeginAtom()->getIdx() == 1, "");
CHECK_INVARIANT(m.getBondWithIdx(1)->getEndAtom()->getIdx() == 2, "");
testBookmarks(m);
// Using operator<< on a non-sanitized molecule is a test of Issue156:
ROMol::ADJ_ITER ai1, ai2;
boost::tie(ai1, ai2) = m.getAtomNeighbors(m.getAtomWithIdx(1));
m.updatePropertyCache();
boost::logging::disable_logs("rdApp.info");
while (ai1 != ai2) {
BOOST_LOG(rdInfoLog) << *m.getAtomWithIdx(*ai1) << endl;
ai1++;
}
m.addAtom(new Atom(6), true, true);
Bond *bsp = m.createPartialBond(2);
m.setBondBookmark(bsp, 47);
m.finishPartialBond(3, 47, Bond::SINGLE);
m.clearBondBookmark(47);
BOOST_LOG(rdInfoLog) << "partial bond added:" << endl;
unsigned int i;
m.updatePropertyCache();
for (i = 0; i < m.getNumAtoms(); i++) {
Atom *a = m.getAtomWithIdx(i);
BOOST_LOG(rdInfoLog) << "\t" << *a << endl;
}
int newAtNum = m.addAtom(new Atom(6), true, true);
m.addBond(0, newAtNum, Bond::SINGLE);
BOOST_LOG(rdInfoLog) << "Again:" << endl;
m.updatePropertyCache();
for (i = 0; i < m.getNumAtoms(); i++) {
Atom *a = m.getAtomWithIdx(i);
BOOST_LOG(rdInfoLog) << "\t" << *a << endl;
}
RWMol m2;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
// QueryAtom *qA = new QueryAtom;
// qA->setAtomicNum(7);
// m2.addAtom(qA);
m2.addAtom(new QueryAtom(7), true, true);
m2.addBond(0, 1, Bond::TRIPLE);
m2.addBond(1, 2, Bond::SINGLE);
m.insertMol(m2);
m.updatePropertyCache();
BOOST_LOG(rdInfoLog) << "post-insert:" << endl;
for (i = 0; i < m.getNumAtoms(); i++) {
Atom *a = m.getAtomWithIdx(i);
BOOST_LOG(rdInfoLog) << "\t" << *a << endl;
}
BOOST_LOG(rdInfoLog) << " ------------------- " << endl;
auto *newA = new Atom(12);
int newIdx = m.addAtom(newA, true, true);
m.addBond(newIdx - 1, newIdx, Bond::AROMATIC);
// m.debugMol(cout);
BOOST_LOG(rdInfoLog) << " trying a replace " << endl;
auto *repA = new Atom(22);
m.replaceAtom(newIdx, repA);
delete repA;
TEST_ASSERT(m.getAtomWithIdx(newIdx)->getAtomicNum() == 22);
auto *nbnd = new Bond(Bond::DOUBLE);
TEST_ASSERT(m.getBondWithIdx(m.getNumBonds() - 1)->getBondType() ==
Bond::AROMATIC);
m.replaceBond(m.getNumBonds() - 1, nbnd);
m.debugMol(std::cerr);
TEST_ASSERT(m.getBondWithIdx(m.getNumBonds() - 1)->getBondType() ==
nbnd->getBondType());
delete nbnd;
delete bsp;
}
{
RWMol m;
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
m.addBond(0, 1, Bond::SINGLE);
auto *conf = new Conformer(m.getNumAtoms());
m.addConformer(conf);
m.getConformer().setAtomPos(0, RDGeom::Point3D(1.0, 0.0, 0.0));
m.getConformer().setAtomPos(1, RDGeom::Point3D(0.0, 1.0, 0.0));
RWMol m2;
// insert molecule without a conf:
m2.addAtom(new Atom(6), true, true);
m.insertMol(m2);
TEST_ASSERT(m.getConformer().getNumAtoms() == m.getNumAtoms());
TEST_ASSERT(feq(m.getConformer().getAtomPos(2).x, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(2).y, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(2).z, 0.0));
// insert molecule with a conf:
conf = new Conformer(m2.getNumAtoms());
m2.addConformer(conf);
m2.getConformer().setAtomPos(0, RDGeom::Point3D(1.0, 1.0, 0.0));
m.insertMol(m2);
TEST_ASSERT(m.getConformer().getNumAtoms() == m.getNumAtoms());
TEST_ASSERT(feq(m.getConformer().getAtomPos(2).x, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(2).y, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(2).z, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(3).x, 1.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(3).y, 1.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(3).z, 0.0));
}
{
// start with a molecule with no conf
RWMol m;
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
m.addBond(0, 1, Bond::SINGLE);
TEST_ASSERT(m.getNumConformers() == 0);
RWMol m2;
// insert molecule without a conf:
m2.addAtom(new Atom(6), true, true);
m.insertMol(m2);
TEST_ASSERT(m.getNumConformers() == 0);
// insert molecule with a conf:
auto *conf = new Conformer(m2.getNumAtoms());
m2.addConformer(conf);
m2.getConformer().setAtomPos(0, RDGeom::Point3D(1.0, 1.0, 0.0));
m.insertMol(m2);
TEST_ASSERT(m.getNumConformers() == 1);
TEST_ASSERT(m.getConformer().getNumAtoms() == m.getNumAtoms());
TEST_ASSERT(feq(m.getConformer().getAtomPos(0).x, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(0).y, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(0).z, 0.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(3).x, 1.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(3).y, 1.0));
TEST_ASSERT(feq(m.getConformer().getAtomPos(3).z, 0.0));
}
}
void testPeriodicTable() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing properties from periodic table" << std::endl;
TEST_ASSERT(PeriodicTable::getTable()->getDefaultValence(6) == 4);
TEST_ASSERT(PeriodicTable::getTable()->getNouterElecs(6) == 4);
TEST_ASSERT(PeriodicTable::getTable()->getMostCommonIsotope(6) == 12);
TEST_ASSERT(PeriodicTable::getTable()->getMostCommonIsotopeMass(6) == 12.0);
TEST_ASSERT(PeriodicTable::getTable()->getMostCommonIsotopeMass(6) == 12.0);
TEST_ASSERT(feq(PeriodicTable::getTable()->getMostCommonIsotopeMass(4),
9.0122, 1e-4));
TEST_ASSERT(feq(PeriodicTable::getTable()->getRb0(6), 0.77, 1e-2));
TEST_ASSERT(PeriodicTable::getTable()->getDefaultValence(26) == -1);
TEST_ASSERT(PeriodicTable::getTable()->getDefaultValence(57) == -1);
// this was sf.net issue 269
int anum;
anum = PeriodicTable::getTable()->getAtomicNumber("C");
TEST_ASSERT(anum == 6);
try {
anum = PeriodicTable::getTable()->getAtomicNumber("Xx");
} catch (...) {
anum = -1;
}
TEST_ASSERT(anum == -1);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAddAtomWithConf() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing issue 264: adding atoms to molecules that "
"already have conformers"
<< std::endl;
{
RWMol m;
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
auto *conf = new Conformer(m.getNumAtoms());
m.addConformer(conf);
m.addAtom(new Atom(6), true, true);
TEST_ASSERT(m.getConformer().getNumAtoms() == m.getNumAtoms());
}
{
RWMol m;
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
auto *conf = new Conformer(m.getNumAtoms());
m.addConformer(conf);
m.addAtom();
TEST_ASSERT(m.getConformer().getNumAtoms() == m.getNumAtoms());
}
{ // make sure things are ok even if there is no conformer
RWMol m;
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
TEST_ASSERT(m.getNumConformers() == 0);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue267() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing issue 267: default valence of *"
<< std::endl;
{
RWMol m;
m.addAtom(new Atom(0), true, true);
m.updatePropertyCache();
TEST_ASSERT(m.getAtomWithIdx(0)->getImplicitValence() == 0);
}
{
RWMol m;
m.addAtom(new Atom(0), true, true);
for (unsigned int i = 0; i < 8; ++i) {
m.addAtom(new Atom(1), true, true);
m.addBond(0, i + 1, Bond::SINGLE);
}
m.updatePropertyCache();
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue284() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing issue 284: removeBond not updating indices"
<< std::endl;
{
RWMol m;
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
m.addAtom(new Atom(6), true, true);
m.addBond(0, 1, Bond::SINGLE);
m.addBond(1, 2, Bond::SINGLE);
m.updatePropertyCache();
TEST_ASSERT(m.getBondBetweenAtoms(0, 1)->getIdx() == 0);
TEST_ASSERT(m.getBondBetweenAtoms(1, 2)->getIdx() == 1);
m.removeBond(0, 1);
TEST_ASSERT(!m.getBondBetweenAtoms(0, 1));
TEST_ASSERT(m.getBondBetweenAtoms(1, 2)->getIdx() == 0);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAtomResidues() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing residue information handling on atoms"
<< std::endl;
{
auto *m = new RWMol();
m->addAtom(new Atom(6), true, true);
m->addAtom(new Atom(6), true, true);
m->addBond(0, 1, Bond::SINGLE);
m->addAtom(new Atom(6), true, true);
m->addBond(1, 2, Bond::SINGLE);
m->addAtom(new Atom(6), true, true);
m->addBond(2, 3, Bond::SINGLE);
TEST_ASSERT(!(m->getAtomWithIdx(0)->getMonomerInfo()));
TEST_ASSERT(!(m->getAtomWithIdx(1)->getMonomerInfo()));
TEST_ASSERT(!(m->getAtomWithIdx(2)->getMonomerInfo()));
TEST_ASSERT(!(m->getAtomWithIdx(3)->getMonomerInfo()));
m->getAtomWithIdx(0)->setMonomerInfo(
new AtomMonomerInfo(AtomMonomerInfo::OTHER, "m1"));
TEST_ASSERT((m->getAtomWithIdx(0)->getMonomerInfo()));
TEST_ASSERT(m->getAtomWithIdx(0)->getMonomerInfo()->getName() == "m1");
m->getAtomWithIdx(1)->setMonomerInfo(new AtomPDBResidueInfo("Ca", 3));
TEST_ASSERT((m->getAtomWithIdx(1)->getMonomerInfo()));
TEST_ASSERT(m->getAtomWithIdx(1)->getMonomerInfo()->getName() == "Ca");
TEST_ASSERT(static_cast<const AtomPDBResidueInfo *>(
m->getAtomWithIdx(1)->getMonomerInfo())
->getSerialNumber() == 3);
auto *m2 = new RWMol(*m);
delete m;
TEST_ASSERT((m2->getAtomWithIdx(0)->getMonomerInfo()));
TEST_ASSERT(m2->getAtomWithIdx(0)->getMonomerInfo()->getName() == "m1");
TEST_ASSERT((m2->getAtomWithIdx(1)->getMonomerInfo()));
TEST_ASSERT(m2->getAtomWithIdx(1)->getMonomerInfo()->getName() == "Ca");
TEST_ASSERT(static_cast<const AtomPDBResidueInfo *>(
m2->getAtomWithIdx(1)->getMonomerInfo())
->getSerialNumber() == 3);
TEST_ASSERT(!(m2->getAtomWithIdx(2)->getMonomerInfo()));
TEST_ASSERT(!(m2->getAtomWithIdx(3)->getMonomerInfo()));
delete m2;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testNeedsUpdatePropertyCache() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing function needsUpdatePropertyCache"
<< std::endl;
{
RWMol m;
m.addAtom(new Atom(0), true, true);
TEST_ASSERT(m.needsUpdatePropertyCache() == true);
m.updatePropertyCache();
TEST_ASSERT(m.getAtomWithIdx(0)->getImplicitValence() == 0);
TEST_ASSERT(m.needsUpdatePropertyCache() == false);
}
{
RWMol m;
m.addAtom(new Atom(6), true, true);
for (ROMol::AtomIterator atomIt = m.beginAtoms(); atomIt != m.endAtoms();
++atomIt) {
(*atomIt)->calcExplicitValence(false);
(*atomIt)->calcImplicitValence(false);
}
m.addAtom(new Atom(6), true, true);
m.addBond(0, 1, Bond::SINGLE);
TEST_ASSERT(m.needsUpdatePropertyCache() == true);
m.updatePropertyCache();
TEST_ASSERT(m.needsUpdatePropertyCache() == false);
}
{
RWMol m;
m.addAtom(new Atom(6), true, true);
m.getAtomWithIdx(0)->calcExplicitValence(false);
TEST_ASSERT(m.getAtomWithIdx(0)->needsUpdatePropertyCache());
m.getAtomWithIdx(0)->setNoImplicit(true);
TEST_ASSERT(!m.getAtomWithIdx(0)->needsUpdatePropertyCache());
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
namespace {
std::string qhelper(Atom::QUERYATOM_QUERY *q, unsigned int depth = 0) {
std::string res = "";
if (q) {
for (unsigned int i = 0; i < depth; ++i) {
res += " ";
}
res += q->getFullDescription() + "\n";
for (auto ci = q->beginChildren(); ci != q->endChildren(); ++ci) {
res += qhelper((*ci).get(), depth + 1);
}
}
return res;
}
} // namespace
const char *m_als_mol =
"\n"
" Marvin 08200814552D \n"
"\n"
" 9 8 0 0 0 0 999 V2000\n"
" -1.9152 1.6205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.0902 1.6205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.5068 2.2039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.3277 0.9061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.3277 2.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.1527 2.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.6830 2.8727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.1527 0.9061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.6771 0.2814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 2 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 1 4 1 0 0 0 0\n"
" 1 5 1 0 0 0 0\n"
" 5 6 2 0 0 0 0\n"
" 6 7 1 0 0 0 0\n"
" 4 8 2 0 0 0 0\n"
" 8 9 1 0 0 0 0\n"
"M ALS 4 2 F O Cl \n"
"M END\n";
void testAtomListLineRoundTrip() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Test AtomListLine RoundTrip" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/test_data/m_als_round_trip.mol";
const bool sanitize = false;
const bool removeHs = true;
const bool strictParsing = true;
unsigned int line = 0;
std::istringstream inStream(m_als_mol);
RWMol *m =
MolDataStreamToMol(inStream, line, sanitize, removeHs, strictParsing);
std::string desc = qhelper(m->getAtomWithIdx(3)->getQuery());
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 9);
std::string molblock = MolToMolBlock(*m);
TEST_ASSERT(molblock.find(" ALS ") != std::string::npos);
std::istringstream inStream2(molblock);
RWMol *m2 =
MolDataStreamToMol(inStream2, line, sanitize, removeHs, strictParsing);
TEST_ASSERT(m2);
TEST_ASSERT(desc == qhelper(m2->getAtomWithIdx(3)->getQuery()));
Atom *cl(new Atom(17));
Atom *o(new Atom(8));
TEST_ASSERT(dynamic_cast<QueryAtom *>(m->getAtomWithIdx(3))->Match(cl));
TEST_ASSERT(dynamic_cast<QueryAtom *>(m->getAtomWithIdx(3))->Match(o));
TEST_ASSERT(dynamic_cast<QueryAtom *>(m2->getAtomWithIdx(3))->Match(cl));
TEST_ASSERT(dynamic_cast<QueryAtom *>(m2->getAtomWithIdx(3))->Match(o));
delete cl;
delete o;
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAtomListLineWithOtherQueries() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Test AtomListLine with other queries" << std::endl;
const std::list<std::string> molblocks{R"MOL(
SciTegic06022014352D
4 3 0 0 0 0 999 V2000
14.8926 -7.5485 0.0000 N 0 3 0 0 0 0 0 0 0 1 0 0
13.8697 -6.9579 0.0000 L 0 0 0 0 0 0 0 0 0 4 0 0
15.9154 -6.9579 0.0000 A 0 0 0 0 0 0 0 0 0 3 0 0
14.8926 -8.7296 0.0000 L 0 5 0 0 0 0 0 0 0 2 0 0
2 1 5 0 0 0 2
1 3 1 0 0 0 2
4 1 1 0 0 0 8
M CHG 2 1 1 4 -1
M SUB 1 4 1
M ALS 2 2 F O S 0
M ALS 4 2 F O S 0
M END
)MOL",
R"MOL(
SciTegic06022014352D
4 3 0 0 0 0 999 V2000
14.8926 -7.5485 0.0000 N 0 3 0 0 0 0 0 0 0 1 0 0
13.8697 -6.9579 0.0000 L 0 0 0 0 0 0 0 0 0 4 0 0
15.9154 -6.9579 0.0000 A 0 0 0 0 0 0 0 0 0 3 0 0
14.8926 -8.7296 0.0000 L 0 5 0 0 0 0 0 0 0 2 0 0
2 1 5 0 0 0 2
1 3 1 0 0 0 2
4 1 1 0 0 0 8
M CHG 2 1 1 4 -1
M ALS 2 2 F O S 0
M ALS 4 2 F O S 0
M SUB 1 4 1
M END
)MOL"};
const bool sanitize = false;
const bool removeHs = true;
const bool strictParsing = true;
for (const auto &molblock : molblocks) {
RWMOL_SPTR m(MolBlockToMol(molblock, sanitize, removeHs, strictParsing));
TEST_ASSERT(m->getNumAtoms() == 4);
const Atom *a = m->getAtomWithIdx(3);
TEST_ASSERT(a->hasQuery());
const QueryAtom *qa = dynamic_cast<const QueryAtom *>(a);
TEST_ASSERT(qa);
TEST_ASSERT(describeQuery(a) == R"MOL(AtomAnd
AtomAnd
AtomOr
AtomAtomicNum 8 = val
AtomAtomicNum 16 = val
AtomFormalCharge -1 = val
AtomExplicitDegree 1 = val
)MOL");
TEST_ASSERT(SmartsWrite::GetAtomSmarts(qa) == "[#8,#16;-;D1:2]");
}
}
void testReplaceChargedAtomWithQueryAtom() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Test replaceAtomWithQueryAtom on a charged atom"
<< std::endl;
auto mol = "[NH3+]C"_smiles;
TEST_ASSERT(mol.get());
auto a = mol->getAtomWithIdx(0);
TEST_ASSERT(a);
const QueryAtom *qa = dynamic_cast<const QueryAtom *>(
QueryOps::replaceAtomWithQueryAtom(mol.get(), a));
TEST_ASSERT(qa);
TEST_ASSERT(SmartsWrite::GetAtomSmarts(qa) == "[#7&+]");
}
void testGithub608() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Test github 608: stereo bonds wrong after insertMol"
<< std::endl;
{
RWMol *m = SmilesToMol("N1NN1");
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
RWMol *f = SmilesToMol("C/C=C/C");
TEST_ASSERT(f);
TEST_ASSERT(f->getNumAtoms() == 4);
TEST_ASSERT(f->getBondBetweenAtoms(1, 2)->getStereoAtoms().size() == 2);
TEST_ASSERT(f->getBondBetweenAtoms(1, 2)->getStereoAtoms()[0] == 0);
TEST_ASSERT(f->getBondBetweenAtoms(1, 2)->getStereoAtoms()[1] == 3);
m->insertMol(*f);
TEST_ASSERT(m->getNumAtoms() == 7);
TEST_ASSERT(m->getBondBetweenAtoms(4, 5)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(4, 5)->getStereoAtoms().size() == 2);
TEST_ASSERT(m->getBondBetweenAtoms(4, 5)->getStereoAtoms()[0] == 3);
TEST_ASSERT(m->getBondBetweenAtoms(4, 5)->getStereoAtoms()[1] == 6);
delete m;
delete f;
}
{
INT_VECT nAtoms;
RWMol *m = SmilesToMol("N1NN1");
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
RWMol *f = SmilesToMol("C[C@]1(F)CC[C@](Cl)(Br)CC1");
TEST_ASSERT(f);
TEST_ASSERT(f->getNumAtoms() == 10);
TEST_ASSERT(f->getAtomWithIdx(1)->getPropIfPresent(
common_properties::_ringStereoAtoms, nAtoms));
TEST_ASSERT(std::find(nAtoms.begin(), nAtoms.end(), 6) != nAtoms.end());
m->insertMol(*f);
TEST_ASSERT(m->getNumAtoms() == 13);
TEST_ASSERT(m->getAtomWithIdx(4)->getPropIfPresent(
common_properties::_ringStereoAtoms, nAtoms));
TEST_ASSERT(std::find(nAtoms.begin(), nAtoms.end(), 9) != nAtoms.end());
delete m;
delete f;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
#ifdef RDK_TEST_MULTITHREADED
#include <thread>
#include <future>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>
namespace {
void runblock(std::vector<const PeriodicTable *> *pts, int idx) {
const PeriodicTable *pt = PeriodicTable::getTable();
(*pts)[idx] = pt;
TEST_ASSERT(pt->getAtomicNumber("C") == 6);
TEST_ASSERT(pt->getAtomicNumber("N") == 7);
TEST_ASSERT(pt->getAtomicNumber("O") == 8);
};
} // namespace
void testGithub381() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test github381: thread-safe initialization of the periodic table"
<< std::endl;
std::vector<std::future<void>> tg;
unsigned int count = 32;
std::vector<const PeriodicTable *> pts(count);
#if 1
for (unsigned int i = 0; i < count; ++i) {
std::cerr.flush();
tg.emplace_back(std::async(std::launch::async, runblock, &pts, i));
}
for (auto &fut : tg) {
fut.get();
}
TEST_ASSERT(pts[0] != nullptr);
for (unsigned int i = 1; i < count; ++i) {
TEST_ASSERT(pts[i] == pts[0]);
}
#endif
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#else
void testGithub381() {}
#endif
void testGithub1041() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test github1041: Segfault for atom with no "
"owner (expect some warnings)"
<< std::endl;
{
Atom at(6);
bool ok = false;
try {
at.getOwningMol();
} catch (const Invar::Invariant &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
Bond b;
bool ok = false;
try {
b.getOwningMol();
} catch (const Invar::Invariant &) {
ok = true;
}
TEST_ASSERT(ok);
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGithub1453() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test github1453: RWMol.clear() should reset the numBonds count."
<< std::endl;
RWMol m2;
m2.addAtom(new Atom(6), true, true);
m2.addAtom(new Atom(6), true, true);
m2.addBond(0, 1, Bond::TRIPLE);
TEST_ASSERT(m2.getNumAtoms() == 2);
TEST_ASSERT(m2.getNumBonds() == 1);
m2.clear();
TEST_ASSERT(m2.getNumAtoms() == 0);
TEST_ASSERT(m2.getNumBonds() == 0);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testRanges() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test range-based for loops." << std::endl;
RWMol *m = SmilesToMol("C1CC1");
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 3);
// For by value (ok since the atoms are pointers)
unsigned int i = 0;
for (auto atom : m->atoms()) {
TEST_ASSERT(atom->getIdx() == i);
i++;
}
// try refs
i = 0;
for (auto &atom : m->atoms()) {
TEST_ASSERT(atom->getIdx() == i);
i++;
}
// try const refs
i = 0;
for (auto const &atom : m->atoms()) {
TEST_ASSERT(atom->getIdx() == i);
i++;
}
const RWMol *cm = m;
i = 0;
for (auto atom : cm->atoms()) {
TEST_ASSERT(atom->getIdx() == i);
i++;
}
i = 0;
for (auto bond : m->bonds()) {
TEST_ASSERT(bond->getIdx() == i);
i++;
}
i = 0;
for (auto bond : cm->bonds()) {
TEST_ASSERT(bond->getIdx() == i);
i++;
}
const auto atom = m->getAtomWithIdx(0);
i = 0;
for (const auto &nbri :
boost::make_iterator_range(m->getAtomNeighbors(atom))) {
const auto &nbr = (*m)[nbri];
TEST_ASSERT(nbr->getAtomicNum() == 6);
i++;
}
TEST_ASSERT(i == 2);
i = 0;
for (const auto &nbri : boost::make_iterator_range(m->getAtomBonds(atom))) {
const auto &bnd = (*m)[nbri];
TEST_ASSERT(bnd->getBondType() == Bond::SINGLE);
i++;
}
TEST_ASSERT(i == 2);
// non-const versions of the same things
i = 0;
for (const auto &nbri :
boost::make_iterator_range(m->getAtomNeighbors(atom))) {
auto nbr = (*m)[nbri];
TEST_ASSERT(nbr->getAtomicNum() == 6);
nbr->setAtomicNum(7);
nbr->setAtomicNum(6);
i++;
}
TEST_ASSERT(i == 2);
i = 0;
for (const auto &nbri : boost::make_iterator_range(m->getAtomBonds(atom))) {
auto bnd = (*m)[nbri];
TEST_ASSERT(bnd->getBondType() == Bond::SINGLE);
bnd->setBondType(Bond::DOUBLE);
bnd->setBondType(Bond::SINGLE);
i++;
}
TEST_ASSERT(i == 2);
delete m;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGithub1642() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test github1642: Atom index type is too low for big molecules."
<< std::endl;
RWMol m2;
unsigned int big_num_atoms = 70000;
Atom *carbon = new Atom(6);
for (unsigned int i = 0; i < big_num_atoms; ++i) {
m2.addAtom(carbon);
}
TEST_ASSERT(m2.getNumAtoms() == big_num_atoms);
for (int i = big_num_atoms; i > 0; --i) {
m2.removeAtom(i - 1);
}
TEST_ASSERT(m2.getNumAtoms() == 0);
delete carbon;
BOOST_LOG(rdErrorLog) << "Finished" << std::endl;
}
void testGithub1843() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test github1843: RWMol.clear() should not destroy ring pointer."
<< std::endl;
RWMol *m = SmilesToMol("N1NN1");
m->clear();
MolOps::sanitizeMol(*m);
delete m;
BOOST_LOG(rdErrorLog) << "Finished" << std::endl;
}
void testHasValenceViolation() {
BOOST_LOG(rdInfoLog) << " ----------> Testing Atom::hasValenceViolation()"
<< std::endl;
auto to_mol = [](const auto &smiles) {
int debugParse = 0;
bool sanitize = false;
std::unique_ptr<RWMol> mol(
RDKit::SmilesToMol(smiles, debugParse, sanitize));
TEST_ASSERT(mol != nullptr);
mol->updatePropertyCache(false);
return mol;
};
// All valid atoms
for (const auto &smiles : {
"C",
"C(C)(C)(C)C",
"S(C)(C)(C)(C)(C)C",
"O(C)C",
"[H]",
"[H+]", // proton
"[H-]",
"[HH]",
"[He]",
"[C][C] |^5:0,1|",
"[H][Si] |^5:1|",
"[CH3+]",
"[CH3-]",
"[NH4+]",
"[Na]",
"[Na][H]",
"[Na]([H])[H]",
"[Og][Og]([Og])([Og])([Og])([Og])([Og])[Og]",
"[Lv-2]",
"[Lv+4]",
"[Lv+8]"
"*", // dummy atom, which also accounts for wildcards
"*C |$_AP1;$|]", // attachment point
"[*] |$_R1$|", // rgroup
}) {
auto mol = to_mol(smiles);
for (auto atom : mol->atoms()) {
TEST_ASSERT(!atom->hasValenceViolation());
}
}
// First atom has a valence error!
for (const auto &smiles : {
// FIXME: commented out cases do not raise AtomValenceException
// when passing through the valence calculation code; will file
// RDKit issues to address within the valence code separately.
// "[C+5]",
"C(C)(C)(C)(C)C",
"S(C)(C)(C)(C)(C)(C)C",
// "[C+](C)(C)(C)C",
"[C-](C)(C)(C)C",
// "[C](C)(C)(C)C |^1:0|", // pentavalent due to unpaired electron
"O(C)=C",
// "[H+] |^1:0|", // same as [H]
// "[H+] |^2:0|", // non-physical radical count
"[H+2]",
// "[H-2]",
// "[He+]",
// "[He+2]",
// "[He][He]",
"[O-3]",
// "[O+7]",
"[F-2]",
// "[F+2]",
"[Lv-4]",
}) {
auto mol = to_mol(smiles);
auto atom = mol->getAtomWithIdx(0);
TEST_ASSERT(atom->hasValenceViolation());
}
// Queries never have valence errors
for (const auto &smarts : {
"[#6](C)(C)(C)(C)C", // query pentavalent carbon
"[#8](-,=[#6])=[#6]", // S/D query bond present
"[!#6&!#1](-[#6])=[#6]", // Q query atom
"[#6,#7,#8](-[#6])=[#6]", // allowed list
"[!#6&!#7&!#8](-[#6])=[#6]", // disallowed list
"[#6&R](-[#6])=[#6]", // advanced query features
}) {
auto mol = v2::SmilesParse::MolFromSmarts(smarts);
for (auto atom : mol->atoms()) {
TEST_ASSERT(!atom->hasValenceViolation());
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testGithub6370() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test Github 6370: non-physical radical counts being preserved"
<< std::endl;
auto testRadicalsForSingleAtom = [](const std::string &element, int valence) {
for (int explicitHCount = 0; explicitHCount <= valence; explicitHCount++) {
for (int radicalType = 1; radicalType <= 7; radicalType++) {
std::string smi;
if (explicitHCount == 0) {
smi = (boost::format("[%s] |^%d:0|") % element % radicalType).str();
} else {
smi = (boost::format("[%sH%d] |^%d:0|") % element % explicitHCount %
radicalType)
.str();
}
auto m = v2::SmilesParse::MolFromSmiles(smi);
TEST_ASSERT(
static_cast<int>(m->getAtomWithIdx(0)->getNumRadicalElectrons()) ==
valence - explicitHCount);
}
}
};
// Checks CXSMILES in the form of [XHn] |^m:0|
// where X is the element symbol,
// n = 0, ..., valence,
// m = 1, ..., 7 denotes the radical type
for (int atomicNum = 2; atomicNum <= 118; atomicNum++) {
const auto &defaultVs =
PeriodicTable::getTable()->getValenceList(atomicNum);
if (defaultVs.size() != 1) {
// Skips elements with multiple valences, e.g., transition metals
continue;
}
int valence = defaultVs[0];
std::string element =
PeriodicTable::getTable()->getElementSymbol(atomicNum);
testRadicalsForSingleAtom(element, valence);
}
// Checks CXSMILES in the form of [NH4+] |^m:0|
// where m = 1, ..., 7 denotes the radical type
for (int radicalType = 1; radicalType <= 7; radicalType++) {
std::string smi = (boost::format("[NH4+] |^%d:0|") % radicalType).str();
auto m = v2::SmilesParse::MolFromSmiles(smi);
TEST_ASSERT(
static_cast<int>(m->getAtomWithIdx(0)->getNumRadicalElectrons()) == 0);
}
BOOST_LOG(rdErrorLog) << "Finished" << std::endl;
}
// -------------------------------------------------------------------
int main() {
RDLog::InitLogs();
boost::logging::enable_logs("rdApp.info");
test1();
testPropLeak();
testMolProps();
testAtomProps();
testBondProps();
testMisc();
testDegree();
testIssue1993296();
testIssue2381580();
testIssue2840217();
testPeriodicTable();
testAddAtomWithConf();
testIssue267();
testIssue284();
testClearMol();
testAtomResidues();
testNeedsUpdatePropertyCache();
testGithub608();
testGithub381();
testGithub1041();
testGithub1041();
testGithub1453();
testRanges();
testGithub1642();
testGithub1843();
testGithub6370();
testAtomListLineRoundTrip();
testAtomListLineWithOtherQueries();
testReplaceChargedAtomWithQueryAtom();
testHasValenceViolation();
return 0;
}
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