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b35538599f0a39a536e344f4f5600d55568fa5da
rdkit/Code/GraphMol/test1.cpp
Paolo Tosco b35538599f - Added AMBER trajectory reader and relevant tests
2016-04-16 20:28:45 +01:00

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// $Id$
//
// Copyright (C) 2001-2008 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 <GraphMol/RDKitBase.h>
#include <GraphMol/MonomerInfo.h>
#include <GraphMol/RDKitQueries.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDLog.h>
//#include <boost/log/functions.hpp>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/MMFF/Builder.h>
#include <ForceField/ForceField.h>
#include <Geometry/Trajectory.h>
#include <sstream>
#include <iostream>
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));
m2.addAtom(new Atom(6));
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(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(detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
m2.clearComputedProps();
CHECK_INVARIANT(!m2.hasProp("cprop2"), "");
m2.getProp(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));
m2.addAtom(new Atom(6));
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(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(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));
m2.addAtom(new Atom(6));
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 boost::bad_any_cast &e) {
ok = true;
}
TEST_ASSERT(ok);
a1->setProp<int>("iprop", 4);
TEST_ASSERT(a1->hasProp("iprop"));
ok = false;
try {
a1->getProp<double>("iprop");
} catch (const boost::bad_any_cast &e) {
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(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(detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
a1->clearComputedProps();
CHECK_INVARIANT(!a1->hasProp("cprop2"), "");
a1->getProp(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));
m2.addAtom(new Atom(6));
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(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(detail::computedPropName, cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
b1->clearComputedProps();
CHECK_INVARIANT(!b1->hasProp("cprop2"), "");
b1->getProp(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));
m2.addAtom(new Atom(6));
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));
m2.addAtom(new Atom(6));
m2.addAtom(new Atom(6));
m2.addAtom(new Atom(6));
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));
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_SPTR 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));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(1));
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);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue1993296() {
RWMol *m = new RWMol();
bool ok;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 1993296" << std::endl;
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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;
}
Bond *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;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue2381580() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 2381580" << std::endl;
{
RWMol *m = new RWMol();
m->addAtom(new Atom(5));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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;
}
{
RWMol *m = new RWMol();
m->addAtom(new Atom(5));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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;
}
{
RWMol *m = new RWMol();
m->addAtom(new Atom(5));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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 &e) {
ok = true;
}
TEST_ASSERT(ok);
delete m;
}
{
RWMol *m = new RWMol();
m->addAtom(new Atom(5));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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 &e) {
ok = true;
}
TEST_ASSERT(ok);
delete m;
}
{
RWMol *m = new RWMol();
m->addAtom(new Atom(5));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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;
}
{
RWMol *m = new RWMol();
m->addAtom(new Atom(5));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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;
{
RWMol *m = new RWMol();
for (unsigned int i = 0; i < 200; ++i) {
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
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;
Atom *newAtom = new Atom(8);
m.addAtom(newAtom);
CHECK_INVARIANT(m.getAtomWithIdx(0)->getIdx() == 0, "");
newAtom = new Atom(6);
m.addAtom(newAtom);
CHECK_INVARIANT(m.getAtomWithIdx(0)->getIdx() == 0, "");
CHECK_INVARIANT(m.getAtomWithIdx(1)->getIdx() == 1, "");
newAtom = new Atom(7);
m.addAtom(newAtom);
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));
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));
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));
m2.addAtom(new Atom(6));
// QueryAtom *qA = new QueryAtom;
// qA->setAtomicNum(7);
// m2.addAtom(qA);
m2.addAtom(new QueryAtom(7));
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;
Atom *newA = new Atom(12);
int newIdx = m.addAtom(newA);
m.addBond(newIdx - 1, newIdx, Bond::AROMATIC);
// m.debugMol(cout);
BOOST_LOG(rdInfoLog) << " trying a replace " << endl;
Atom *repA = new Atom(22);
m.replaceAtom(newIdx, repA);
}
{
RWMol m;
m.addAtom(new Atom(6));
m.addAtom(new Atom(6));
m.addBond(0, 1, Bond::SINGLE);
Conformer *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));
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));
m.addAtom(new Atom(6));
m.addBond(0, 1, Bond::SINGLE);
TEST_ASSERT(m.getNumConformers() == 0);
RWMol m2;
// insert molecule without a conf:
m2.addAtom(new Atom(6));
m.insertMol(m2);
TEST_ASSERT(m.getNumConformers() == 0);
// insert molecule with a conf:
Conformer *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 testAddConformersFromTrajectory() {
BOOST_LOG(rdInfoLog) << "-----------------------\n";
BOOST_LOG(rdInfoLog) << "Testing adding conformers from a trajectory" << std::endl;
std::string molBlock =
"\n"
" RDKit 3D\n"
"\n"
" 71 74 0 0 0 0 0 0 0 0999 V2000\n"
" 8.2543 3.1901 -0.3005 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.4558 1.9712 0.0938 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.3934 1.0441 -0.9483 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 6.6660 -0.0533 -0.4641 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.1928 0.2346 -0.4609 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.3713 -0.9410 -0.5770 N 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.1852 -1.0034 -1.2291 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.2914 0.1276 -1.6316 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.9308 -0.4468 -1.9908 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.1417 -0.7821 -0.7545 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.1848 0.3695 0.0456 N 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.5661 0.7686 -0.0745 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.4768 -0.0640 0.8206 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.8874 0.1143 0.3941 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.6333 -0.9984 0.0264 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.0127 -0.9516 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.7062 0.1599 0.3963 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.0408 0.4828 -0.1977 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -7.7914 1.1180 -1.5591 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.7622 1.4403 0.7265 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.8409 -0.7397 -0.4395 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.9121 -1.6637 0.4258 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -9.7414 -0.7636 -1.5059 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -5.9736 1.2357 0.8565 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.5843 1.2252 0.8530 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.6263 1.4884 -0.3942 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.0541 1.0258 -0.4230 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.9225 -2.3317 -1.2963 N 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6061 -2.9745 -0.3180 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.3554 -4.1536 0.3735 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.7653 -4.2712 1.6948 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.8254 -3.4613 2.0796 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.1978 -2.3436 1.3419 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.5694 -2.0799 0.1305 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 9.3138 3.1372 0.0031 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.8117 4.0754 0.1798 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 8.2358 3.3535 -1.4074 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 6.4027 2.2146 0.3634 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.9270 1.5444 1.0040 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 7.0677 -0.2415 0.5615 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 6.9530 -0.9105 -1.1025 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.9578 0.7259 0.5137 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.9985 0.9430 -1.3033 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.7171 0.7264 -2.4494 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.3994 0.2339 -2.6810 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.1342 -1.4171 -2.5076 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.7632 -1.3370 -1.0391 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.7845 -1.4394 -0.1311 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0125 0.1989 1.0673 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.6672 1.8215 0.2925 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.8705 0.7271 -1.1337 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.3045 0.3159 1.8590 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.1980 -1.1367 0.7635 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.1513 -1.9468 -0.2114 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.6138 -1.7460 -0.4718 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -7.0727 0.4399 -2.0858 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -7.3144 2.1076 -1.4482 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.7609 1.1720 -2.1135 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.3137 2.4504 0.5729 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -8.6170 1.0817 1.7580 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -9.8244 1.4444 0.4200 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -6.4629 2.0541 1.3719 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.0445 2.0563 1.3058 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.3329 1.8224 -1.3991 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.4920 2.3164 0.3160 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.2025 0.3766 0.4766 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.7945 1.8369 -0.3969 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4404 -4.6964 0.1303 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.3157 -5.0055 2.3587 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.4272 -3.7654 2.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 5.5668 -1.5069 1.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0\n"
" 2 3 1 0\n"
" 3 4 1 0\n"
" 4 5 1 0\n"
" 5 6 1 0\n"
" 6 7 1 0\n"
" 7 8 1 0\n"
" 8 9 1 0\n"
" 9 10 1 0\n"
" 10 11 1 0\n"
" 11 12 1 0\n"
" 12 13 1 0\n"
" 13 14 1 0\n"
" 14 15 2 0\n"
" 15 16 1 0\n"
" 16 17 2 0\n"
" 17 18 1 0\n"
" 18 19 1 0\n"
" 18 20 1 0\n"
" 18 21 1 0\n"
" 21 22 2 0\n"
" 21 23 1 0\n"
" 17 24 1 0\n"
" 24 25 2 0\n"
" 11 26 1 0\n"
" 26 27 1 0\n"
" 7 28 2 0\n"
" 28 29 1 0\n"
" 29 30 2 0\n"
" 30 31 1 0\n"
" 31 32 2 0\n"
" 32 33 1 0\n"
" 33 34 2 0\n"
" 34 6 1 0\n"
" 27 8 1 0\n"
" 34 29 1 0\n"
" 25 14 1 0\n"
" 1 35 1 0\n"
" 1 36 1 0\n"
" 1 37 1 0\n"
" 2 38 1 0\n"
" 2 39 1 0\n"
" 4 40 1 0\n"
" 4 41 1 0\n"
" 5 42 1 0\n"
" 5 43 1 0\n"
" 8 44 1 0\n"
" 9 45 1 0\n"
" 9 46 1 0\n"
" 10 47 1 0\n"
" 10 48 1 0\n"
" 11 49 1 0\n"
" 12 50 1 0\n"
" 12 51 1 0\n"
" 13 52 1 0\n"
" 13 53 1 0\n"
" 15 54 1 0\n"
" 16 55 1 0\n"
" 19 56 1 0\n"
" 19 57 1 0\n"
" 19 58 1 0\n"
" 20 59 1 0\n"
" 20 60 1 0\n"
" 20 61 1 0\n"
" 24 62 1 0\n"
" 25 63 1 0\n"
" 26 64 1 0\n"
" 26 65 1 0\n"
" 27 66 1 0\n"
" 27 67 1 0\n"
" 30 68 1 0\n"
" 31 69 1 0\n"
" 32 70 1 0\n"
" 33 71 1 0\n"
"M CHG 2 11 1 23 -1\n"
"M END\n";
RWMol *mol = MolBlockToMol(molBlock, true, false);
const unsigned int everySteps = 10;
const unsigned int maxIts = 1000;
double gradTol = 0.01;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/test_data/bilastine_trajectory.sdf";
SDWriter w(fName);
ForceFields::ForceField *field = MMFF::constructForceField(*mol);
field->initialize();
RDGeom::Trajectory traj(3, mol->getNumAtoms());
traj.setFreePosOnDestroy(true);
field->minimize(everySteps, &traj, maxIts, gradTol);
mol->removeConformer(0);
mol->addConformersFromTrajectory(&traj);
for (unsigned int nConf = 0;
nConf < mol->getNumConformers(); ++nConf) {
std::stringstream ss;
ss << std::fixed << std::setprecision(4)
<< traj.getSnapshot(nConf).getEnergy();
mol->setProp("ENERGY", ss.str(), false);
w.write(*mol, nConf);
}
w.close();
delete field;
delete mol;
}
void testAddConformersFromAmberTrajectory() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "testAddConformersFromAmberTrajectory" << std::endl;
ROMol *mol = SmilesToMol("CCC");
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/Geometry/testData/water_coords.trx";
{
RDGeom::Trajectory traj(3, mol->getNumAtoms(), RDGeom::Trajectory::FREE_POS_ON_DESTROY);
std::cerr << "1a) traj.size()" << traj.size() << std::endl;
traj.readAmber(fName);
std::cerr << "1) traj.size()" << traj.size() << std::endl;
TEST_ASSERT(traj.size() == 1);
for (unsigned int i = 0; i < 2; ++i) {
mol->addConformersFromTrajectory(&traj);
TEST_ASSERT(mol->getNumConformers() == i + 1);
TEST_ASSERT(mol->getConformer(i).getNumAtoms() == 3);
TEST_ASSERT(RDKit::feq(mol->getConformer(i).getAtomPos(0).x, 0.1941767));
TEST_ASSERT(RDKit::feq(mol->getConformer(i).getAtomPos(2).z, -0.4088006));
}
mol->clearConformers();
mol->addConformersFromTrajectory(&traj, 0);
TEST_ASSERT(mol->getNumConformers() == 0);
}
fName = rdbase + "/Code/Geometry/testData/water_coords2.trx";
{
RDGeom::Trajectory traj(3, mol->getNumAtoms(), RDGeom::Trajectory::FREE_POS_ON_DESTROY);
std::cerr << "2) traj.size()" << traj.size() << std::endl;
traj.readAmber(fName);
TEST_ASSERT(traj.size() == 2);
mol->addConformersFromTrajectory(&traj);
TEST_ASSERT(mol->getNumConformers() == 2);
mol->clearConformers();
mol->addConformersFromTrajectory(&traj, 1);
TEST_ASSERT(mol->getNumConformers() == 1);
}
delete mol;
BOOST_LOG(rdErrorLog) << "done" << std::endl;
}
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));
m.addAtom(new Atom(6));
Conformer *conf = new Conformer(m.getNumAtoms());
m.addConformer(conf);
m.addAtom(new Atom(6));
TEST_ASSERT(m.getConformer().getNumAtoms() == m.getNumAtoms());
}
{
RWMol m;
m.addAtom(new Atom(6));
m.addAtom(new Atom(6));
Conformer *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));
m.addAtom(new Atom(6));
m.addAtom(new Atom(6));
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));
m.updatePropertyCache();
TEST_ASSERT(m.getAtomWithIdx(0)->getImplicitValence() == 0);
}
{
RWMol m;
m.addAtom(new Atom(0));
for (unsigned int i = 0; i < 8; ++i) {
m.addAtom(new Atom(1));
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));
m.addAtom(new Atom(6));
m.addAtom(new Atom(6));
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;
{
RWMol *m = new RWMol();
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addBond(0, 1, Bond::SINGLE);
m->addAtom(new Atom(6));
m->addBond(1, 2, Bond::SINGLE);
m->addAtom(new Atom(6));
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);
RWMol *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()));
}
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));
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));
for (ROMol::AtomIterator atomIt = m.beginAtoms(); atomIt != m.endAtoms();
++atomIt) {
(*atomIt)->calcExplicitValence(false);
(*atomIt)->calcImplicitValence(false);
}
m.addAtom(new Atom(6));
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));
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 (Atom::QUERYATOM_QUERY::CHILD_VECT_CI ci = q->beginChildren();
ci != q->endChildren(); ++ci) {
res += qhelper((*ci).get(), depth + 1);
}
}
return res;
}
}
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);
std::istringstream inStream2(molblock);
RWMol *m2 =
MolDataStreamToMol(inStream2, line, sanitize, removeHs, strictParsing);
TEST_ASSERT(m2);
TEST_ASSERT(desc == qhelper(m2->getAtomWithIdx(3)->getQuery()));
Atom::ATOM_SPTR cl(new Atom(17));
Atom::ATOM_SPTR o(new Atom(17));
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 m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
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;
}
// -------------------------------------------------------------------
int main() {
RDLog::InitLogs();
// boost::logging::enable_logs("rdApp.info");
#if 1
test1();
testAddConformersFromTrajectory();
testAddConformersFromAmberTrajectory();
testPropLeak();
testMolProps();
testAtomProps();
testBondProps();
testMisc();
testDegree();
testIssue1993296();
testIssue2381580();
testIssue2840217();
#endif
testPeriodicTable();
testAddAtomWithConf();
testIssue267();
testIssue284();
testClearMol();
testAtomResidues();
testNeedsUpdatePropertyCache();
testAtomListLineRoundTrip();
testGithub608();
return 0;
}
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