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85e2e94d202a0303a5fabc169ea63d0d07def140
rdkit/Code/GraphMol/test1.cpp
Brian Kelley 85e2e94d20 Fix MolFile Atom Line List Writer 
Only the first element in the atom one was being
written correctly, the remainder were not being
padded correctly and could not be round tripped.
2015-04-05 20:47:02 -04:00

1177 lines
34 KiB
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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 <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()>=0);
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()==m->getAtomWithIdx(0)->getTotalValence());
TEST_ASSERT(m->getAtomWithIdx(1)->getExplicitValence()+m->getAtomWithIdx(1)->getImplicitValence()==m->getAtomWithIdx(1)->getTotalValence());
TEST_ASSERT(m->getAtomWithIdx(2)->getExplicitValence()+m->getAtomWithIdx(2)->getImplicitValence()==m->getAtomWithIdx(2)->getTotalValence());
TEST_ASSERT(m->getAtomWithIdx(3)->getExplicitValence()+m->getAtomWithIdx(3)->getImplicitValence()==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));
}
}
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;
}
}
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;
RWMol *m = MolFileToMol(fName, sanitize);
std::string desc = qhelper(m->getAtomWithIdx(3)->getQuery());
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
std::string molblock = MolToMolBlock(*m);
std::istringstream inStream(molblock);
const bool removeHs=true;
const bool strictParsing=true;
unsigned int line = 0;
RWMol *m2 = MolDataStreamToMol(inStream, 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;
}
// -------------------------------------------------------------------
int main()
{
RDLog::InitLogs();
//boost::logging::enable_logs("rdApp.info");
// test1(); // <- this doesn't seem to actually do anything
#if 1
testPropLeak();
testMolProps();
testAtomProps();
testBondProps();
testMisc();
testDegree();
testIssue1993296();
testIssue2381580();
testIssue2840217();
#endif
testPeriodicTable();
testAddAtomWithConf();
testIssue267();
testIssue284();
testClearMol();
testAtomResidues();
testNeedsUpdatePropertyCache();
testAtomListLineRoundTrip();
return 0;
}
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