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4ea3b4430fd7d262bc48b68f084de53c6104edbc
rdkit/Code/GraphMol/test1.cpp
Greg Landrum 4ea82818a6 switch away from using the old, unsupported boost::log stuff. 
This "lookalike" implementation is much cruder than the real thing and does not really support
enabling and disabling logs, or associating them with files, but those components were not being
particularly used in the RDKit anyway.
2008-04-06 09:12:02 +00:00

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// $Id$
//
// Copyright (C) 2001-2006 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDLog.h>
//#include <boost/log/functions.hpp>
#include <iostream>
using namespace std;
using namespace RDKit;
// -------------------------------------------------------------------
void testBookmarks(ROMol m){
int i;
// ------------------------
// simple bookmark stuff
ROMol::GRAPH_NODE_TYPE a1 = m.getAtomWithIdx(1);
m.setAtomBookmark(a1,666);
ROMol::GRAPH_NODE_TYPE 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");
//----------------------------
// now do bond bookmarks
ROMol::GRAPH_EDGE_TYPE b1 = m.getBondWithIdx(0);
m.setBondBookmark(b1,23);
ROMol::GRAPH_EDGE_TYPE 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");
}
void testMolProps()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Mol Property Caches" << std::endl;
RWMol m2;
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"),"");
CHECK_INVARIANT(!m2.hasProp("prop2"),"");
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"),"");
CHECK_INVARIANT(!m2.hasProp("prop2"),"");
m2.getProp("prop1",tmpS);
CHECK_INVARIANT(tmpS=="2","");
std::string tmpString("2");
m2.setProp("prop1",tmpString.c_str());
CHECK_INVARIANT(m2.hasProp("prop1"),"");
CHECK_INVARIANT(!m2.hasProp("prop2"),"");
m2.getProp("prop1",tmpS);
CHECK_INVARIANT(tmpS=="2","");
// check for computed properties
m2.setProp("cprop1", 1, true);
m2.setProp("cprop2", 2, true);
STR_VECT cplst;
m2.getProp("computedProps", cplst);
CHECK_INVARIANT(cplst.size() == 2, "");
CHECK_INVARIANT(cplst[0] == "cprop1", "");
CHECK_INVARIANT(cplst[1] == "cprop2", "");
m2.clearProp("cprop1");
CHECK_INVARIANT(!m2.hasProp("cprop1"), "");
m2.getProp("computedProps", cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
m2.clearComputedProps();
CHECK_INVARIANT(!m2.hasProp("cprop2"), "");
m2.getProp("computedProps", cplst);
CHECK_INVARIANT(cplst.size() == 0, "");
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);
ROMol::GRAPH_NODE_TYPE a1 = m2.getAtomWithIdx(0);
ROMol::GRAPH_NODE_TYPE a2 = m2.getAtomWithIdx(0);
ROMol::GRAPH_NODE_TYPE 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"),"");
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,"");
// ceck for computed properties
a1->setProp("cprop1", 1, true);
a1->setProp("cprop2", 2, true);
STR_VECT cplst;
a1->getProp("computedProps", 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("computedProps", cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
a1->clearComputedProps();
CHECK_INVARIANT(!a1->hasProp("cprop2"), "");
a1->getProp("computedProps", 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);
ROMol::GRAPH_EDGE_TYPE b1 = m2.getBondWithIdx(0);
ROMol::GRAPH_EDGE_TYPE 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("computedProps", 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("computedProps", cplst);
CHECK_INVARIANT(cplst.size() == 1, "");
b1->clearComputedProps();
CHECK_INVARIANT(!b1->hasProp("cprop2"), "");
b1->getProp("computedProps", 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);
ROMol::GRAPH_NODE_TYPE a1 = m2.getAtomWithIdx(0);
ROMol::GRAPH_NODE_TYPE 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,"");
ROMol::GRAPH_EDGE_TYPE b1 = m2.getBondWithIdx(0);
ROMol::GRAPH_EDGE_TYPE 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);
ROMol::GRAPH_EDGE_TYPE 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,"");
ROMol::GRAPH_EDGE_CONST_TYPE 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::GRAPH_MOL_BOND_PMAP::type pMap = m2.getBondPMap();
ROMol::OEDGE_ITER begin,end;
boost::tie(begin,end) = m2.getAtomBonds(at);
while(begin!=end){
const Atom *at2 = pMap[*begin]->getOtherAtom(at);
TEST_ASSERT(at2);
begin++;
}
ROMol::GRAPH_MOL_ATOM_PMAP::type atomMap = m2.getAtomPMap();
ROMol::VERTEX_ITER atBegin,atEnd;
boost::tie(atBegin,atEnd) = m2.getVertices();
TEST_ASSERT(atBegin!=atEnd);
while(atBegin!=atEnd){
const Atom *at2=atomMap[*atBegin];
TEST_ASSERT(at2->getIdx()>=0);
atBegin++;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
// -------------------------------------------------------------------
int main()
{
RDLog::InitLogs();
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++){
ROMol::GRAPH_NODE_TYPE 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++){
ROMol::GRAPH_NODE_TYPE 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++){
ROMol::GRAPH_NODE_TYPE 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);
#if 0
//m.debugMol(cout);
MolOps::sanitizeMol(m);
BOOST_LOG(rdInfoLog) << "\n\n\n********************************\n";
string pickle;
m.debugMol(cout);
MolPickler::pickleMol(m,pickle);
ROMol *mFromP = new ROMol(pickle);
TEST_ASSERT(mFromP->getNumAtoms()==m.getNumAtoms());
//mFromP->debugMol(cout);
#endif
boost::logging::enable_logs("rdApp.info");
testPropLeak();
testMolProps();
testAtomProps();
testBondProps();
testMisc();
return 0;
}
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