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rdkit/Code/GraphMol/Subgraphs/test1.cpp
Greg Landrum 853d8f4750 fix and test sf.net issue 250
2012-09-11 06:39:21 +00:00

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// $Id$
//
// Copyright (C) 2003-2006 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/Subgraphs/Subgraphs.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <iostream>
using namespace std;
using namespace RDKit;
void testSubgraphs()
{
std::cout << "-----------------------\n Subgraph retrieval" << std::endl;
// build: CCC(C)CC
RWMol mol;
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addBond(0,1,Bond::SINGLE);
mol.addBond(1,2,Bond::SINGLE);
mol.addBond(2,3,Bond::SINGLE);
mol.addBond(2,4,Bond::SINGLE);
mol.addBond(3,5,Bond::SINGLE);
PATH_LIST tmp;
PATH_LIST::iterator i;
PATH_TYPE::iterator j;
int totPs = 0;
tmp = findAllSubgraphsOfLengthN(mol,1);
CHECK_INVARIANT(tmp.size()==5,"");
totPs += tmp.size();
tmp = findAllSubgraphsOfLengthN(mol,2);
CHECK_INVARIANT(tmp.size()==5,"");
totPs += tmp.size();
tmp = findAllSubgraphsOfLengthN(mol,3);
CHECK_INVARIANT(tmp.size()==5,"");
totPs += tmp.size();
tmp = findAllSubgraphsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==3,"");
totPs += tmp.size();
tmp = findAllSubgraphsOfLengthN(mol,5);
CHECK_INVARIANT(tmp.size()==1,"");
totPs += tmp.size();
tmp = findAllSubgraphsOfLengthN(mol,6);
CHECK_INVARIANT(tmp.size()==0,"");
totPs += tmp.size();
// now use the direct range function and check that we get the
// same anwswer
INT_PATH_LIST_MAP tmpm;
tmpm = findAllSubgraphsOfLengthsMtoN(mol, 1, 6);
int newTot, idx;
newTot = 0;
for (idx = 1; idx <= 6; idx++) {
newTot += tmpm[idx].size();
}
CHECK_INVARIANT(totPs==newTot, "");
// add an H and make sure things don't change:
mol.addAtom(new Atom(1));
mol.addBond(5,6,Bond::SINGLE);
tmp = findAllSubgraphsOfLengthN(mol,1);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllSubgraphsOfLengthN(mol,2);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllSubgraphsOfLengthN(mol,3);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllSubgraphsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==3,"");
tmp = findAllSubgraphsOfLengthN(mol,5);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findAllSubgraphsOfLengthN(mol,6);
CHECK_INVARIANT(tmp.size()==0,"");
std::cout << "Finished" << std::endl;
}
void testSubgraphs2a() {
// these have been moved here from test2.cpp
std::cout << "-----------------------\n testSubgraphs2a" << std::endl;
RWMol *mol=SmilesToMol("C1CC2C1N2");
CHECK_INVARIANT(mol,"");
int nAll=0;
int nUnique=0;
for(unsigned int i=1;i<7;++i){
PATH_LIST tmp;
tmp = findAllSubgraphsOfLengthN(*mol,i);
nAll += tmp.size();
tmp = findUniqueSubgraphsOfLengthN(*mol,i);
nUnique += tmp.size();
}
CHECK_INVARIANT(nAll==49,"");
CHECK_INVARIANT(nUnique==21,"");
delete mol;
std::cout << "Finished" << std::endl;
}
void testSubgraphs2 () {
// these have been moved here from test2.cpp
std::cout << "-----------------------\n testSubgraphs2" << std::endl;
RWMol *mol=SmilesToMol("C12C3C4C1C1C2C3N41");
CHECK_INVARIANT(mol,"");
int nAll=0;
int nUnique=0;
int i;
for(i=1;i<13;i++){
PATH_LIST tmp;
tmp = findAllSubgraphsOfLengthN(*mol,i);
nAll += tmp.size();
tmp = findUniqueSubgraphsOfLengthN(*mol,i);
nUnique += tmp.size();
}
CHECK_INVARIANT(nAll==2433,"");
CHECK_INVARIANT(nUnique==300,"");
delete mol;
mol=SmilesToMol("CCC(O)C(c1ccccc1)CC(C)N(C)C");
CHECK_INVARIANT(mol,"");
nAll=0;
nUnique=0;
for(i=1;i<18;i++){
PATH_LIST tmp;
tmp = findAllSubgraphsOfLengthN(*mol,i);
nAll += tmp.size();
tmp = findUniqueSubgraphsOfLengthN(*mol,i);
nUnique += tmp.size();
}
CHECK_INVARIANT(nAll==1990,"");
CHECK_INVARIANT(nUnique==907,"");
std::cout << "Finished" << std::endl;
}
void dumpVIV(PATH_LIST v){
PATH_LIST::iterator i;
PATH_TYPE::iterator j;
for(i=v.begin();i!=v.end();i++){
for(j=i->begin();j!=i->end();j++){
std::cout << *j << " ";
}
std::cout << std::endl;
}
}
void testPaths()
{
std::cout << "-----------------------\n Path retrieval" << std::endl;
// build: CCC(C)CC
RWMol mol;
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addBond(0,1,Bond::SINGLE);
mol.addBond(1,2,Bond::SINGLE);
mol.addBond(2,3,Bond::SINGLE);
mol.addBond(2,4,Bond::SINGLE);
mol.addBond(3,5,Bond::SINGLE);
PATH_LIST tmp;
//
// Retrieve using bonds
//
tmp = findAllPathsOfLengthN(mol,1);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllPathsOfLengthN(mol,2);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllPathsOfLengthN(mol,3);
CHECK_INVARIANT(tmp.size()==4,"");
tmp = findAllPathsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findAllPathsOfLengthN(mol,5);
CHECK_INVARIANT(tmp.size()==0,"");
tmp = findAllPathsOfLengthN(mol,6);
CHECK_INVARIANT(tmp.size()==0,"");
//
// Retrieve using atoms, which gives the results shifted by
// one (it takes two atoms to make one bond)
//
tmp = findAllPathsOfLengthN(mol,1,false);
CHECK_INVARIANT(tmp.size()==6,"");
tmp = findAllPathsOfLengthN(mol,2,false);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllPathsOfLengthN(mol,3,false);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllPathsOfLengthN(mol,4,false);
CHECK_INVARIANT(tmp.size()==4,"");
tmp = findAllPathsOfLengthN(mol,5,false);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findAllPathsOfLengthN(mol,6,false);
CHECK_INVARIANT(tmp.size()==0,"");
//
// try m->n
//
INT_PATH_LIST_MAP pths;
pths = findAllPathsOfLengthsMtoN(mol,1,6);
CHECK_INVARIANT(pths[1].size()==5,"");
CHECK_INVARIANT(pths[2].size()==5,"");
CHECK_INVARIANT(pths[3].size()==4,"");
CHECK_INVARIANT(pths[4].size()==1,"");
CHECK_INVARIANT(pths[5].size()==0,"");
CHECK_INVARIANT(pths[6].size()==0,"");
pths = findAllPathsOfLengthsMtoN(mol,1,6,false);
CHECK_INVARIANT(pths[1].size()==6,"");
CHECK_INVARIANT(pths[2].size()==5,"");
CHECK_INVARIANT(pths[3].size()==5,"");
CHECK_INVARIANT(pths[4].size()==4,"");
CHECK_INVARIANT(pths[5].size()==1,"");
CHECK_INVARIANT(pths[6].size()==0,"");
//
// add an atom, close the ring and re-check a couple indices:
// (leaves us with CC1CCCCC1)
//
mol.addAtom(new Atom(6));
mol.addBond(5,6,Bond::SINGLE);
mol.addBond(0,6,Bond::SINGLE);
tmp = findAllPathsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==8,"");
tmp = findAllPathsOfLengthN(mol,5,false);
CHECK_INVARIANT(tmp.size()==8,"");
std::cout << "Finished" << std::endl;
}
void testPaths2()
{
std::cout << "-----------------------\n Path retrieval2" << std::endl;
// build: CCC(C)CC
RWMol mol;
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addBond(0,1,Bond::SINGLE);
mol.addBond(1,2,Bond::SINGLE);
mol.addBond(2,3,Bond::SINGLE);
mol.addBond(2,0,Bond::SINGLE);
//
// Retrieve using bonds
//
PATH_LIST tmp = findAllPathsOfLengthN(mol,3);
//std::cout << "\n3:" << std::endl;
//dumpVIV(tmp);
CHECK_INVARIANT(tmp.size()==3,"");
std::cout << "Finished" << std::endl;
}
void testUniqueSubgraphs()
{
std::cout << "-----------------------\n Unique Subgraph retrieval" << std::endl;
// build: CCC(C)CC
RWMol mol;
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addAtom(new Atom(6));
mol.addBond(0,1,Bond::SINGLE);
mol.addBond(1,2,Bond::SINGLE);
mol.addBond(2,3,Bond::SINGLE);
mol.addBond(2,4,Bond::SINGLE);
mol.addBond(3,5,Bond::SINGLE);
PATH_LIST tmp;
PATH_LIST::iterator i;
PATH_TYPE::iterator j;
tmp = findAllSubgraphsOfLengthN(mol,1);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findAllSubgraphsOfLengthN(mol,2);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findUniqueSubgraphsOfLengthN(mol,2);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findAllSubgraphsOfLengthN(mol,3);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findUniqueSubgraphsOfLengthN(mol,3);
CHECK_INVARIANT(tmp.size()==2,"");
tmp = findAllSubgraphsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==3,"");
tmp = findUniqueSubgraphsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==2,"");
tmp = findAllSubgraphsOfLengthN(mol,5);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findUniqueSubgraphsOfLengthN(mol,5);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findAllSubgraphsOfLengthN(mol,6);
CHECK_INVARIANT(tmp.size()==0,"");
tmp = findUniqueSubgraphsOfLengthN(mol,6);
CHECK_INVARIANT(tmp.size()==0,"");
// add an H and make sure things don't change:
mol.addAtom(new Atom(1));
mol.addBond(5,6,Bond::SINGLE);
tmp = findAllSubgraphsOfLengthN(mol,2);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findUniqueSubgraphsOfLengthN(mol,2);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findAllSubgraphsOfLengthN(mol,3);
CHECK_INVARIANT(tmp.size()==5,"");
tmp = findUniqueSubgraphsOfLengthN(mol,3);
CHECK_INVARIANT(tmp.size()==2,"");
tmp = findAllSubgraphsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==3,"");
tmp = findUniqueSubgraphsOfLengthN(mol,4);
CHECK_INVARIANT(tmp.size()==2,"");
tmp = findAllSubgraphsOfLengthN(mol,5);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findUniqueSubgraphsOfLengthN(mol,5);
CHECK_INVARIANT(tmp.size()==1,"");
tmp = findAllSubgraphsOfLengthN(mol,6);
CHECK_INVARIANT(tmp.size()==0,"");
tmp = findUniqueSubgraphsOfLengthN(mol,6);
CHECK_INVARIANT(tmp.size()==0,"");
std::cout << "Finished" << std::endl;
}
void testUniqueSubgraphs2() {
// moved here from test2.cpp
std::cout << "-----------------------\n testUniqueSubgraphs2" << std::endl;
RWMol *mol=SmilesToMol("O=C(O)CCCC=CC(C1C(O)CC(O)C1(C=CC(O)CCCCC))");
CHECK_INVARIANT(mol,"");
int nAll=0;
int nUnique=0;
for(int i=1;i<26;i++){
PATH_LIST tmp;
tmp = findAllSubgraphsOfLengthN(*mol,i);
//std::cout << i << "\t" << tmp.size();
nAll += tmp.size();
tmp = findUniqueSubgraphsOfLengthN(*mol,i);
//std::cout << "\t" << tmp.size() << std::endl;;
nUnique += tmp.size();
}
CHECK_INVARIANT(nAll==6435,"");
CHECK_INVARIANT(nUnique==5618,"");
delete mol;
std::cout << "Finished" << std::endl;
}
void testLeak() {
// moved here from test2.cpp
std::cout << "-----------------------\n testing for a core leak (Issue 42) " << std::endl;
RWMol *mol=SmilesToMol("O=C(O)CCCC=CC(C1C(O)CC(O)C1(C=CC(O)CCCCC))");
CHECK_INVARIANT(mol,"");
for(int rep=0;rep<100;rep++){
int nAll=0;
int nUnique=0;
for(int i=1;i<26;i++){
PATH_LIST tmp;
tmp = findAllSubgraphsOfLengthN(*mol,i);
//std::cout << i << "\t" << tmp.size();
nAll += tmp.size();
tmp = findUniqueSubgraphsOfLengthN(*mol,i);
//std::cout << "\t" << tmp.size() << std::endl;;
nUnique += tmp.size();
}
CHECK_INVARIANT(nAll==6435,"");
CHECK_INVARIANT(nUnique==5618,"");
}
delete mol;
std::cout << "Finished" << std::endl;
}
void testRootedSubgraphs () {
std::cout << "-----------------------\n testRootedSubgraphs" << std::endl;
{
RWMol *mol=SmilesToMol("CC1CC1");
TEST_ASSERT(mol);
PATH_LIST tmp;
tmp = findAllSubgraphsOfLengthN(*mol,1,false,0);
TEST_ASSERT(tmp.size()==1);
tmp = findAllSubgraphsOfLengthN(*mol,2,false,0);
TEST_ASSERT(tmp.size()==2);
tmp = findAllSubgraphsOfLengthN(*mol,3,false,0);
TEST_ASSERT(tmp.size()==3);
tmp = findUniqueSubgraphsOfLengthN(*mol,2,false,false,0);
TEST_ASSERT(tmp.size()==1);
tmp = findUniqueSubgraphsOfLengthN(*mol,3,false,false,0);
TEST_ASSERT(tmp.size()==2);
INT_PATH_LIST_MAP tmpm;
tmpm = findAllSubgraphsOfLengthsMtoN(*mol,1,3,false,0);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==2);
TEST_ASSERT(tmpm[3].size()==3);
// edge case:
tmp = findAllSubgraphsOfLengthN(*mol,1,false,10);
TEST_ASSERT(tmp.size()==0);
delete mol;
}
{ // tests for sf.net issue 250
RWMol *mol=SmilesToMol("C1CC1C");
TEST_ASSERT(mol);
PATH_LIST tmp;
tmp = findAllSubgraphsOfLengthN(*mol,1,false,3);
TEST_ASSERT(tmp.size()==1);
tmp = findAllSubgraphsOfLengthN(*mol,2,false,3);
TEST_ASSERT(tmp.size()==2);
tmp = findAllSubgraphsOfLengthN(*mol,3,false,3);
TEST_ASSERT(tmp.size()==3);
tmp = findUniqueSubgraphsOfLengthN(*mol,2,false,false,3);
TEST_ASSERT(tmp.size()==1);
tmp = findUniqueSubgraphsOfLengthN(*mol,3,false,false,3);
TEST_ASSERT(tmp.size()==2);
INT_PATH_LIST_MAP tmpm;
tmpm = findAllSubgraphsOfLengthsMtoN(*mol,1,3,false,3);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==2);
TEST_ASSERT(tmpm[3].size()==3);
// edge case:
tmp = findAllSubgraphsOfLengthN(*mol,1,false,10);
TEST_ASSERT(tmp.size()==0);
delete mol;
}
{
RWMol *mol=SmilesToMol("CC1CC1");
TEST_ASSERT(mol);
INT_PATH_LIST_MAP tmpm;
tmpm = findAllSubgraphsOfLengthsMtoN(*mol,1,2,false,0);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==2);
TEST_ASSERT(tmpm[3].size()==0);
tmpm = findAllSubgraphsOfLengthsMtoN(*mol,1,3,false,0);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==2);
TEST_ASSERT(tmpm[3].size()==3);
delete mol;
}
{ // tests for sf.net issue 250
RWMol *mol=SmilesToMol("C1CC1C");
TEST_ASSERT(mol);
INT_PATH_LIST_MAP tmpm;
tmpm = findAllSubgraphsOfLengthsMtoN(*mol,1,2,false,3);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==2);
TEST_ASSERT(tmpm[3].size()==0);
tmpm = findAllSubgraphsOfLengthsMtoN(*mol,1,3,false,3);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==2);
TEST_ASSERT(tmpm[3].size()==3);
delete mol;
}
std::cout << "Finished" << std::endl;
}
void testRootedPaths () {
std::cout << "-----------------------\n testRootedPaths" << std::endl;
{
RWMol *mol=SmilesToMol("CC1CC1");
TEST_ASSERT(mol);
PATH_LIST tmp;
// bond paths:
tmp = findAllPathsOfLengthN(*mol,1,true,false,0);
TEST_ASSERT(tmp.size()==1);
tmp = findAllPathsOfLengthN(*mol,2,true,false,0);
TEST_ASSERT(tmp.size()==2);
tmp = findAllPathsOfLengthN(*mol,3,true,false,0);
TEST_ASSERT(tmp.size()==2);
// edge case:
tmp = findAllPathsOfLengthN(*mol,1,true,false,10);
TEST_ASSERT(tmp.size()==0);
// atom paths:
tmp = findAllPathsOfLengthN(*mol,1,false,false,0);
TEST_ASSERT(tmp.size()==1);
tmp = findAllPathsOfLengthN(*mol,2,false,false,0);
TEST_ASSERT(tmp.size()==1);
tmp = findAllPathsOfLengthN(*mol,3,false,false,0);
TEST_ASSERT(tmp.size()==2);
tmp = findAllPathsOfLengthN(*mol,4,false,false,0);
TEST_ASSERT(tmp.size()==2);
delete mol;
}
{ // tests for sf.net issue 250
RWMol *mol=SmilesToMol("C1CC1C");
TEST_ASSERT(mol);
PATH_LIST tmp;
// bond paths:
tmp = findAllPathsOfLengthN(*mol,1,true,false,3);
TEST_ASSERT(tmp.size()==1);
tmp = findAllPathsOfLengthN(*mol,2,true,false,3);
TEST_ASSERT(tmp.size()==2);
tmp = findAllPathsOfLengthN(*mol,3,true,false,3);
TEST_ASSERT(tmp.size()==2);
// edge case:
tmp = findAllPathsOfLengthN(*mol,1,true,false,10);
TEST_ASSERT(tmp.size()==0);
// atom paths:
tmp = findAllPathsOfLengthN(*mol,1,false,false,3);
TEST_ASSERT(tmp.size()==1);
tmp = findAllPathsOfLengthN(*mol,2,false,false,3);
TEST_ASSERT(tmp.size()==1);
tmp = findAllPathsOfLengthN(*mol,3,false,false,3);
TEST_ASSERT(tmp.size()==2);
tmp = findAllPathsOfLengthN(*mol,4,false,false,3);
TEST_ASSERT(tmp.size()==2);
delete mol;
}
{
RWMol *mol=SmilesToMol("CC1CC1");
TEST_ASSERT(mol);
INT_PATH_LIST_MAP tmpm;
tmpm = findAllPathsOfLengthsMtoN(*mol,1,2,false,false,0);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==1);
TEST_ASSERT(tmpm[3].size()==0);
tmpm = findAllPathsOfLengthsMtoN(*mol,1,3,false,false,0);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==1);
TEST_ASSERT(tmpm[3].size()==2);
delete mol;
}
{ // tests for sf.net issue 250
RWMol *mol=SmilesToMol("C1CC1C");
TEST_ASSERT(mol);
INT_PATH_LIST_MAP tmpm;
tmpm = findAllPathsOfLengthsMtoN(*mol,1,2,false,false,3);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==1);
TEST_ASSERT(tmpm[3].size()==0);
tmpm = findAllPathsOfLengthsMtoN(*mol,1,3,false,false,3);
TEST_ASSERT(tmpm[1].size()==1);
TEST_ASSERT(tmpm[2].size()==1);
TEST_ASSERT(tmpm[3].size()==2);
delete mol;
}
std::cout << "Finished" << std::endl;
}
// -------------------------------------------------------------------
int main()
{
#if 1
testSubgraphs();
testSubgraphs2a();
testSubgraphs2();
testPaths();
testPaths2();
testUniqueSubgraphs();
testUniqueSubgraphs2();
testRootedSubgraphs();
testRootedPaths();
#endif
//testLeak();
return 0;
}
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