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/vf2match.cpp

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vf2match.cpp
#include <openbabel/obiter.h>
#include <vf2/argraph.h>
#include <vf2/argedit.h>
#include <vf2/match.h>
#include <vf2/vf2_sub_state.h>
#include <vf2/vf2_state.h>
#include <vf2/vf2.h>
#define VERTEX_UNUSED -1
using namespace std;
namespace OpenBabel
{
class _OBAtomComparator: public AttrComparator
{
public:
_OBAtomComparator()
{
}
virtual bool compatible(void* aa, void* ab)
{
OBAtom* _aa = (OBAtom*)aa;
OBAtom* _ab = (OBAtom*)ab;
if (_aa->GetAtomicNum() != _ab->GetAtomicNum()) return false;
if (_aa->IsInRing()) {
if (!_ab->IsInRing()) return false;
}
if (_aa->IsAromatic()) {
if (!_ab->IsAromatic()) return false;
}
//if (_aa->GetIsotope() != _ab->GetIsotope()) return false;
return true;
}
};
class _OBBondComparator: public AttrComparator
{
public:
_OBBondComparator()
{
}
virtual bool compatible(void* ba, void* bb)
{
OBBond* _ba = (OBBond*)ba;
OBBond* _bb = (OBBond*)bb;
if (_ba->IsUp() != _bb->IsUp()) return false;
if (_ba->IsDown() !=_bb->IsDown()) return false;
if (_ba->IsHash() !=_bb->IsHash()) return false;
if (_ba->IsWedge() != _bb->IsWedge()) return false;
if (_ba->IsInRing()) {
if (!_bb->IsInRing()) return false;
}
if (_ba->IsAromatic()) {
if (_bb->IsAromatic()) return true;
else
return false;
}
if (_ba->GetBondOrder() != _bb->GetBondOrder()) return false;
return true;
}
};
class _OBAtomComparatorEx: public AttrComparator
{
public:
_OBAtomComparatorEx()
{
}
virtual bool compatible(void* aa, void* ab)
{
OBAtom* _aa = (OBAtom*)aa;
OBAtom* _ab = (OBAtom*)ab;
if (_aa->GetAtomicNum() != _ab->GetAtomicNum()) return false;
if (_aa->IsInRing() != _ab->IsInRing()) return false;
if (_aa->GetHyb() != _ab->GetHyb()) return false;
if (_aa->IsChiral() !=_ab->IsChiral()) return false;
if (_aa->GetIsotope() != _ab->GetIsotope()) return false;
if (_aa->GetFormalCharge() != _ab->GetFormalCharge()) return false;
if (_aa->IsAromatic() !=_ab->IsAromatic()) return false;
return true;
}
};
class _OBBondComparatorEx: public AttrComparator
{
public:
_OBBondComparatorEx()
{
}
virtual bool compatible(void* ba, void* bb)
{
OBBond* _ba = (OBBond*)ba;
OBBond* _bb = (OBBond*)bb;
bool _baa, _bba;
if (_ba->IsUp() != _bb->IsUp()) return false;
if (_ba->IsDown() !=_bb->IsDown()) return false;
if (_ba->IsHash() !=_bb->IsHash()) return false;
if (_ba->IsWedge() !=_bb->IsWedge()) return false;
if (_ba->IsInRing() != _bb->IsInRing()) return false;
_baa = _ba->IsAromatic();
_bba = _bb->IsAromatic();
if (_baa || _bba) {
if (_baa == _bba) return true;
else
return false;
}
if (_ba->GetBondOrder() != _bb->GetBondOrder()) return false;
return true;
}
};
VF2::VF2() {};
bool VF2::Match(OBMol &mol,OBMol &mol_sarg)
{
OBAtom *start_atom, *end_atom;
ARGEdit ed_target, ed_sarg;//, ed_target2;
int n,s,e;
unsigned int i;
if((mol.NumHvyAtoms() < mol_sarg.NumHvyAtoms()) || (mol.NumBonds() < mol_sarg.NumBonds())) return false;
node_id ni_target[mol.NumAtoms()], ni_sarg[mol_sarg.NumAtoms()], start_idx, end_idx;
vector<unsigned int> lt_target(mol.NumAtoms()+1,VERTEX_UNUSED);
vector<unsigned int> lt_sarg(mol_sarg.NumAtoms()+1,VERTEX_UNUSED);
//map<int, node_id> node_id_map_target, node_id_map_sarg;
//map<int, node_id>::iterator i;
FOR_BONDS_OF_MOL(b, mol_sarg) {
//cout << b->GetBondOrder() << endl;
//cout << "A:" << b->IsAromatic() << endl;
start_atom = b->GetBeginAtom();
end_atom = b->GetEndAtom();
s = start_atom->GetIdx();
e = end_atom->GetIdx();
i = lt_sarg[s];
if(i!=VERTEX_UNUSED) {
start_idx = i;
} else {
start_idx=ed_sarg.InsertNode(start_atom);
//node_id_map_sarg.insert(make_pair(s,start_idx));
lt_sarg[s]=start_idx;
}
i = lt_sarg[e];
if(i!=VERTEX_UNUSED) {
end_idx = i;
} else {
end_idx=ed_sarg.InsertNode(end_atom);
//node_id_map_sarg.insert(make_pair(e,end_idx));
lt_sarg[e]=end_idx;
}
ed_sarg.InsertEdge(start_idx,end_idx,(OBBond*)&*b);
ed_sarg.InsertEdge(end_idx,start_idx,(OBBond*)&*b);
}
//}
FOR_BONDS_OF_MOL(b, mol) {
start_atom = b->GetBeginAtom();
end_atom = b->GetEndAtom();
s = start_atom->GetIdx();
e = end_atom->GetIdx();
i = lt_target[s];
if(i!=VERTEX_UNUSED) {
start_idx = i;
} else {
start_idx=ed_target.InsertNode(start_atom);
//node_id_map_target.insert(make_pair(s,start_idx));
lt_target[s]=start_idx;
}
i = lt_target[e];
if(i!=VERTEX_UNUSED) {
end_idx = i;
} else {
end_idx=ed_target.InsertNode(end_atom);
//node_id_map_target.insert(make_pair(e,end_idx));
lt_target[e]=end_idx;
}
ed_target.InsertEdge(start_idx,end_idx,(OBBond*)&*b);
ed_target.InsertEdge(end_idx,start_idx,(OBBond*)&*b);
}
//}
ARGraph<OBAtom*, OBBond*> g_target(&ed_target), g_sarg(&ed_sarg);
g_sarg.SetNodeComparator(new _OBAtomComparator());
g_sarg.SetEdgeComparator(new _OBBondComparator());
VF2SubState s0(&g_sarg, &g_target);
if (match(&s0, &n, ni_sarg, ni_target)) return true;
return false;
}
bool VF2::ExactMatch(OBMol &mol,OBMol &mol_sarg)
{
OBAtom *start_atom, *end_atom;
ARGEdit ed_target, ed_sarg;//, ed_target2;
int n,s,e;
unsigned int i;
if((mol.NumHvyAtoms() != mol_sarg.NumHvyAtoms()) || (mol.NumBonds() != mol_sarg.NumBonds())) return false;
node_id ni_target[mol.NumAtoms()], ni_sarg[mol_sarg.NumAtoms()], start_idx, end_idx;
//map<int, node_id> node_id_map_target, node_id_map_sarg;
//map<int, node_id>::iterator i;
vector<unsigned int> lt_target(mol.NumAtoms()+1,VERTEX_UNUSED);
vector<unsigned int> lt_sarg(mol_sarg.NumAtoms()+1,VERTEX_UNUSED);
FOR_BONDS_OF_MOL(b, mol_sarg) {
//cout << b->GetBondOrder() << endl;
//cout << "A:" << b->IsAromatic() << endl;
start_atom = b->GetBeginAtom();
end_atom = b->GetEndAtom();
s = start_atom->GetIdx();
e = end_atom->GetIdx();
i = lt_sarg[s];
if(i!=VERTEX_UNUSED) {
start_idx = i;
} else {
start_idx=ed_sarg.InsertNode(start_atom);
//node_id_map_sarg.insert(make_pair(s,start_idx));
lt_sarg[s]=start_idx;
}
i = lt_sarg[e];
if(i != VERTEX_UNUSED) {
end_idx = i;
} else {
end_idx=ed_sarg.InsertNode(end_atom);
//node_id_map_sarg.insert(make_pair(e,end_idx));
lt_sarg[e]=end_idx;
}
ed_sarg.InsertEdge(start_idx,end_idx,(OBBond*)&*b);
ed_sarg.InsertEdge(end_idx,start_idx,(OBBond*)&*b);
}
//}
FOR_BONDS_OF_MOL(b, mol) {
start_atom = b->GetBeginAtom();
end_atom = b->GetEndAtom();
s = start_atom->GetIdx();
e = end_atom->GetIdx();
i = lt_target[s];
if(i != VERTEX_UNUSED) {
start_idx = i;
} else {
start_idx=ed_target.InsertNode(start_atom);
//node_id_map_target.insert(make_pair(s,start_idx));
lt_target[s]=start_idx;
}
i = lt_target[e];
if(i != VERTEX_UNUSED) {
end_idx = i;
} else {
end_idx=ed_target.InsertNode(end_atom);
//node_id_map_target.insert(make_pair(e,end_idx));
lt_target[e]=end_idx;
}
ed_target.InsertEdge(start_idx,end_idx,(OBBond*)&*b);
ed_target.InsertEdge(end_idx,start_idx,(OBBond*)&*b);
}
//}
ARGraph<OBAtom*, OBBond*> g_target(&ed_target), g_sarg(&ed_sarg);
g_sarg.SetNodeComparator(new _OBAtomComparatorEx());
g_sarg.SetEdgeComparator(new _OBBondComparatorEx());
VF2State s0(&g_sarg, &g_target);
if (match(&s0, &n, ni_sarg, ni_target)) return true;
return false;
}
}
Raw
vf2match.h
#include <openbabel/mol.h>
namespace OpenBabel
{
class OBAPI VF2
{
public:
VF2();
bool Match(OBMol &mol,OBMol &mol_sarg);
bool ExactMatch(OBMol &mol,OBMol &mol_sarg);
};
}
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