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// $Id$
#include "pairlist.h"
namespace PTools
{
AttractPairList::AttractPairList(const AttractRigidbody & receptor , const AttractRigidbody & ligand, dbl cutoff )
{
mp_ligand = &ligand;
mp_receptor = &receptor;
squarecutoff = cutoff*cutoff;
no_update = false;
update();
}
AttractPairList::AttractPairList(const AttractRigidbody & receptor, const AttractRigidbody & ligand)
{
mp_ligand = &ligand;
mp_receptor = &receptor;
no_update = true ; //if infinite cutoff
for (uint i = 0 ; i < mp_ligand->Size(); i++)
for (uint j = 0; j < mp_receptor->Size(); j++)
{
vectl.push_back(i);
vectr.push_back(j);
}
}
AttractPairList::~AttractPairList()
{
}
/**
Very basic implementation of an atom pairlist.
*/
void AttractPairList::update()
{
if (no_update) return ;
vectl.clear(); // clears the pairlist
vectr.clear();
//basic implementation of a pairlist generation:
std::vector<uint> activelig;
std::vector<uint> activerec;
for (uint i=0; i<mp_ligand->Size(); i++)
{
if (mp_ligand->isAtomActive(i))
{
activelig.push_back(i);
}
}
for (uint i=0; i<mp_receptor->Size(); i++)
{
if (mp_receptor->isAtomActive(i))
{
activerec.push_back(i);
}
}
uint activeligsize = activelig.size();
uint activerecsize = activerec.size();
for (uint ii = 0 ; ii < activeligsize ; ii++)
{
for (uint jj = 0; jj < activerecsize; jj++)
{
uint i=activelig[ii];
uint j=activerec[jj];
Coord3D c1 = mp_ligand->GetCoords(i) ;
Coord3D c2 = mp_receptor->GetCoords(j);
if (Norm2(c1-c2) <= squarecutoff)
{
vectl.push_back(i);
vectr.push_back(j);
}
}
}
}
void AttractPairList::addPair(const AttractRigidbody & ligand, const AttractRigidbody & receptor, const AtomPair& pair)
{
if (&ligand==mp_ligand && &receptor==mp_receptor)
{
vectl.push_back(pair.atlig);
vectr.push_back(pair.atrec);
}
else
{
std::cerr << "error in PairList::add() : wrong receptor or ligand " << std::endl;
abort();
}
};
} //namespace PTools
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