static inline void BondTypes(ParmHolder<int>& ParmIndices, Topology const& top, BondArray const& bonds) {
for (BondArray::const_iterator b = bonds.begin(); b != bonds.end(); ++b)
{
AtomTypeHolder types(2);
types.AddName( top[b->A1()].Type() );
types.AddName( top[b->A2()].Type() );
ParmIndices.AddParm( types, b->Idx(), false );
}
}
/** Set up bond arrays in a sorted list for easy access during loop
* over all pairs of atoms. Only use bonds for which both atoms are in
* the mask.
*/
void Action_CheckStructure::ProcessBondArray(BondArray const& Bonds, BondParmArray const& Parm,
CharMask const& cMask)
{
BondType BT;
for (BondArray::const_iterator bnd = Bonds.begin(); bnd != Bonds.end(); ++bnd)
{
if ( cMask.AtomInCharMask(bnd->A1()) && cMask.AtomInCharMask(bnd->A2()) ) {
if (bnd->Idx() < 0)
mprintf("Warning: Bond parameters not present for atoms %i-%i, skipping.\n",
bnd->A1()+1, bnd->A2()+1);
else {
BT.Req_off2_ = Parm[ bnd->Idx() ].Req() + bondoffset_;
BT.Req_off2_ *= BT.Req_off2_; // Store squared values.
BT.a1_ = bnd->A1();
BT.a2_ = bnd->A2();
bondList_.push_back(BT);
}
}
}
}