/** 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);
}
}
}
}
/** Check that at least 1 atom in the range is in Mask1 */
static inline void CheckRange(Image::PairType& atomPairs, CharMask const& MaskIn,
int firstAtom, int lastAtom)
{
bool rangeIsValid = false;
for (int atom = firstAtom; atom < lastAtom; ++atom) {
if (MaskIn.AtomInCharMask(atom)) {
rangeIsValid = true;
break;
}
}
if (rangeIsValid) {
atomPairs.push_back( firstAtom );
atomPairs.push_back( lastAtom );
}
}
