u_int8_t
maxblock(u_int32_t addr, u_int8_t bits)
{
u_int32_t m;
while (bits > 0) {
m = imask(bits - 1);
if ((addr & m) != addr)
return (bits);
bits--;
}
return (bits);
}
u_int8_t
maxdiff(u_int32_t a, u_int32_t b)
{
u_int8_t bits = 0;
u_int32_t m;
b++;
while (bits < 32) {
m = imask(bits);
if ((a & m) != (b & m))
return (bits);
bits++;
}
return (bits);
}
/** An atom pair list consists of 2 values for each entry, a beginning
* index and ending index. For molecules and residues this is the first
* and just beyond the last atom; for atoms it is just the atom itself
* twice.
*/
Image::PairType Image::CreatePairList(Topology const& Parm, Mode modeIn,
std::string const& maskExpression)
{
PairType atomPairs;
// Set up mask based on desired imaging mode.
if ( modeIn == BYMOL || modeIn == BYRES ) {
CharMask cmask( maskExpression );
if ( Parm.SetupCharMask( cmask ) ) return atomPairs;
cmask.MaskInfo();
if (cmask.None()) return atomPairs;
// Set up atom range for each entity to be imaged.
if (modeIn == BYMOL) {
atomPairs.reserve( Parm.Nmol()*2 );
for (Topology::mol_iterator mol = Parm.MolStart();
mol != Parm.MolEnd(); ++mol)
CheckRange( atomPairs, cmask, mol->BeginAtom(), mol->EndAtom());
} else { // BYRES
atomPairs.reserve( Parm.Nres()*2 );
for (Topology::res_iterator residue = Parm.ResStart();
residue != Parm.ResEnd(); ++residue)
CheckRange( atomPairs, cmask, residue->FirstAtom(), residue->LastAtom() );
}
} else { // BYATOM
AtomMask imask( maskExpression );
if ( Parm.SetupIntegerMask( imask ) ) return atomPairs;
imask.MaskInfo();
if (imask.None()) return atomPairs;
atomPairs.reserve( Parm.Natom()*2 );
for (AtomMask::const_iterator atom = imask.begin(); atom != imask.end(); ++atom) {
atomPairs.push_back( *atom );
atomPairs.push_back( (*atom)+1 );
}
}
// mprintf("\tNumber of %ss to be imaged is %zu based on mask '%s'\n",
// ModeString[modeIn], atomPairs.size()/2, maskIn.MaskString());
return atomPairs;
}
