/** Set up masks. */
int Cpptraj::MaskArray::SetupMasks(AtomMask const& maskIn, Topology const& topIn)
{
if (type_ == BY_MOLECULE && topIn.Nmol() < 1) {
mprintf("Warning: '%s' has no molecule information, cannot setup by molecule.\n",
topIn.c_str());
return 1;
}
masks_.clear();
if ( maskIn.None() ) {
mprintf("Warning: Nothing selected by mask '%s'\n", maskIn.MaskString());
return 0;
}
int last = -1;
int current = 0;
maxAtomsPerMask_ = 0;
sameNumAtomsPerMask_ = true;
for (AtomMask::const_iterator atm = maskIn.begin(); atm != maskIn.end(); ++atm)
{
switch (type_) {
case BY_ATOM : current = *atm; break;
case BY_RESIDUE : current = topIn[*atm].ResNum(); break;
case BY_MOLECULE : current = topIn[*atm].MolNum(); break;
}
if (current != last) {
if (!masks_.empty())
checkAtomsPerMask( masks_.back().Nselected() );
masks_.push_back( AtomMask() );
masks_.back().SetNatoms( topIn.Natom() );
}
masks_.back().AddSelectedAtom( *atm );
last = current;
}
if (!masks_.empty())
checkAtomsPerMask( masks_.back().Nselected() );
return 0;
}
/** 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;
}
/** Search for bonds between atoms in residues and atoms in adjacent residues
* using distance-based criterion that depends on atomic elements.
* \param top Topology to add bonds to.
* \param frameIn Frame containing atomic coordinates.
* \param offset Offset to add when determining if a bond is present.
* \param debug If > 0 print extra info.
*/
int BondSearch( Topology& top, Frame const& frameIn, double offset, int debug) {
mprintf("\tDetermining bond info from distances.\n");
if (frameIn.empty()) {
mprinterr("Internal Error: No coordinates set; cannot search for bonds.\n");
return 1;
}
# ifdef TIMER
Timer time_total, time_within, time_between;
time_total.Start();
time_within.Start();
# endif
// ----- STEP 1: Determine bonds within residues
for (Topology::res_iterator res = top.ResStart(); res != top.ResEnd(); ++res)
{
int stopatom = res->LastAtom();
// Check for bonds between each atom in the residue.
for (int atom1 = res->FirstAtom(); atom1 != stopatom; ++atom1) {
Atom::AtomicElementType a1Elt = top[atom1].Element();
// If this is a hydrogen and it already has a bond, move on.
if (a1Elt==Atom::HYDROGEN && top[atom1].Nbonds() > 0 )
continue;
for (int atom2 = atom1 + 1; atom2 != stopatom; ++atom2) {
Atom::AtomicElementType a2Elt = top[atom2].Element();
double D2 = DIST2_NoImage(frameIn.XYZ(atom1), frameIn.XYZ(atom2) );
double cutoff2 = Atom::GetBondLength(a1Elt, a2Elt) + offset;
cutoff2 *= cutoff2;
if (D2 < cutoff2) {
top.AddBond(atom1, atom2);
// Once a bond has been made to hydrogen move on.
if (a1Elt==Atom::HYDROGEN) break;
}
}
}
}
# ifdef TIMER
time_within.Stop();
time_between.Start();
# endif
// ----- STEP 2: Determine bonds between adjacent residues
Topology::mol_iterator nextmol = top.MolStart();
if (top.Nmol() > 0)
++nextmol;
for (Topology::res_iterator res = top.ResStart() + 1; res != top.ResEnd(); ++res)
{
// If molecule information is already present, check if first atom of
// this residue >= first atom of next molecule, which indicates this
// residue and the previous residue are in different molecules.
if ( (nextmol != top.MolEnd()) &&
(res->FirstAtom() >= nextmol->BeginAtom()) )
{
++nextmol;
continue;
}
// If this residue is recognized as solvent, no need to check previous or
// next residue
if ( res->NameIsSolvent() ) {
++res;
if (res == top.ResEnd()) break;
continue;
}
// Get previous residue
Topology::res_iterator previous_res = res - 1;
// If previous residue is recognized as solvent, no need to check previous.
if ( previous_res->NameIsSolvent() ) continue;
// Get previous residue start atom
int startatom = previous_res->FirstAtom();
// Previous residue stop atom, this residue start atom
int midatom = res->FirstAtom();
// This residue stop atom
int stopatom = res->LastAtom();
// Check for bonds between adjacent residues
for (int atom1 = startatom; atom1 != midatom; atom1++) {
Atom::AtomicElementType a1Elt = top[atom1].Element();
if (a1Elt==Atom::HYDROGEN) continue;
for (int atom2 = midatom; atom2 != stopatom; atom2++) {
Atom::AtomicElementType a2Elt = top[atom2].Element();
if (a2Elt==Atom::HYDROGEN) continue;
double D2 = DIST2_NoImage(frameIn.XYZ(atom1), frameIn.XYZ(atom2) );
double cutoff2 = Atom::GetBondLength(a1Elt, a2Elt) + offset;
cutoff2 *= cutoff2;
if (D2 < cutoff2)
top.AddBond(atom1, atom2);
}
}
}
# ifdef TIMER
time_between.Stop();
time_total.Stop();
time_within.WriteTiming(2, "Distances within residues", time_total.Total());
time_between.WriteTiming(2, "Distances between residues", time_total.Total());
time_total.WriteTiming(1, "Total for determining bonds via distances");
# endif
if (debug > 0)
mprintf("\t%s: %zu bonds to hydrogen, %zu other bonds.\n", top.c_str(),
top.BondsH().size(), top.Bonds().size());
return 0;
}
