/** Set up bond parameters for bonds for which both atoms present in mask. */
void Action_CheckStructure::SetupBondList(AtomMask const& iMask, Topology const& top) {
CharMask cMask( iMask.ConvertToCharMask(), iMask.Nselected() );
ProcessBondArray(top.Bonds(), top.BondParm(), cMask);
ProcessBondArray(top.BondsH(), top.BondParm(), cMask);
}
int Parm_CharmmPsf::WriteParm(FileName const& fname, Topology const& parm) {
// TODO: CMAP etc info
CpptrajFile outfile;
if (outfile.OpenWrite(fname)) return 1;
// Write PSF
outfile.Printf("PSF\n\n");
// Write title
std::string titleOut = parm.ParmName();
titleOut.resize(78);
outfile.Printf("%8i !NTITLE\n* %-78s\n\n", 1, titleOut.c_str());
// Write NATOM section
outfile.Printf("%8i !NATOM\n", parm.Natom());
unsigned int idx = 1;
// Make fake segment ids for now.
char segid[2];
segid[0] = 'A';
segid[1] = '\0';
mprintf("Warning: Assigning single letter segment IDs.\n");
int currentMol = 0;
bool inSolvent = false;
for (Topology::atom_iterator atom = parm.begin(); atom != parm.end(); ++atom, ++idx) {
int resnum = atom->ResNum();
if (atom->MolNum() != currentMol) {
if (!inSolvent) {
inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
currentMol = atom->MolNum();
segid[0]++;
} else
inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
}
// TODO: Print type name for xplor-like PSF
int typeindex = atom->TypeIndex() + 1;
// If type begins with digit, assume charmm numbers were read as
// type. Currently Amber types all begin with letters.
if (isdigit(atom->Type()[0]))
typeindex = convertToInteger( *(atom->Type()) );
// ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
outfile.Printf("%8i %-4s %-4i %-4s %-4s %4i %14.6G %9g %10i\n", idx, segid,
parm.Res(resnum).OriginalResNum(), parm.Res(resnum).c_str(),
atom->c_str(), typeindex, atom->Charge(),
atom->Mass(), 0);
}
outfile.Printf("\n");
// Write NBOND section
outfile.Printf("%8u !NBOND: bonds\n", parm.Bonds().size() + parm.BondsH().size());
idx = 1;
for (BondArray::const_iterator bond = parm.BondsH().begin();
bond != parm.BondsH().end(); ++bond, ++idx)
{
outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
if ((idx % 4)==0) outfile.Printf("\n");
}
for (BondArray::const_iterator bond = parm.Bonds().begin();
bond != parm.Bonds().end(); ++bond, ++idx)
{
outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
if ((idx % 4)==0) outfile.Printf("\n");
}
if ((idx % 4)!=0) outfile.Printf("\n");
outfile.Printf("\n");
// Write NTHETA section
outfile.Printf("%8u !NTHETA: angles\n", parm.Angles().size() + parm.AnglesH().size());
idx = 1;
for (AngleArray::const_iterator ang = parm.AnglesH().begin();
ang != parm.AnglesH().end(); ++ang, ++idx)
{
outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
if ((idx % 3)==0) outfile.Printf("\n");
}
for (AngleArray::const_iterator ang = parm.Angles().begin();
ang != parm.Angles().end(); ++ang, ++idx)
{
outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
if ((idx % 3)==0) outfile.Printf("\n");
}
if ((idx % 3)==0) outfile.Printf("\n");
outfile.Printf("\n");
// Write out NPHI section
outfile.Printf("%8u !NPHI: dihedrals\n", parm.Dihedrals().size() + parm.DihedralsH().size());
idx = 1;
for (DihedralArray::const_iterator dih = parm.DihedralsH().begin();
dih != parm.DihedralsH().end(); ++dih, ++idx)
{
outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
if ((idx % 2)==0) outfile.Printf("\n");
}
for (DihedralArray::const_iterator dih = parm.Dihedrals().begin();
dih != parm.Dihedrals().end(); ++dih, ++idx)
{
outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
if ((idx % 2)==0) outfile.Printf("\n");
}
if ((idx % 2)==0) outfile.Printf("\n");
outfile.Printf("\n");
outfile.CloseFile();
return 0;
}
/** 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;
}
