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);
}
}
}
}
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;
}