C++ Topology::Bonds方法代码示例

/** 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;
}

//.........这里部分代码省略.........
  * \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;
}