C++ Topology::Nsolvent方法代码示例

/** Like the strip action, closest will modify the current parm keeping info
  * for atoms in mask plus the closestWaters solvent molecules. Set up the
  * vector of MolDist objects, one for every solvent molecule in the original
  * parm file. Atom masks for each solvent molecule will be set up.
  */
Action_Closest::RetType Action_Closest::Setup(Topology const& topIn, CoordinateInfo const& cInfoIn)
{
  // If there are no solvent molecules this action is not valid.
  if (topIn.Nsolvent()==0) {
    mprintf("Warning: Parm %s does not contain solvent.\n",topIn.c_str());
    return Action_Closest::SKIP;
  }
  // If # solvent to keep >= solvent in this parm the action is not valid.
  if (closestWaters_ >= topIn.Nsolvent()) {
    mprintf("Warning: # solvent to keep (%i) >= # solvent molecules in '%s' (%i)\n",
            closestWaters_, topIn.c_str(), topIn.Nsolvent());
    return Action_Closest::SKIP;
  }
  image_.SetupImaging( cInfoIn.TrajBox().Type() );
  if (image_.ImagingEnabled())
    mprintf("\tDistances will be imaged.\n");
  else
    mprintf("\tImaging off.\n"); 
  // LOOP OVER MOLECULES
  // 1: Check that all solvent molecules contain same # atoms. Solvent 
  //    molecules must be identical for the command to work properly; 
  //    the prmtop strip occurs only once so the solvent params become fixed.
  // 2: Set up a mask for all solvent molecules.
  SolventMols_.clear();
  // NOTE: May not be necessary to init 'solvent'
  MolDist solvent;
  solvent.D = 0.0;
  solvent.mol = 0;
  SolventMols_.resize(topIn.Nsolvent(), solvent);
  std::vector<MolDist>::iterator mdist = SolventMols_.begin();
  // 3: Set up the soluteMask for all non-solvent molecules.
  int molnum = 1;
  int nclosest = 0;
  int NsolventAtoms = -1;
  for (Topology::mol_iterator Mol = topIn.MolStart();
                              Mol != topIn.MolEnd(); ++Mol)
  {
    if ( Mol->IsSolvent() ) {
      // Solvent, check for same # of atoms.
      if (NsolventAtoms == -1)
        NsolventAtoms = Mol->NumAtoms();
      else if ( NsolventAtoms != Mol->NumAtoms() ) {
        mprinterr("Error: Solvent molecules in '%s' are not of uniform size.\n"
                  "Error:   First solvent mol = %i atoms, solvent mol %i = %i atoms.\n",
                  topIn.c_str(), NsolventAtoms, molnum, (*Mol).NumAtoms());
        return Action_Closest::ERR;
      }
      // mol here is the output molecule number which is why it starts from 1.
      mdist->mol = molnum;
      // Solvent molecule mask
      mdist->mask.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() );
      // Atoms in the solvent molecule to actually calculate distances to.
      if (firstAtom_) {
        mdist->solventAtoms.assign(1, Mol->BeginAtom() );
      } else {
        mdist->solventAtoms.clear();
        mdist->solventAtoms.reserve( Mol->NumAtoms() );
        for (int svatom = Mol->BeginAtom(); svatom < Mol->EndAtom(); svatom++)
          mdist->solventAtoms.push_back( svatom );
      }
      if (debug_ > 0) {
        mprintf("DEBUG:\tSet up mol %i:", mdist->mol); // DEBUG
        mdist->mask.PrintMaskAtoms("solvent"); // DEBUG
        mprintf("\n"); // DEBUG
      }
      ++mdist;
    }
    ++molnum;
  }

  // Setup distance atom mask
  // NOTE: Should ensure that no solvent atoms are selected!
  if ( topIn.SetupIntegerMask(distanceMask_) ) return Action_Closest::ERR;
  if (distanceMask_.None()) {
    mprintf("Warning: Distance mask '%s' contains no atoms.\n",
            distanceMask_.MaskString());
    return Action_Closest::SKIP;
  }
  distanceMask_.MaskInfo();

  // Check the total number of solvent atoms to be kept.
  NsolventAtoms *= closestWaters_;
  mprintf("\tKeeping %i solvent atoms.\n",NsolventAtoms);
  if (NsolventAtoms < 1) {
    mprintf("Warning: # of solvent atoms to be kept is < 1.\n");
    return Action_Closest::SKIP;
  }
  NsolventMolecules_ = (int)SolventMols_.size();

  return Action_Closest::OK;
}