C++ Topology::SoluteResidues方法代码示例

/** Perform setup required for per residue rmsd calculation.
  * Need to set up a target mask, reference mask, and dataset for each
  * residue specified in ResRange.
  * NOTE: Residues in the range arguments from user start at 1, internal
  *       res nums start from 0.
  */
int Action_Rmsd::perResSetup(Topology const& currentParm, Topology const& refParm) {
  Range tgt_range; // Selected target residues
  Range ref_range; // Selected reference residues

  // If no target range previously specified do all solute residues
  if (TgtRange_.Empty()) { 
    tgt_range = currentParm.SoluteResidues();
    tgt_range.ShiftBy(1); // To match user range arg which would start from 1
  } else
    tgt_range = TgtRange_;
  // If the reference range is empty, set it to match the target range
  if (RefRange_.Empty()) 
    ref_range = tgt_range;
  else
    ref_range = RefRange_;
  // Check that the number of reference residues matches number of target residues
  if (tgt_range.Size() != ref_range.Size()) {
    mprintf("Warning: Number of target residues %i does not match\n"
            "Warning:   number of reference residues %i.\n",
            tgt_range.Size(), ref_range.Size());
    return 1;
  }

  // Setup a dataset, target mask, and reference mask for each residue.
  int maxNatom = 0;
  Range::const_iterator ref_it = ref_range.begin();
  MetaData md(rmsd_->Meta().Name(), "res");
  md.SetScalarMode( MetaData::M_RMS );
  for (Range::const_iterator tgt_it = tgt_range.begin();
                             tgt_it != tgt_range.end(); ++tgt_it, ++ref_it)
  {
    int tgtRes = *tgt_it;
    int refRes = *ref_it;
    // Check if either the residue num or the reference residue num out of range.
    if ( tgtRes < 1 || tgtRes > currentParm.Nres()) {
      mprintf("Warning: Specified residue # %i is out of range.\n", tgtRes);
      continue;
    }
    if ( refRes < 1 || refRes > refParm.Nres() ) {
      mprintf("Warning: Specified reference residue # %i is out of range.\n", refRes);
      continue;
    }
    // Check if a perResType has been set for this residue # yet.
    perResArray::iterator PerRes;
    for (PerRes = ResidueRMS_.begin(); PerRes != ResidueRMS_.end(); ++PerRes)
      if ( PerRes->data_->Meta().Idx() == tgtRes ) break;
    // If necessary, create perResType for residue
    if (PerRes == ResidueRMS_.end()) {
      perResType p;
      md.SetIdx( tgtRes );
      md.SetLegend( currentParm.TruncResNameNum(tgtRes-1) );
      p.data_ = (DataSet_1D*)masterDSL_->AddSet(DataSet::DOUBLE, md);
      if (p.data_ == 0) {
        mprinterr("Internal Error: Could not set up per residue data set.\n");
        return 2;
      }
      if (perresout_ != 0) perresout_->AddDataSet( p.data_ );
      // Setup mask strings. Note that masks are based off user residue nums
      p.tgtResMask_.SetMaskString(":" + integerToString(tgtRes) + perresmask_);
      p.refResMask_.SetMaskString(":" + integerToString(refRes) + perresmask_);
      ResidueRMS_.push_back( p );
      PerRes = ResidueRMS_.end() - 1;
    }
    PerRes->isActive_ = false;
    // Setup the reference mask
    if (refParm.SetupIntegerMask(PerRes->refResMask_)) {
      mprintf("Warning: Could not setup reference mask for residue %i\n",refRes);
      continue;
    }
    if (PerRes->refResMask_.None()) {
      mprintf("Warning: No atoms selected for reference residue %i\n",refRes);
      continue;
    }
    // Setup the target mask
    if (currentParm.SetupIntegerMask(PerRes->tgtResMask_)) {
      mprintf("Warning: Could not setup target mask for residue %i\n",tgtRes);
      continue;
    }
    if (PerRes->tgtResMask_.None()) {
      mprintf("Warning: No atoms selected for target residue %i\n",tgtRes);
      continue;
    }
    // Check that # atoms in target and reference masks match
    if (PerRes->tgtResMask_.Nselected() != PerRes->refResMask_.Nselected()) {
      mprintf("Warning: Res %i: # atoms in Tgt (%i) != # atoms in Ref (%i)\n",
              tgtRes, PerRes->tgtResMask_.Nselected(), PerRes->refResMask_.Nselected());
      if (debug_ > 0) {
        mprintf("    Target Atoms:\n");
        for (AtomMask::const_iterator t = PerRes->tgtResMask_.begin();
                                      t != PerRes->tgtResMask_.end(); ++t)
          mprintf("\t%s\n", currentParm.AtomMaskName(*t).c_str());
        mprintf("    Ref Atoms:\n");
        for (AtomMask::const_iterator r = PerRes->refResMask_.begin();
                                      r != PerRes->refResMask_.end(); ++r)
//.........这里部分代码省略.........