C++ PDB::readFromFilepointer方法代码示例

PathMSDBase::PathMSDBase(const ActionOptions&ao):
PLUMED_COLVAR_INIT(ao),
neigh_size(-1),
neigh_stride(-1),
nframes(0)
{
  parse("LAMBDA",lambda);
  parse("NEIGH_SIZE",neigh_size);
  parse("NEIGH_STRIDE",neigh_stride);
  parse("REFERENCE",reference);

  // open the file
  FILE* fp=fopen(reference.c_str(),"r");
  std::vector<AtomNumber> aaa;
  if (fp!=NULL)
  {
    log<<"Opening reference file "<<reference.c_str()<<"\n";
    bool do_read=true;
    while (do_read){
         PDB mypdb; 
         RMSD mymsd(log); 
         do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
         if(do_read){
            unsigned nat=0;
            nframes++;
            if(mypdb.getAtomNumbers().size()==0) error("number of atoms in a frame should be more than zero");
            if(nat==0) nat=mypdb.getAtomNumbers().size();
            if(nat!=mypdb.getAtomNumbers().size()) error("frames should have the same number of atoms");
            if(aaa.empty()) aaa=mypdb.getAtomNumbers();
            if(aaa!=mypdb.getAtomNumbers()) error("frames should contain same atoms in same order");
            log<<"Found PDB: "<<nframes<<" containing  "<<mypdb.getAtomNumbers().size()<<" atoms\n"; 
	    pdbv.push_back(mypdb); 
//            requestAtoms(mypdb.getAtomNumbers()); // is done in non base classes 
            derivs_s.resize(mypdb.getAtomNumbers().size());
            derivs_z.resize(mypdb.getAtomNumbers().size());
            mymsd.set(mypdb,"OPTIMAL");
            msdv.push_back(mymsd); // the vector that stores the frames
            //log<<mypdb; 
         }else{break ;}
    }
    fclose (fp);
    log<<"Found TOTAL "<<nframes<< " PDB in the file "<<reference.c_str()<<" \n"; 
    if(nframes==0) error("at least one frame expected");
  } 
  if(neigh_stride>0 || neigh_size>0){
           if(neigh_size>int(nframes)){
           	log.printf(" List size required ( %d ) is too large: resizing to the maximum number of frames required: %u  \n",neigh_size,nframes);
 		neigh_size=nframes;
           }
           log.printf("  Neighbor list enabled: \n");
           log.printf("                size   :  %d elements\n",neigh_size);
           log.printf("                stride :  %d timesteps \n",neigh_stride);
  }else{
           log.printf("  Neighbor list NOT enabled \n");
  }

}

Mapping::Mapping(const ActionOptions&ao):
Action(ao),
ActionAtomistic(ao),
ActionWithArguments(ao),
ActionWithValue(ao),
ActionWithVessel(ao)
{
  // Read the input
  std::string mtype; parse("TYPE",mtype);
  bool skipchecks; parseFlag("DISABLE_CHECKS",skipchecks);
  // Setup the object that does the mapping
  mymap = new PointWiseMapping( mtype, skipchecks ); 
 
  // Read the properties we require
  if( keywords.exists("PROPERTY") ){
     std::vector<std::string> property;
     parseVector("PROPERTY",property);
     if(property.size()==0) error("no properties were specified");
     mymap->setPropertyNames( property, false );
  } else {
     std::vector<std::string> property(1); 
     property[0]="sss";
     mymap->setPropertyNames( property, true );
  }

  // Open reference file
  std::string reference; parse("REFERENCE",reference); 
  FILE* fp=fopen(reference.c_str(),"r"); 
  if(!fp) error("could not open reference file " + reference );

  // Read all reference configurations 
  bool do_read=true; std::vector<double> weights; 
  unsigned nfram=0, wnorm=0., ww;
  while (do_read){
     PDB mypdb; 
     // Read the pdb file
     do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
     // Fix argument names
     expandArgKeywordInPDB( mypdb );
     if(do_read){
        mymap->readFrame( mypdb ); ww=mymap->getWeight( nfram ); 
        weights.push_back( ww );
        wnorm+=ww; nfram++;
     } else {
        break;
     }
  }
  fclose(fp); 

  if(nfram==0 ) error("no reference configurations were specified");
  log.printf("  found %d configurations in file %s\n",nfram,reference.c_str() );
  for(unsigned i=0;i<weights.size();++i) weights[i] /= wnorm;
  mymap->setWeights( weights );

  // Finish the setup of the mapping object
  // Get the arguments and atoms that are required
  std::vector<AtomNumber> atoms; std::vector<std::string> args;
  mymap->getAtomAndArgumentRequirements( atoms, args );
  requestAtoms( atoms ); std::vector<Value*> req_args;
  interpretArgumentList( args, req_args ); requestArguments( req_args );
  // Duplicate all frames (duplicates are used by sketch-map)
  mymap->duplicateFrameList(); 
  fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
  plumed_assert( !mymap->mappingNeedsSetup() );
  // Resize all derivative arrays
  mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
  // Resize forces array
  if( getNumberOfAtoms()>0 ){ 
     forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
  } else {
     forcesToApply.resize( getNumberOfArguments() );
  }
}