Esempio n. 1
0
void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb, const bool allowblocks  ){
  if( !allowblocks && pdb.getNumberOfAtomBlocks()!=1 ) error("found multi-atom-block pdb format but expecting only one block of atoms");  

  for(unsigned i=0;i<pdb.size();++i){
     indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );
     align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] );
  }
  atom_der_index.resize( reference_atoms.size() );
}
Esempio n. 2
0
void MultiDomainRMSD::read( const PDB& pdb ) {
  unsigned nblocks =  pdb.getNumberOfAtomBlocks();
  if( nblocks<2 ) error("multidomain RMSD only has one block of atoms");

  std::vector<Vector> positions; std::vector<double> align, displace;
  std::string num; blocks.resize( nblocks+1 ); blocks[0]=0;
  for(unsigned i=0; i<nblocks; ++i) blocks[i+1]=pdb.getAtomBlockEnds()[i];

  double tmp, lower=0.0, upper=std::numeric_limits<double>::max( );
  if( pdb.getArgumentValue("LOWER_CUTOFF",tmp) ) lower=tmp;
  if( pdb.getArgumentValue("UPPER_CUTOFF",tmp) ) upper=tmp;
  bool nopbc=pdb.hasFlag("NOPBC");

  domains.resize(0); weights.resize(0);
  for(unsigned i=1; i<=nblocks; ++i) {
    Tools::convert(i,num);
    if( ftype=="RMSD" ) {
      // parse("TYPE"+num, ftype );
      lower=0.0; upper=std::numeric_limits<double>::max( );
      if( pdb.getArgumentValue("LOWER_CUTOFF"+num,tmp) ) lower=tmp;
      if( pdb.getArgumentValue("UPPER_CUTOFF"+num,tmp) ) upper=tmp;
      nopbc=pdb.hasFlag("NOPBC");
    }
    domains.emplace_back( metricRegister().create<SingleDomainRMSD>( ftype ) );
    positions.resize( blocks[i] - blocks[i-1] );
    align.resize( blocks[i] - blocks[i-1] );
    displace.resize( blocks[i] - blocks[i-1] );
    unsigned n=0;
    for(unsigned j=blocks[i-1]; j<blocks[i]; ++j) {
      positions[n]=pdb.getPositions()[j];
      align[n]=pdb.getOccupancy()[j];
      displace[n]=pdb.getBeta()[j];
      n++;
    }
    domains[i-1]->setBoundsOnDistances( !nopbc, lower, upper );
    domains[i-1]->setReferenceAtoms( positions, align, displace );
    domains[i-1]->setupRMSDObject();

    double ww=0;
    if( !pdb.getArgumentValue("WEIGHT"+num,ww) ) weights.push_back( 1.0 );
    else weights.push_back( ww );
  }
  // And set the atom numbers for this object
  indices.resize(0); atom_der_index.resize(0);
  for(unsigned i=0; i<pdb.size(); ++i) { indices.push_back( pdb.getAtomNumbers()[i] ); atom_der_index.push_back(i); }
  // setAtomNumbers( pdb.getAtomNumbers() );
}
Esempio n. 3
0
void MultiDomainRMSD::read( const PDB& pdb ){
   unsigned nblocks =  pdb.getNumberOfAtomBlocks();
   if( nblocks<2 ) error("multidomain RMSD only has one block of atoms");
  
   std::vector<AtomNumber> atomnumbers;
   std::vector<Vector> positions; std::vector<double> align, displace;
   std::string num; blocks.resize( nblocks+1 ); blocks[0]=0;
   for(unsigned i=0;i<nblocks;++i) blocks[i+1]=pdb.getAtomBlockEnds()[i]; 

   double lower=0.0, upper=std::numeric_limits<double>::max( );
   parse("LOWER_CUTOFF",lower,true); 
   parse("UPPER_CUTOFF",upper,true);

   for(unsigned i=1;i<=nblocks;++i){
       Tools::convert(i,num);
       if( ftype=="RMSD" ){
          parse("TYPE"+num, ftype );
          parse("LOWER_CUTOFF"+num,lower,true); 
          parse("UPPER_CUTOFF"+num,upper,true); 
       }
       domains.push_back( metricRegister().create<SingleDomainRMSD>( ftype ) );
       positions.resize( blocks[i] - blocks[i-1] + 1 );
       align.resize( blocks[i] - blocks[i-1] + 1 );
       displace.resize( blocks[i] - blocks[i-1] + 1 );
       unsigned n=0;
       for(unsigned j=blocks[i-1];j<blocks[i];++j){
           positions[n]=pdb.getPositions()[j];
           align[n]=pdb.getOccupancy()[j];
           displace[n]=pdb.getBeta()[j];
           n++;
       }
       domains[i-1]->setBoundsOnDistances( true, lower, upper );  // Currently no option for nopbc
       domains[i-1]->setReferenceAtoms( positions, align, displace );
       domains[i-1]->setNumberOfAtoms( positions.size() );
       
       double ww=0; parse("WEIGHT"+num, ww, true );
       if( ww==0 ) weights.push_back( 1.0 );
       else weights.push_back( ww );
   }   
   // And set the atom numbers for this object
   setAtomNumbers( pdb.getAtomNumbers() );
}