Fixed bugs that prevent reading in of metrics in analysis methods correctly

src/dimred/SmacoffMDS.cpp

@@ -65,7 +65,6 @@ DimensionalityReductionBase(ao)
 }
 
 void SmacofMDS::calculateProjections( const Matrix<double>& targets, Matrix<double>& projections ){
-abort();
    // Take the square root of all the distances and the weights
    Matrix<double> weights( targets.nrows(), targets.ncols() );
    Matrix<double> distances( targets.nrows(), targets.ncols() ); 

src/tools/PDB.cpp

@@ -49,7 +49,7 @@ void PDB::setAtomPositions( const std::vector<Vector>& pos ){
 void PDB::setArgumentValue( const std::string& argname, const double& val ){
   bool replaced=false; std::string num; Tools::convert( val, num );
   for(unsigned i=0;i<remark.size();++i){
-      if( remark[i].find(argname+"=")!=std::string::npos){
+      if( remark[i].find(argname+"=")!=std::string::npos && remark[i].find("sigma_")==std::string::npos ){
           remark[i]=argname + "=" + num; replaced=true;
       }
   }