Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2019 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #ifndef __PLUMED_reference_DRMSD_h
      23             : #define __PLUMED_reference_DRMSD_h
      24             : 
      25             : #include <vector>
      26             : #include <string>
      27             : #include <map>
      28             : #include "SingleDomainRMSD.h"
      29             : 
      30             : namespace PLMD {
      31             : 
      32          84 : class DRMSD : public SingleDomainRMSD {
      33             : private:
      34             :   bool nopbc;
      35             : protected:
      36             :   bool bounds_were_set;
      37             :   double lower, upper;
      38             :   std::map< std::pair <unsigned,unsigned>, double> targets;
      39             : /// Read in NOPBC, LOWER_CUTOFF and UPPER_CUTOFF
      40             :   void readBounds();
      41             : public:
      42             :   explicit DRMSD( const ReferenceConfigurationOptions& ro );
      43             : /// This sets upper and lower bounds on distances to be used in DRMSD
      44             :   void setBoundsOnDistances( bool dopbc, double lbound=0.0, double ubound=std::numeric_limits<double>::max( ) );
      45             : /// Check that similar comparisons are being performed - perhaps this is needed ask Davide? GAT
      46             : //  void check( ReferenceConfiguration* , ReferenceConfiguration* );
      47             :   virtual void read( const PDB& );
      48             :   virtual void setup_targets();
      49             :   void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in );
      50             :   double calc( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const ;
      51             : };
      52             : 
      53             : }
      54             : #endif
      55             :