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_SingleDomainRMSD_h
      23             : #define __PLUMED_reference_SingleDomainRMSD_h
      24             : 
      25             : #include "ReferenceAtoms.h"
      26             : 
      27             : namespace PLMD {
      28             : 
      29             : class Pbc;
      30             : 
      31        1033 : class SingleDomainRMSD : public ReferenceAtoms {
      32             : protected:
      33             :   void readReference( const PDB& pdb );
      34             : public:
      35             :   explicit SingleDomainRMSD( const ReferenceConfigurationOptions& ro );
      36             : /// Set the reference structure
      37             :   virtual void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in );
      38             : /// Calculate
      39             :   double calc( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals, const std::vector<double>& arg, ReferenceValuePack& myder, const bool& squared ) const;
      40             :   double calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const;
      41             : /// Calculate the distance using the input position
      42             :   virtual double calc( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const=0;
      43             : /// This sets upper and lower bounds on distances to be used in DRMSD (here it does nothing)
      44          32 :   virtual void setBoundsOnDistances( bool dopbc, double lbound=0.0, double ubound=std::numeric_limits<double>::max( ) ) {};
      45             : /// This is used by MultiDomainRMSD to setup the RMSD object in Optimal RMSD type
      46          31 :   virtual void setupRMSDObject() {};
      47             : };
      48             : 
      49             : }
      50             : 
      51             : #endif