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_MultiDomainRMSD_h
      23             : #define __PLUMED_reference_MultiDomainRMSD_h
      24             : 
      25             : #include "SingleDomainRMSD.h"
      26             : 
      27             : namespace PLMD {
      28             : 
      29             : class Pbc;
      30             : 
      31          15 : class MultiDomainRMSD : public ReferenceAtoms {
      32             : private:
      33             : /// The type of RMSD we are using
      34             :   std::string ftype;
      35             : /// The weight of a block
      36             :   std::vector<double> weights;
      37             : /// Blocks containing start and end points for all the domains
      38             :   std::vector<unsigned> blocks;
      39             : /// Each of the domains we are calculating the distance from
      40             :   std::vector<std::unique_ptr<SingleDomainRMSD>> domains;
      41             : public:
      42             :   explicit MultiDomainRMSD( const ReferenceConfigurationOptions& ro );
      43             : /// Read in the input from a pdb
      44             :   void read( const PDB& ) override;
      45             : /// Set the input from an analysis object (don't know how this will work yet so currently just a plumed_error)
      46             :   void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in ) override;
      47             : /// Calculate
      48             :   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 override;
      49             :   double calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const ;
      50             : ///
      51             :   bool pcaIsEnabledForThisReference() override;
      52             :   void extractAtomicDisplacement( const std::vector<Vector>& pos, std::vector<Vector>& direction ) const override;
      53             :   double projectAtomicDisplacementOnVector( const bool& normalized, const std::vector<Vector>& vecs, ReferenceValuePack& mypack ) const override;
      54             :   void setupPCAStorage( ReferenceValuePack& mypack ) override;
      55             : };
      56             : 
      57             : }
      58             : 
      59             : #endif