Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2023 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_tools_ERMSD_h
      23             : #define __PLUMED_tools_ERMSD_h
      24             : 
      25             : #include "Tensor.h"
      26             : #include "Vector.h"
      27             : #include <vector>
      28             : #include <limits>
      29             : #include <string>
      30             : #include <map>
      31             : #include <utility>
      32             : #include <cstddef>
      33             : 
      34             : namespace PLMD {
      35             : 
      36             : class PDB;
      37             : class Pbc;
      38             : 
      39             : /// A class that implements ERMSD calculations
      40             : class ERMSD {
      41             :   //std::map< std::pair <unsigned,unsigned> , double> targets;
      42             :   //unsigned natoms;
      43             :   std::vector<Vector4d> reference_mat;
      44             :   std::size_t natoms;
      45             :   std::size_t nresidues;
      46             :   std::vector<std::pair <unsigned,unsigned> > pairs;
      47             :   double cutoff;
      48             : 
      49             : public:
      50             : /// Constructor
      51           4 :   ERMSD(): natoms(0),nresidues(0), cutoff(0.0) {}
      52             : 
      53             : /// clear the structure
      54             :   void clear();
      55             : 
      56             :   bool inPair(unsigned i, unsigned j);
      57             : 
      58             : /// set reference coordinates
      59             :   void setReference(const std::vector<Vector> & reference, const std::vector<unsigned> & pairs_vec,double mycutoff=0.24);
      60             : 
      61             :   void calcMat(const std::vector<Vector> & positions, const Pbc& pbc,std::vector<Vector4d> &mat,std::vector<TensorGeneric<4,3> > & Gderivatives);
      62             : 
      63             : /// Compute ermsd ( no pbc )
      64             : //  double calculate(const std::vector<Vector> & positions,
      65             : //                   std::vector<Vector> &derivatives, Tensor& virial) const ;
      66             : /// Compute ermsd ( with pbc )
      67             :   double calculate(const std::vector<Vector>& positions, const Pbc& pbc,std::vector<Vector> &derivatives, Tensor& virial);
      68             : };
      69             : 
      70             : }
      71             : 
      72             : #endif
      73             :