Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2019 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_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             : 
      33             : namespace PLMD {
      34             : 
      35             : class PDB;
      36             : class Pbc;
      37             : 
      38             : /// A class that implements ERMSD calculations
      39           8 : class ERMSD {
      40             :   //std::map< std::pair <unsigned,unsigned> , double> targets;
      41             :   //unsigned natoms;
      42             :   std::vector<Vector4d> reference_mat;
      43             :   unsigned natoms;
      44             :   unsigned nresidues;
      45             :   std::vector<std::pair <unsigned,unsigned> > pairs;
      46             :   double cutoff;
      47             : 
      48             : public:
      49             : /// Constructor
      50          12 :   ERMSD(): natoms(0),nresidues(0), cutoff(0.0) {}
      51             : 
      52             : /// clear the structure
      53             :   void clear();
      54             : 
      55             :   bool inPair(unsigned i, unsigned j);
      56             : 
      57             : /// set reference coordinates
      58             :   void setReference(const std::vector<Vector> & reference, const std::vector<unsigned> & pairs_vec,double mycutoff=0.24);
      59             : 
      60             :   void calcMat(const std::vector<Vector> & positions, const Pbc& pbc,std::vector<Vector4d> &mat,std::vector<TensorGeneric<4,3> > & Gderivatives);
      61             : 
      62             : /// Compute ermsd ( no pbc )
      63             : //  double calculate(const std::vector<Vector> & positions,
      64             : //                   std::vector<Vector> &derivatives, Tensor& virial) const ;
      65             : /// Compute ermsd ( with pbc )
      66             :   double calculate(const std::vector<Vector>& positions, const Pbc& pbc,std::vector<Vector> &derivatives, Tensor& virial);
      67             : };
      68             : 
      69             : }
      70             : 
      71             : #endif
      72             :