1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 Copyright (c) 2016-2021 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 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 ERMSD()50 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 73