Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2020 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_secondarystructure_SecondaryStructureRMSD_h
      23             : #define __PLUMED_secondarystructure_SecondaryStructureRMSD_h
      24             : 
      25             : #include "core/ActionWithVector.h"
      26             : #include "tools/RMSD.h"
      27             : #include <vector>
      28             : 
      29             : namespace PLMD {
      30             : 
      31             : class ActionShortcut;
      32             : 
      33             : namespace secondarystructure {
      34             : 
      35             : /// Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
      36             : 
      37             : class SecondaryStructureRMSD : public ActionWithVector {
      38             : private:
      39             : /// Are we operating without periodic boundary conditions
      40             :   bool nopbc;
      41             : /// The type of rmsd we are calculating
      42             :   std::string alignType;
      43             : /// List of all the atoms we require
      44             :   std::vector<AtomNumber> all_atoms;
      45             : /// The list of tasks that we need to do on the round
      46             :   std::vector<unsigned> ss_tasks;
      47             : /// The atoms involved in each of the secondary structure segments
      48             :   std::vector< std::vector<unsigned> > colvar_atoms;
      49             : /// The list of reference configurations
      50             :   std::vector<RMSD> myrmsd;
      51             :   std::vector<std::map<std::pair<unsigned,unsigned>, double> > drmsd_targets;
      52             : /// Variables for strands cutoff
      53             :   bool align_strands;
      54             :   double s_cutoff2;
      55             :   unsigned align_atom_1, align_atom_2;
      56             :   bool verbose_output;
      57             : /// Get the index of an atom
      58             :   unsigned getAtomIndex( const unsigned& current, const unsigned& iatom ) const ;
      59             : public:
      60             :   static void registerKeywords( Keywords& keys );
      61             :   static void readBackboneAtoms( ActionShortcut* action, PlumedMain& plumed, const std::string& backnames, std::vector<unsigned>& chain_lengths, std::string& all_atoms );
      62             :   static bool readShortcutWords( std::string& ltmap, ActionShortcut* action );
      63             :   static void expandShortcut( const bool& uselessthan, const std::string& labout, const std::string& labin, const std::string& ltmap, ActionShortcut* action );
      64             :   explicit SecondaryStructureRMSD(const ActionOptions&);
      65             :   unsigned getNumberOfDerivatives() override ;
      66             :   void areAllTasksRequired( std::vector<ActionWithVector*>& task_reducing_actions ) override;
      67             :   int checkTaskStatus( const unsigned& taskno, int& flag ) const override;
      68             :   void calculate() override;
      69             :   void performTask( const unsigned&, MultiValue& ) const override;
      70             : };
      71             : 
      72             : inline
      73         110 : unsigned SecondaryStructureRMSD::getNumberOfDerivatives() {
      74         110 :   return 3*getNumberOfAtoms()+9;
      75             : }
      76             : 
      77             : inline
      78             : unsigned SecondaryStructureRMSD::getAtomIndex( const unsigned& current, const unsigned& iatom ) const {
      79     4721646 :   return colvar_atoms[current][iatom];
      80             : }
      81             : 
      82             : }
      83             : }
      84             : 
      85             : #endif