Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 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_core_GenericMolInfo_h
      23             : #define __PLUMED_core_GenericMolInfo_h
      24             : 
      25             : #include "ActionSetup.h"
      26             : #include "ActionPilot.h"
      27             : #include "ActionAtomistic.h"
      28             : #include "ActionAnyorder.h"
      29             : #include "tools/Exception.h"
      30             : #include "tools/ForwardDecl.h"
      31             : #include "tools/Subprocess.h"
      32             : #include <memory>
      33             : #include <map>
      34             : 
      35             : namespace PLMD {
      36             : 
      37             : class PDB;
      38             : 
      39             : class GenericMolInfo :
      40             :   public ActionAnyorder,
      41             :   public ActionPilot,
      42             :   public ActionAtomistic {
      43             : private:
      44             :   ForwardDecl<PDB> pdb_fwd;
      45             : /// A pdb file containing the topology
      46             :   PDB& pdb=*pdb_fwd;
      47             : /// The type of molecule in the pdb
      48             :   std::string mytype;
      49             : /// The name of the reference pdb file
      50             :   std::string reference;
      51             : /// The backbone that was read in from the pdb file
      52             :   std::vector< std::vector<AtomNumber> > read_backbone;
      53             : /// Python interpreter is enabled
      54             :   bool enablePythonInterpreter=false;
      55             : /// Python command
      56             :   std::string pythonCmd;
      57             : /// Selector subprocess
      58             :   std::unique_ptr<Subprocess> selector;
      59             : /// Track is selector is running
      60             : /// Needed on Get_rank()>0
      61             :   bool selector_running=false;
      62             : /// Structure in pdb file is whole
      63             :   bool iswhole_;
      64             : public:
      65             :   ~GenericMolInfo();
      66        5357 :   void calculate() override {}
      67        5357 :   void apply() override {}
      68             :   static void registerKeywords( Keywords& keys );
      69             :   static std::map<std::string,std::string> getSpecialKeywords();
      70             :   explicit GenericMolInfo(const ActionOptions&ao);
      71             :   void getBackbone( std::vector<std::string>& resstrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone );
      72             :   std::string getAtomName(AtomNumber a)const;
      73             :   bool checkForAtom(AtomNumber a)const;
      74             :   unsigned getResidueNumber(AtomNumber a)const;
      75             :   std::string getChainID(AtomNumber a)const;
      76             :   Vector getPosition(AtomNumber a)const;
      77             :   bool isWhole() const;
      78             :   unsigned getPDBsize()const ;
      79             :   std::string getResidueName(AtomNumber a)const;
      80             :   void interpretSymbol( const std::string& symbol, std::vector<AtomNumber>& atoms );
      81             : /// Calculate is used to kill the python interpreter.
      82             : /// We do this in order to avoid possible interference or slowing down of the simulation
      83             : /// due to the extra subprocess.
      84             :   void prepare() override;
      85             : };
      86             : 
      87             : }
      88             : 
      89             : #endif