1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 Copyright (c) 2012-2021 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_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 34 namespace PLMD { 35 36 class PDB; 37 38 class GenericMolInfo : 39 public ActionAnyorder, 40 public ActionPilot, 41 public ActionAtomistic { 42 private: 43 ForwardDecl<PDB> pdb_fwd; 44 /// A pdb file containing the topology 45 PDB& pdb=*pdb_fwd; 46 /// The type of molecule in the pdb 47 std::string mytype; 48 /// The name of the reference pdb file 49 std::string reference; 50 /// The backbone that was read in from the pdb file 51 std::vector< std::vector<AtomNumber> > read_backbone; 52 /// Python interpreter is enabled 53 bool enablePythonInterpreter=false; 54 /// Python command 55 std::string pythonCmd; 56 /// Selector subprocess 57 std::unique_ptr<Subprocess> selector; 58 public: 59 ~GenericMolInfo(); calculate()60 void calculate() override {} apply()61 void apply() override {} 62 static void registerKeywords( Keywords& keys ); 63 explicit GenericMolInfo(const ActionOptions&ao); 64 void getBackbone( std::vector<std::string>& resstrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone ); 65 std::string getAtomName(AtomNumber a)const; 66 bool checkForAtom(AtomNumber a)const; 67 unsigned getResidueNumber(AtomNumber a)const; 68 unsigned getPDBsize()const ; 69 std::string getResidueName(AtomNumber a)const; 70 void interpretSymbol( const std::string& symbol, std::vector<AtomNumber>& atoms ); 71 /// Calculate is used to kill the python interpreter. 72 /// We do this in order to avoid possible interference or slowing down of the simulation 73 /// due to the extra subprocess. 74 void prepare() override; 75 }; 76 77 } 78 79 #endif 80