1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 Copyright (c) 2013-2021 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_MolDataClass_h 23 #define __PLUMED_tools_MolDataClass_h 24 25 #include <vector> 26 #include <string> 27 #include "AtomNumber.h" 28 29 namespace PLMD { 30 31 class PDB; 32 33 /// This class provides information on various kinds of molecules 34 /// for instance the kinds of residues that are in a protein 35 /// the atoms involved in the backbone of a particular residue etc 36 class MolDataClass { 37 public: 38 /// Return true if the residue name is one of the allowed reisude names e.g. one of the 20 amino acids for proteins 39 static bool allowedResidue( const std::string& type, const std::string& residuename ); 40 /// Return the number of atoms in the backbone per residue e.g. 5 for proteins 41 static unsigned numberOfAtomsPerResidueInBackbone( const std::string& type ); 42 /// Return the names of the atoms in the backbone e.g. N, CA, CB, C, O for most protein residues 43 static void getBackboneForResidue( const std::string& type, const unsigned& residuenum, const PDB& mypdb, std::vector<AtomNumber>& atoms ); 44 /// Return true if the residue is a terminal group e.g. ACE, NME for proteins 45 static bool isTerminalGroup( const std::string& type, const std::string& residuename ); 46 /// Used to interpret special symbols - currently phi and psi and omega 47 static void specialSymbol( const std::string& type, const std::string& symbol, const PDB& mypdb, std::vector<AtomNumber>& numbers ); 48 }; 49 50 } 51 #endif 52