00001 //------------------------------------------------------------------------------ 00002 // This file is part of the OpenStructure project <www.openstructure.org> 00003 // 00004 // Copyright (C) 2008-2010 by the OpenStructure authors 00005 // 00006 // This library is free software; you can redistribute it and/or modify it under 00007 // the terms of the GNU Lesser General Public License as published by the Free 00008 // Software Foundation; either version 3.0 of the License, or (at your option) 00009 // any later version. 00010 // This library is distributed in the hope that it will be useful, but WITHOUT 00011 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 00012 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more 00013 // details. 00014 // 00015 // You should have received a copy of the GNU Lesser General Public License 00016 // along with this library; if not, write to the Free Software Foundation, Inc., 00017 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 00018 //------------------------------------------------------------------------------ 00019 #ifndef OST_CONOP_BUILDER_HH 00020 #define OST_CONOP_BUILDER_HH 00021 00022 /* 00023 Author: Marco Biasini 00024 */ 00025 #include <ost/mol/mol.hh> 00026 00027 #include <ost/conop/module_config.hh> 00028 #include <ost/conop/builder_fw.hh> 00029 00030 namespace ost { namespace conop { 00031 00050 class DLLEXPORT_OST_CONOP Builder { 00051 public: 00052 public: 00053 virtual ~Builder(); 00054 00057 virtual void CompleteAtoms(const mol::ResidueHandle& rh); 00058 00059 00062 virtual void CheckResidueCompleteness(const mol::ResidueHandle& rh); 00063 00066 virtual bool IsResidueComplete(const mol::ResidueHandle& rh); 00067 00070 virtual mol::ResidueKey IdentifyResidue(const mol::ResidueHandle& rh); 00071 00075 virtual void FillResidueProps(mol::ResidueHandle residue); 00076 00077 virtual void FillAtomProps(mol::AtomHandle atom); 00083 virtual void ConnectAtomsOfResidue(const mol::ResidueHandle& rh); 00090 virtual void ConnectResidueToPrev(const mol::ResidueHandle& rh, 00091 const mol::ResidueHandle& prev); 00093 virtual void ConnectResidueToNext(const mol::ResidueHandle& rh, 00094 const mol::ResidueHandle& next); 00095 00097 virtual void AssignTorsions(const mol::ChainHandle& ch); 00098 00100 virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue); 00101 00103 void AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res); 00104 00113 virtual bool DoesPeptideBondExist(const mol::AtomHandle& n, 00114 const mol::AtomHandle& c); 00115 00121 virtual bool IsBondFeasible(const mol::AtomHandle& atom_a, 00122 const mol::AtomHandle& atom_b); 00123 00125 static String GuessAtomElement(const String& atom_name, bool hetatm); 00126 00128 static bool AreResiduesConsecutive(const mol::ResidueHandle& r1, 00129 const mol::ResidueHandle& r2); 00130 00133 void DistanceBasedConnect(const mol::AtomHandle& atom); 00134 }; 00135 00136 00137 }} // ns 00138 00139 #endif
1.5.8