stage/include/ost/mol/mm/modeller.hh
Go to the documentation of this file.00001 //------------------------------------------------------------------------------ 00002 // This file is part of the OpenStructure project <www.openstructure.org> 00003 // 00004 // Copyright (C) 2008-2015 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 00020 #ifndef OST_MM_MODELLER_HH 00021 #define OST_MM_MODELLER_HH 00022 00023 00024 #include <vector> 00025 #include <set> 00026 00027 #include <ost/platform.hh> 00028 #include <ost/io/mol/pdb_reader.hh> 00029 #include <ost/mol/entity_handle.hh> 00030 #include <ost/mol/residue_handle.hh> 00031 #include <ost/mol/atom_handle.hh> 00032 #include <ost/geom/vec3.hh> 00033 #include <ost/geom/composite.hh> 00034 #include <ost/geom/transform.hh> 00035 #include <ost/mol/xcs_editor.hh> 00036 #include <ost/mol/bond_handle.hh> 00037 #include <ost/message.hh> 00038 #include <ost/mol/bounding_box.hh> 00039 #include <ost/mol/mm/buildingblock.hh> 00040 #include <ost/mol/mm/forcefield.hh> 00041 #include <ost/mol/mm/settings.hh> 00042 #include <ost/mol/mm/index.hh> 00043 #include <ost/mol/mm/topology.hh> 00044 #include <ost/conop/heuristic.hh> 00045 #include <ost/mol/spatial_organizer.hh> 00046 00047 00048 namespace ost { namespace mol{ namespace mm{ 00049 00050 class Modeller{ 00051 public: 00052 00053 static void GenerateDisulfidBonds(ost::mol::EntityHandle& handle); 00054 00055 //may sound pretty stupid... 00056 //But this is necessary if we want to compare our energies with 00057 //the energies calculated by gromacs. When ost writes and entity 00058 //down to disk, it uses 3 digits precision. 00059 //If we feed this into gromacs, it also produces a topology 00060 //with three digits precision. The problem is, that gromacs 00061 //uses nm, therefore the precision gets lowered tenfold. 00062 //To take care of that it is necessary to lower our precision... 00063 static void LowerPrecision(ost::mol::EntityHandle& handle); 00064 00065 static void AssignPDBNaming(ost::mol::EntityHandle& handle); 00066 00067 static void AssignGromacsNaming(ost::mol::EntityHandle& handle); 00068 }; 00069 00070 00071 }}} 00072 00073 #endif
