OpenStructure: stage/include/ost/mol/alg/pdbize.hh Source File

00001 //------------------------------------------------------------------------------
00002 // This file is part of the OpenStructure project <www.openstructure.org>
00003 //
00004 // Copyright (C) 2008-2011 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_MOL_ALG_PDBIZE_HH
00020 #define OST_MOL_ALG_PDBIZE_HH
00021 
00022 #include <ost/mol/entity_view.hh>
00023 #include <ost/mol/entity_handle.hh>
00024 #include <ost/mol/residue_handle.hh>
00025 #include <ost/seq/sequence_list.hh>
00026 #include "module_config.hh"
00027 
00028 namespace ost { namespace mol { namespace alg {
00029 
00030 
00031 extern const char* POLYPEPTIDE_CHAIN_NAMES;
00032 extern const char* LIGAND_CHAIN_NAME;
00033 extern const char* WATER_CHAIN_NAME;
00034 
00035 class DLLEXPORT_OST_MOL_ALG PDBize {
00036 public:
00037   explicit PDBize(int min_polymer_size=10):
00038     min_polymer_size_(min_polymer_size), ent_(mol::CreateEntity()),
00039     curr_chain_name_(POLYPEPTIDE_CHAIN_NAMES), needs_adjustment_(false),
00040     last_rnum_(0)
00041   {}
00042 
00043   void Add(mol::EntityView asu, const geom::Mat4List& transforms,
00044            seq::SequenceList seqres);
00045 
00046   EntityHandle Finish(bool shift_to_fit=true);
00047 private:
00048   int                                   min_polymer_size_;
00049   EntityHandle                          ent_;
00050   ChainHandle                           ligand_chain_;
00051   ChainHandle                           water_chain_;
00052   const char*                           curr_chain_name_;
00053   bool                                  needs_adjustment_;
00054   int                                   last_rnum_;
00055   ResNum                                last_water_rnum_;
00056   std::map<ResidueHandle,ResidueHandle> dst_to_src_map_;
00057 };
00058 
00059 }}}
00060 #endif
00061