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pdbize.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2011 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 #ifndef OST_MOL_ALG_PDBIZE_HH
20 #define OST_MOL_ALG_PDBIZE_HH
21 
22 #include <ost/mol/entity_view.hh>
23 #include <ost/mol/entity_handle.hh>
25 #include <ost/seq/sequence_list.hh>
26 #include "module_config.hh"
27 
28 namespace ost { namespace mol { namespace alg {
29 
30 
31 extern const char* POLYPEPTIDE_CHAIN_NAMES;
32 extern const char* LIGAND_CHAIN_NAME;
33 extern const char* WATER_CHAIN_NAME;
34 
36 public:
37  explicit PDBize(int min_polymer_size=10):
38  min_polymer_size_(min_polymer_size), ent_(mol::CreateEntity()),
39  curr_chain_name_(POLYPEPTIDE_CHAIN_NAMES), needs_adjustment_(false),
40  last_rnum_(0)
41  {}
42 
43  void Add(mol::EntityView asu, const geom::Mat4List& transforms,
44  seq::SequenceList seqres);
45 
46  EntityHandle Finish(bool shift_to_fit=true);
47 private:
48  int min_polymer_size_;
49  EntityHandle ent_;
50  ChainHandle ligand_chain_;
51  ChainHandle water_chain_;
52  const char* curr_chain_name_;
53  bool needs_adjustment_;
54  int last_rnum_;
55  ResNum last_water_rnum_;
56  std::map<ResidueHandle,ResidueHandle> dst_to_src_map_;
57 };
58 
59 }}}
60 #endif
61