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chemdict_parser.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_CONOP_CHEMDICT_PARSER_HH
20 #define OST_CONOP_CHEMDICT_PARSER_HH
21 
22 /*
23  Author: Marco Biasini
24  */
25 
26 
27 #include <ost/mol/chem_class.hh>
28 #include <ost/mol/chem_type.hh>
31 
32 namespace ost { namespace io {
33 
34 typedef enum {
35  ATOM_SPEC,
36  BOND_SPEC,
37  DESC_SPEC,
38  DONT_KNOW
39 } LoopType;
40 
41 class DLLEXPORT_OST_IO ChemdictParser : public StarParser {
42 public:
43  ChemdictParser(std::istream& stream, conop::Compound::Dialect dialect):
44  StarParser(stream), compound_(new conop::Compound("UNK")),
45  last_(0), loop_type_(DONT_KNOW), dialect_(dialect)
46  {
47  this->InitTypeMap();
48  this->InitPDBXTypeMap();
49  }
50 
51  virtual bool OnBeginData(const StringRef& data_name);
52 
53  virtual bool OnBeginLoop(const StarLoopDesc& header);
54 
55  virtual void OnDataRow(const StarLoopDesc& header,
56  const std::vector<StringRef>& columns);
57 
58  virtual void OnDataItem(const StarDataItem& item);
59 
60  virtual void OnEndData();
61 
63  {
64  lib_=lib;
65  }
66 private:
67  void InitTypeMap();
68  void InitPDBXTypeMap();
70  conop::CompoundPtr compound_;
71  typedef enum {
72  ATOM_NAME=0,
73  ALT_ATOM_NAME=1,
74  IS_AROMATIC=2,
75  ORDINAL=3,
76  IS_LEAVING=4,
77  ELE=5,
78  STEREO_CONF=6,
79  ATOM_ID1=0,
80  ATOM_ID2=1,
81  BOND_ORDER=2,
82  DESC_TYPE=0,
83  DESC=1
84  } PropIndex;
85  char last_;
86  int indices_[10];
87  bool insert_;
88  static std::map<String, mol::ChemClass> tm_;
89  static std::map<String, mol::ChemType> xtm_;
90  std::map<String, int> atom_map_;
91  LoopType loop_type_;
92  conop::AtomSpec atom_;
93  conop::Compound::Dialect dialect_;
94 };
95 
96 
97 }}
98 
99 
100 #endif
ChemdictParser(std::istream &stream, conop::Compound::Dialect dialect)
convenient datatype for referencing character data
Definition: string_ref.hh:39
parser for the STAR file format
Definition: star_parser.hh:114
boost::shared_ptr< CompoundLib > CompoundLibPtr
Definition: compound_lib.hh:34
boost::shared_ptr< Compound > CompoundPtr
Definition: compound.hh:131
#define DLLEXPORT_OST_IO
void SetCompoundLib(const conop::CompoundLibPtr &lib)