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MMFF94Processors.h
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1 // -*- Mode: C++; tab-width: 2; -*-
2 // vi: set ts=2:
3 //
4 // $Id: MMFF94Processors.h,v 1.1.8.1 2007/03/25 21:25:18 oliver Exp $
5 //
6 
7 #ifndef BALL_MOLMEC_MMFF94_PROCESSORS_H
8 #define BALL_MOLMEC_MMFF94_PROCESSORS_H
9 
10 #ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
11 # include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
12 #endif
13 
14 #ifndef BALL_DATATYPE_HASHSET_H
15 # include <BALL/DATATYPE/hashSet.h>
16 #endif
17 
18 #ifndef BALL_DATATYPE_STRINGHASHMAP_H
19 # include <BALL/DATATYPE/stringHashMap.h>
20 #endif
21 
22 #ifndef BALL_KERNEL_BOND_H
23 # include <BALL/KERNEL/bond.h>
24 #endif
25 
26 #ifndef BALL_STRUCTURE_ATOMTYPER_H
27 # include <BALL/STRUCTURE/atomTyper.h>
28 #endif
29 
30 #include <vector>
31 
32 namespace BALL
33 {
34  using std::vector;
35 
36  class MMFF94ESParameters;
37  class Molecule;
38  class System;
39 
41  class BALL_EXPORT MMFF94AtomTyper
42  : public AtomTyper
43  {
44  public:
45 
46  struct AromaticType
47  {
48  String new_type;
49  Position atomic_number;
50  bool cation;
51  bool anion;
52  };
53 
54  BALL_CREATE(MMFF94AtomTyper)
55 
56 
57  MMFF94AtomTyper();
58 
60  MMFF94AtomTyper(const MMFF94AtomTyper& t);
61 
63  virtual ~MMFF94AtomTyper() {};
64 
66  virtual void assignTo(System& s);
67 
69  virtual bool setupHydrogenTypes(Parameters& p, const String& section);
70 
72  virtual bool setupSymbolsToTypes(Parameters& p, const String& section);
73 
75  virtual bool setupAromaticTypes(Parameters& p, const String& section);
76 
78  void collectHeteroAtomTypes(const MMFF94AtomTypes& atom_types);
79 
80  protected:
81 
82  bool assignAromaticType_5_(Atom& atom, Position L5, bool anion, bool cation);
83 
84  StringHashMap<String> partner_type_to_htype_;
85  StringHashMap<Position> id_to_type_;
86  HashMap<String, AromaticType> aromatic_types_5_map_;
87  HashSet<String> cation_atoms_;
88  MMFF94AtomTypes* atom_types_;
89  HashSet<Position> hetero_atom_types_;
90  };
91 
92 
96  class BALL_EXPORT MMFF94ChargeProcessor
97  : public UnaryProcessor<Atom>
98  {
99  public:
100 
101  BALL_CREATE(MMFF94ChargeProcessor)
102 
103 
104  MMFF94ChargeProcessor();
105 
107  MMFF94ChargeProcessor(const MMFF94ChargeProcessor& cp);
108 
110  virtual ~MMFF94ChargeProcessor() {};
111 
113  const MMFF94ChargeProcessor& operator = (const MMFF94ChargeProcessor& cp)
114  ;
115 
117  virtual void clear()
118  ;
119 
121  virtual bool start();
122 
124  virtual bool finish();
125 
127  virtual Processor::Result operator () (Atom& atom);
128 
130  void assignFormalCharge(Atom& atom);
131 
133  const HashSet<Atom*>& getUnassignedAtoms() { return unassigned_atoms_;}
134 
136  void setESParameters(const MMFF94ESParameters& es) { es_parameters_ = &es; }
137 
139  void setup(const String& filename);
140 
142  void setAromaticRings(const vector<HashSet<Atom*> >& rings) { aromatic_rings_ = rings;}
143 
144  protected:
145 
146  void assignPartialCharges_();
147 
148  vector<Atom*> atoms_;
149  HashSet<Atom*> unassigned_atoms_;
150  const MMFF94ESParameters* es_parameters_;
151  HashMap<String, float> types_to_charges_;
152  HashSet<String> rule_types_;
153  vector<HashSet<Atom*> > aromatic_rings_;
154  };
155 
156 } // namespace BALL
157 
158 #endif // BALL_MOLMEC_MMFF94_PROCESSORS_H
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