BALL  1.5.0
structurePreparer.h
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1 // -*- Mode: C++; tab-width: 2; -*-
2 // vi: set ts=2:
3 //
4 
5 
6 #ifndef BALL_DOCKING_COMMON_STRUCTUREPREPARER_H
7 #define BALL_DOCKING_COMMON_STRUCTUREPREPARER_H
8 
9 #ifndef BALL_KERNEL_ATOMCONTAINER_H
11 #endif
12 
13 #ifndef BALL_STRUCTURE_ADDHYDROGENSPROCESSOR_H
15 #endif
16 
17 #include <set>
18 
19 namespace BALL
20 {
22  {
23  public:
24 
25  StructurePreparer(String type="", bool ignore = 0);
26 
28  void assignAtomTypes(AtomContainer* at, String iniFile, String AtomType_file="");
29 
32 
35 
37 
38  void setScoringType(String type);
39 
42  void assignCharges(AtomContainer* at, int overwrite_mode);
43 
46  bool assignProteinCharges(AtomContainer* at, String parameterFile, int overwrite_mode);
47 
49 
51 
53 
55  void prepare(AtomContainer* at, String parameterFile, String AtomType_file="");
56 
57  void setSimpleAtomTypes(std::set<String>& new_types);
58 
59  const std::set<String>* getSimpleAtomTypes();
60 
61  private:
62 
63  bool setIonStandardCharge(Atom* atom);
64 
65  bool use_mmff94_;
66 
69  bool ignore_unassigned_;
70 
72  bool use_PLP_;
73 
74  std::set<String> simple_atom_types_;
75  };
76 }
77 
78 #endif // BALL_DOCKING_COMMON_STRUCTUREPREPARER_H
Definition: constants.h:13
void setScoringType(String type)
void setSimpleAtomTypes(std::set< String > &new_types)
void assignCharges(AtomContainer *at, int overwrite_mode)
void assignPLPAtomTypes(AtomContainer *at)
void prepare(AtomContainer *at, String parameterFile, String AtomType_file="")
bool assignProteinCharges(AtomContainer *at, String parameterFile, int overwrite_mode)
StructurePreparer(String type="", bool ignore=0)
void buildBonds(AtomContainer *at)
const std::set< String > * getSimpleAtomTypes()
void selectHeavyAtoms(AtomContainer *at)
void assignSimpleAtomTypes(AtomContainer *at, String iniFile)
void assignMMFF94AtomTypes(AtomContainer *at)
void saturate(AtomContainer *at)
void assignAtomTypes(AtomContainer *at, String iniFile, String AtomType_file="")
#define BALL_EXPORT
Definition: COMMON/global.h:50