BALL 1.5.0
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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
19namespace 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
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
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)
const std::set< String > * getSimpleAtomTypes()
void buildBonds(AtomContainer *at)
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