BALL 1.5.0
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templates.h
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1// -*- Mode: C++; tab-width: 2; -*-
2// vi: set ts=2:
3//
4
5// Molecular Mechanics Parameter: class describing the atom type section of a parameter file
6
7#ifndef BALL_MOLMEC_PARAMETER_TEMPLATES_H
8#define BALL_MOLMEC_PARAMETER_TEMPLATES_H
9
10#ifndef BALL_FORMAT_PARAMETERSECTION_H
12#endif
13
14#ifndef BALL_KERNEL_SYSTEM_H
15# include <BALL/KERNEL/system.h>
16#endif
17
18#ifndef BALL_DATATYPE_HASHSET_H
19# include <BALL/DATATYPE/hashset.h>
20#endif
21
22#include <BALL/KERNEL/atom.h>
23
24namespace BALL
25{
26 class Atom;
27
32 : public ParameterSection
33 {
34 public:
35
39
43
46 Templates(const Templates& templates, bool deep = true);
47
50 virtual ~Templates() ;
51
54 virtual void clear() ;
55
57
60
67 virtual bool extractSection(Parameters& parameters, const String& section_name);
68
71 float getCharge(const String& name) const;
72
75 String getTypeName(const String& name) const;
76
79 bool has(const String& name) const;
80
83 void assign(System& system, bool overwrite_existing_typenames = true,
84 bool overwrite_non_zero_charges = true) const;
85
88 void assignCharges(System& system, bool overwrite_non_zero_charges = true) const;
89
92 void assignTypeNames(System& system, bool overwrite_existing_typenames = true) const;
93
95
98
103 Templates& operator = (const Templates& templates);
104
110
115
118
121
123
124 protected:
125
126 /*_ Contains the charge for each residue/atom combination
127 */
129
130 /*_ Contains the atom type names for each residue/atom combination
131 */
133
134 //_ Atoms, for which the assignment fails
136
137 //_ max number of unassigned atoms
139 };
140} // namespace BALL
141
142#endif // BALL_MOLMEC_PARAMETER_TEMPLATES_H
char Atom[5]
Definition PDBdefs.h:257
virtual bool extractSection(Parameters &parameters, const String &section_name)
Size getMaximumUnassignedAtoms() const
void assignCharges(System &system, bool overwrite_non_zero_charges=true) const
void assignTypeNames(System &system, bool overwrite_existing_typenames=true) const
Templates(const Templates &templates, bool deep=true)
void assign(System &system, bool overwrite_existing_typenames=true, bool overwrite_non_zero_charges=true) const
HashSet< const Atom * > & getUnassignedAtoms()
Get the atoms, for which the assignment failed.
void setMaximumUnassignedAtoms(Size nr)
float getCharge(const String &name) const
HashSet< const Atom * > unassigned_atoms_
Definition templates.h:135
StringHashMap< String > type_names_
Definition templates.h:132
Size getNumberOfUnassignedAtoms() const
Get the number of atoms, for which the assignment failed.
Size max_number_unassigned_atoms_
Definition templates.h:138
bool has(const String &name) const
virtual ~Templates()
virtual void clear()
StringHashMap< float > charges_
Definition templates.h:128
String getTypeName(const String &name) const
#define BALL_EXPORT