OpenStructure
residue_view.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_RESIDUE_VIEW_HH
20 #define OST_RESIDUE_VIEW_HH
21 
22 #include <ost/mol/query.hh>
23 #include <ost/mol/module_config.hh>
24 #include <ost/geom/geom.hh>
25 #include <ost/mol/residue_base.hh>
26 #include <ost/mol/view_type_fw.hh>
30 
31 namespace ost { namespace mol {
32 
40 
41  friend class ChainView;
42 
43 public:
45  ResidueView();
46 
52  ResidueView(const ChainView& chain,
53  const ResidueHandle& residue);
54 
55 public:
56 
58 
59 
60 
61 
62 
63 
64 
65  operator bool() const { return this->IsValid(); }
68  bool IsValid() const { return data_.get()!=0; }
70 
72 
73 
74 
75 
76  ResidueView(const ResidueViewDataPtr& data,
77  const impl::ResidueImplPtr& impl);
78 
80  const ResidueViewDataPtr& ViewData() const {
81  return data_;
82  }
85  return data_;
86  }
88 public:
90 
91 
92 
93 
94 
95 
96 
97 
98 
99 
100 
101  AtomView AddAtom(const AtomView& atom_view,
102  ViewAddFlags flags=0);
103 
113  AtomView AddAtom(const AtomHandle& atom_handle,
114  ViewAddFlags flags=0);
116 
118  AtomView FindAtom(const String& atom_name) const;
119 
121  AtomView FindAtom(const AtomHandle& handle) const;
122 
124  bool IsAtomIncluded(const AtomHandle& handle) const;
125 
129  void RemoveAtom(AtomView view);
130 
135  void RemoveAtoms();
136 
138  void Apply(EntityVisitor& visitor);
139  void Apply(EntityViewVisitor& visitor);
140 
142  int GetAtomCount() const;
143 
145  const AtomViewList& GetAtomList() const;
146 
148  ResidueHandle GetHandle() const;
149 
151  EntityView GetEntity() const;
152 
154  int GetIndex() const;
156  ChainView GetChain() const;
157 
158 
160  double GetMass() const;
161 
163  geom::Vec3 GetCenterOfMass() const;
164 
169  geom::Vec3 GetCenterOfAtoms() const;
170 
172  geom::AlignedCuboid GetBounds() const;
173 
174 
177  EntityView Select(const Query& q, QueryFlags flags=0) const;
178 
181  EntityView Select(const String& query_string, QueryFlags flags=0) const;
182 
183  bool operator==(const ResidueView& rhs) const;
184 
185  bool operator!=(const ResidueView& rhs) const;
186 
187 protected:
190  void SetIndex(int index);
191 
192 private:
193  ResidueViewDataPtr data_;
194 };
195 
196 }} // ns
197 
198 #endif // OST_RESIDUE_VIEW_HH
199