OpenStructure
chain_handle.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
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12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
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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_CHAIN_HANDLE_HS
20 #define OST_CHAIN_HANDLE_HS
21 
22 #include <vector>
23 
24 #include <ost/mol/module_config.hh>
25 
26 #include <ost/geom/geom.hh>
27 
28 #include "chain_base.hh"
29 
30 #include "query.hh"
31 #include "view_type_fw.hh"
32 #include "handle_type_fw.hh"
33 #include "residue_prop.hh"
34 #include "entity_visitor_fw.hh"
35 #include "iterator_fw.hh"
36 #include "sec_structure.hh"
37 
38 namespace ost { namespace mol {
39 
54 
55 public:
56  ChainHandle();
57 
58  ChainHandle(const impl::ChainImplPtr& impl);
59 
60 
62  EntityHandle GetEntity() const;
63 
67  void Apply(EntityVisitor& visitor);
68 
70 
75  ResidueHandle GetPrev(const ResidueHandle& rh);
76  ResidueHandle GetNext(const ResidueHandle& rh);
77 
79 
80 
81 
82 
83 
84  ResidueHandle FindResidue(const ResNum& num) const;
85 
93  AtomHandle FindAtom(const ResNum& num,
94  const String& atom_name) const;
98  ResidueHandle GetResidueByIndex(int index) const;
100 
102  //
103  // To count all atoms of the entity the chain belongs to, use
104  // \c EntityHandle::GetAtomCount(). For count of specific residues, use
105  // \c ResidueHandle::GetResidueCount().
106  int GetAtomCount() const;
107 
114  int GetBondCount() const;
115 
119  int GetResidueCount() const;
120 
126 
127 
128  AtomHandleList GetAtomList() const;
129 
135  ResidueHandleList GetResidueList() const;
136 
150  ResidueHandleIter ResiduesBegin() const;
151 
154  ResidueHandleIter ResiduesEnd() const;
155 
156  AtomHandleIter AtomsBegin() const;
157  AtomHandleIter AtomsEnd() const;
158 
160  Real GetMass() const;
161 
163  geom::Vec3 GetCenterOfMass() const;
164 
169  geom::Vec3 GetCenterOfAtoms() const;
170 
171  geom::AlignedCuboid GetBounds() const;
174  void AssignSecondaryStructure(SecStructure ss,
175  const ResNum& start,
176  const ResNum& end);
177 
180  EntityView Select(const Query& q, QueryFlags flags=0) const;
181 
184  EntityView Select(const String& query_string, QueryFlags flags=0) const;
185 
189  ChainHandle GetHandle() const;
192  bool InSequence() const;
193  bool operator==(const ChainHandle& ref) const;
194  bool operator!=(const ChainHandle& ref) const;
195 
196 
197 };
198 
199 }} // ns
200 
201 #endif // OST_CHAIN_HANDLE_HH
202