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residue_handle.hh
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4 // Copyright (C) 2008-2020 by the OpenStructure authors
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18 //------------------------------------------------------------------------------
19 #ifndef OST_RESIDUE_HANDLE_HU
20 #define OST_RESIDUE_HANDLE_HU
21 
22 #include <ost/geom/vec3.hh>
24 
25 #include <ost/mol/query.hh>
26 #include <ost/mol/module_config.hh>
27 #include <ost/mol/residue_base.hh>
29 
30 namespace ost { namespace mol {
31 
55 public:
56  ResidueHandle();
57 
60  : ResidueBase(impl) {}
61  EntityHandle GetEntity() const;
62 
64  double GetMass() const;
65 
67  geom::Vec3 GetCenterOfMass() const;
68 
73  geom::Vec3 GetCenterOfAtoms() const;
74 
76  geom::AlignedCuboid GetBounds() const;
77 
79  ChainHandle GetChain() const;
80 
83  ResidueHandle GetPrev() const;
84 
87  ResidueHandle GetNext() const;
88 
92  AtomHandle FindAtom(const String& aname) const;
93 
98  void Apply(EntityVisitor& visitor);
99 
103  AtomHandleList GetAtomList() const;
104 
106  int GetAtomCount() const;
107 
113  int GetBondCount() const;
114 
124  TorsionHandle FindTorsion(const String& torsion_name) const;
125 
127  TorsionHandleList GetTorsionList() const;
128 
130  int GetIndex() const;
131 
138 
139  bool HasAltAtomGroup(const String& group) const;
142 
147  const String& GetCurrentAltGroupName() const;
148 
150  std::vector<String> GetAltAtomGroupNames() const;
151 
153  bool HasAltAtoms() const;
154 
158  geom::Vec3 GetAltAtomPos(const AtomHandle& atom, const String& group) const;
159 
166  bool SwitchAtomPos(const String& group);
168 
172  ResidueHandle GetHandle() const;
173  unsigned long GetHashCode() const;
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 ResidueHandle& ref) const;
184  bool operator!=(const ResidueHandle& ref) const;
185 
186 
187 
188 };
189 
194 bool DLLEXPORT_OST_MOL InSequence(const ResidueHandle& residue_one,
195  const ResidueHandle& residue_two);
196 
197 
198 }} //ns
199 
200 #endif // OST_RESIDUE_HANDLE_HH
201 
std::string String
Definition: base.hh:54
Handle to atom datatype.
Definition: atom_handle.hh:37
axis-aligned cuboid
Protein or molecule.
boost::shared_ptr< ResidueImpl > ResidueImplPtr
bool DLLEXPORT_OST_GEOM operator==(const Line2 &l1, const Line2 &l2)
bool DLLEXPORT_OST_MOL InSequence(const ResidueHandle &residue_one, const ResidueHandle &residue_two)
Test if two residues are in next in sequence.
DLLEXPORT_OST_IMG_BASE bool operator!=(const ImageHandle &lhs, const ConstImageHandle &rhs)
EntityVisitor interface.
Selection Query.
Definition: query.hh:74
uint QueryFlags
Definition: query.hh:69
std::vector< TorsionHandle > TorsionHandleList
linear chain of residues
Definition: chain_handle.hh:52
Three dimensional vector class, using Real precision.
Definition: vec3.hh:43
#define DLLEXPORT_OST_MOL
Named torsion (dihedral) angle.
ResidueHandle(const impl::ResidueImplPtr &impl)
std::vector< AtomHandle > AtomHandleList
definition of EntityView
Definition: entity_view.hh:86
base class for ResidueHandle and ResidueView
Definition: residue_base.hh:65