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entity_impl.hh
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18 //------------------------------------------------------------------------------
19 #ifndef OST_ENTITY_IMPL_HH
20 #define OST_ENTITY_IMPL_HH
21 
22 #include <map>
23 #include <vector>
24 
25 #include <boost/enable_shared_from_this.hpp>
26 
27 #include <ost/mol/module_config.hh>
28 #include <ost/geom/geom.hh>
29 
31 
32 #include <ost/mol/entity_view.hh>
33 
34 #include <ost/mol/residue_prop.hh>
44 #include <ost/mol/entity_view.hh>
45 #include <ost/mol/entity_handle.hh>
47 
48 
49 #include <ost/generic_property.hh>
50 
51 namespace ost { namespace mol { namespace impl {
52 
54 typedef std::map<AtomImpl*,AtomImplPtr> AtomImplMap;
56 typedef std::map<ResidueImpl*,ResidueImplPtr> ResidueImplMap;
58 typedef std::vector<ChainImplPtr> ChainImplList;
60 typedef std::map<ConnectorImpl*,ConnectorImplP> ConnectorImplMap;
62 typedef std::map<TorsionImpl*,TorsionImplP> TorsionImplMap;
64 typedef std::vector<FragmentImplP> FragmentImplList;
66 typedef std::map<EntityObserver*,EntityObserverPtr> EntityObserverMap;
69 
71 typedef enum {
74  // dirty trace (implies dirty ICS)
79 
80 
83  public boost::enable_shared_from_this<EntityImpl>
84 {
85 public:
86  EntityImpl();
87  ~EntityImpl();
88 
91 
92  Real GetMass() const;
97 
98 
99 
100  // default copy ctor and assignment op should work for now
101  AtomImplPtr CreateAtom(const ResidueImplPtr& rp, const String& name,
102  const geom::Vec3& pos, const String& ele);
103 
105  const ResNum& n,
106  const ResidueKey& k);
107 
108  ChainImplPtr InsertChain(const String& cname);
112  // force deep to be set explicitely, because it is better than implicit
113  // (and since we are on the impl level interface consistency isn't that critical)
114  ChainImplPtr InsertChain(const String& chain_name, const ChainImplPtr& chain, bool deep);
115  ConnectorImplP Connect(const AtomImplPtr& first, const AtomImplPtr& second,
116  Real len, Real theta, Real phi,
117  unsigned char bond_order);
118 
119  TorsionImplP AddTorsion(const String& name, const AtomImplPtr& a1,
120  const AtomImplPtr& a2, const AtomImplPtr& a3,
121  const AtomImplPtr& a4);
122 
123  void TraceDirectionality();
124 
127  const AtomImplPtr& a2,
128  const AtomImplPtr& a3,
129  const AtomImplPtr& a4) const;
130 
131  void RenameChain(ChainImplPtr chain, const String& new_name);
132  bool SetAngle(const AtomImplPtr& a1, const AtomImplPtr& a2,
133  const AtomImplPtr& a3, Real angle);
134 
135  Real GetAngle(const AtomImplPtr& a1, const AtomImplPtr& a2,
136  const AtomImplPtr& a3) const;
137  Real GetAngleXCS(const AtomImplPtr& a1, const AtomImplPtr& a2,
138  const AtomImplPtr& a3) const;
139  Real GetAngleICS(const AtomImplPtr& a1, const AtomImplPtr& a2,
140  const AtomImplPtr& a3) const;
141  // update positions from internal coordinate system
142  void UpdateFromICS();
143 
144  // update internal coordinate system from positions
145  void UpdateFromXCS();
146 
147  void Apply(EntityVisitor& v);
148  void ApplyTransform(const geom::Transform& t);
149 
150  void SetTransform(const geom::Transform& t);
151  const geom::Transform& GetTransform() const {return transform_;}
152  bool HasTransform() const {return has_transform_;}
153  void ClearTransform();
154  void FixTransform();
155 
156  void AttachObserver(const EntityObserverPtr& o);
157  void DetachObserver(const EntityObserverPtr& o);
158  void NotifyObserver();
159 
160 
161  void UpdateOrganizer();
162 
163  AtomImplList FindWithin(const geom::Vec3& pos, Real radius);
164  // use query flag defaults
165  EntityView Select(const EntityHandle& h, const Query& q) const;
166  // override query flag defaults with given flags
167  EntityView Select(const EntityHandle& h, const Query& q,
168  QueryFlags flags) const;
169  EntityView CreateFullView(const EntityHandle& h) const;
170  void SetDefaultQueryFlags(QueryFlags f) {default_query_flags_=f;}
171  QueryFlags GetDefaultQueryFlags() const {return default_query_flags_;}
172 
173 
176  ChainImplPtr FindChain(const String& name) const;
177 
178  ResidueImplPtr FindResidue(const String& chain_name,
179  const ResNum& residue) const;
180 
181  AtomImplPtr FindAtom(const String& chain_name,
182  const ResNum& residue,
183  const String& atom_name) const;
184  /*
185  this is a deep-swap which will exchange the internal structure
186  of two implementations, which by design affects _all_ entity handles
187  that point two either of these two implementations
188  */
189  void Swap(EntityImpl& impl);
190 
192  int GetAtomCount() const;
193 
195  int GetBondCount() const;
196 
199 
200 
202  int GetResidueCount() const;
203 
205  int GetChainCount() const;
206 
207  const ChainImplList& GetChainList() const { return chain_list_; }
208 
209  ChainImplList& GetChainList() { return chain_list_; }
210 
211  void DeleteFromConnMap(const ConnectorImplP& conn);
212 
213  void DeleteChain(const ChainImplPtr& chain);
214 
215  void DeleteAtom(const AtomImplPtr& atom);
216 
217  void IncXCSEditorCount();
218  void DecXCSEditorCount();
219 
220  void IncICSEditorCount();
221  void DecICSEditorCount();
222 
224 
225  void UpdateXCSIfNeeded();
226 
227  void UpdateICSIfNeeded();
228 
230 
231  void EnableICS();
232 
233  bool HasICS() const;
234 
235  bool IsXCSDirty() const;
236 
237  void MarkXCSDirty();
238  void MarkICSDirty();
239  void MarkTraceDirty();
240  void MarkOrganizerDirty();
241 
242  void UpdateTransformedPos();
243 
244  const String& GetName() const;
245 
246  impl::ChainImplList::iterator GetChain(const String& name);
247 
249  void SetName(const String& ent_name);
250 
251  void ReorderAllResidues();
252 
253  void RenumberAllResidues(int start, bool keep_spacing);
254 
255  void RenumberChain(const String& name, int start, bool keep_spacing);
256 
257 private:
258  void DoCopy(EntityImplPtr dest);
259 
260  void ReplicateHierarchy(EntityImplPtr dest);
261 
262  void DoCopyBondsAndTorsions(EntityImplPtr dest);
263 
264  AtomImplMap atom_map_;
265  ChainImplList chain_list_;
266  ConnectorImplMap connector_map_;
267  TorsionImplMap torsion_map_;
268 
269  geom::Transform transform_;
270  bool has_transform_;
271 
272  SpatialAtomOrganizer atom_organizer_;
273  FragmentImplList fragment_list_;
274  EntityObserverMap observer_map_;
275 
276  int xcs_editor_count_;
277  int ics_editor_count_;
278  int dirty_flags_;
279  String name_;
280 
281  unsigned long next_index_;
282 
283  QueryFlags default_query_flags_;
284 
285  template <bool always_true>
286  EntityView do_selection(const EntityHandle&, const Query&, QueryFlags) const;
287 };
288 
289 }}} // ns
290 
291 #endif
ResidueImplPtr FindResidue(const String &chain_name, const ResNum &residue) const
std::vector< FragmentImplP > FragmentImplList
Definition: entity_impl.hh:64
geom::Vec3 GetCenterOfAtoms() const
String ResidueKey
geom::Vec3 GetCenterOfMass() const
std::map< ResidueImpl *, ResidueImplPtr > ResidueImplMap
Definition: entity_impl.hh:56
std::vector< ChainImplPtr > ChainImplList
Definition: entity_impl.hh:58
std::map< ConnectorImpl *, ConnectorImplP > ConnectorImplMap
Definition: entity_impl.hh:60
Real GetAngleICS(const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const
void DeleteAtom(const AtomImplPtr &atom)
const ChainImplList & GetChainList() const
Definition: entity_impl.hh:207
std::string String
Definition: base.hh:54
float Real
Definition: base.hh:44
void ApplyTransform(const geom::Transform &t)
axis-aligned cuboid
int GetAtomCount() const
Get total number of atoms of all chains belonging to this entity.
const String & GetName() const
Real GetAngleXCS(const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const
void Apply(EntityVisitor &v)
void RenumberAllResidues(int start, bool keep_spacing)
ConnectorImplP Connect(const AtomImplPtr &first, const AtomImplPtr &second, Real len, Real theta, Real phi, unsigned char bond_order)
Protein or molecule.
boost::shared_ptr< ResidueImpl > ResidueImplPtr
int GetBondCount() const
Get total number of bonds belonging to this entity.
boost::shared_ptr< ConnectorImpl > ConnectorImplP
AtomImplPtr FindAtom(const String &chain_name, const ResNum &residue, const String &atom_name) const
ChainImplPtr FindChain(const String &name) const
EntityImplPtr Copy()
copy entity
std::map< EntityObserver *, EntityObserverPtr > EntityObserverMap
Definition: entity_impl.hh:66
impl::ChainImplList::iterator GetChain(const String &name)
boost::shared_ptr< ChainImpl > ChainImplPtr
ResidueImplPtr CreateResidue(const ChainImplPtr &cp, const ResNum &n, const ResidueKey &k)
TorsionImplP FindTorsion(const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, const AtomImplPtr &a4) const
Search for torsion.
pointer_it< ChainImplPtr > GetChainIter(const String &name)
EntityVisitor interface.
Selection Query.
Definition: query.hh:74
void RenameChain(ChainImplPtr chain, const String &new_name)
Real GetAngle(const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const
void DeleteFromConnMap(const ConnectorImplP &conn)
uint QueryFlags
Definition: query.hh:69
boost::shared_ptr< AtomImpl > AtomImplPtr
Definition: atom_impl_fw.hh:33
TorsionImplMap & GetTorsionMap()
basic and essential transformation class, including translation, rotation and center of rotation ...
Definition: transform.hh:39
boost::shared_ptr< EntityImpl > EntityImplPtr
std::map< TorsionImpl *, TorsionImplP > TorsionImplMap
Definition: entity_impl.hh:62
EntityView Select(const EntityHandle &h, const Query &q) const
SpatialOrganizer< AtomImplPtr > SpatialAtomOrganizer
Definition: entity_impl.hh:68
void AttachObserver(const EntityObserverPtr &o)
boost::shared_ptr< TorsionImpl > TorsionImplP
Three dimensional vector class, using Real precision.
Definition: vec3.hh:43
std::map< AtomImpl *, AtomImplPtr > AtomImplMap
Definition: entity_impl.hh:54
geom::AlignedCuboid GetBounds() const
returns the axis-aligned bounding box of the entity
std::vector< BondHandle > BondHandleList
bool SetAngle(const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, Real angle)
ChainImplPtr InsertChain(const String &cname)
EntityView CreateFullView(const EntityHandle &h) const
void SetDefaultQueryFlags(QueryFlags f)
Definition: entity_impl.hh:170
const geom::Transform & GetTransform() const
Definition: entity_impl.hh:151
void RenumberChain(const String &name, int start, bool keep_spacing)
QueryFlags GetDefaultQueryFlags() const
Definition: entity_impl.hh:171
TorsionImplP AddTorsion(const String &name, const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, const AtomImplPtr &a4)
std::vector< AtomImplPtr > AtomImplList
Definition: atom_impl_fw.hh:38
definition of EntityView
Definition: entity_view.hh:86
AtomImplList FindWithin(const geom::Vec3 &pos, Real radius)
void SetName(const String &ent_name)
int GetChainCount() const
Get number of chains.
base class for the implementation
void Swap(EntityImpl &impl)
AtomImplPtr CreateAtom(const ResidueImplPtr &rp, const String &name, const geom::Vec3 &pos, const String &ele)
void DetachObserver(const EntityObserverPtr &o)
void SetTransform(const geom::Transform &t)
int GetResidueCount() const
Get total number of residues of all chains belonging to this entity.
boost::shared_ptr< EntityObserver > EntityObserverPtr
void DeleteChain(const ChainImplPtr &chain)
ChainImplList & GetChainList()
Definition: entity_impl.hh:209
mol::BondHandleList GetBondList() const
Get list of bonds.