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| EntityImpl () |
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| ~EntityImpl () |
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EntityImplPtr | Copy () |
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Real | GetMass () const |
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geom::Vec3 | GetCenterOfMass () const |
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geom::Vec3 | GetCenterOfAtoms () const |
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geom::AlignedCuboid | GetBounds () const |
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AtomImplPtr | CreateAtom (const ResidueImplPtr &rp, const String &name, const geom::Vec3 &pos, const String &ele) |
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ResidueImplPtr | CreateResidue (const ChainImplPtr &cp, const ResNum &n, const ResidueKey &k) |
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ChainImplPtr | InsertChain (const String &cname) |
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ChainImplPtr | InsertChain (const String &chain_name, const ChainImplPtr &chain, bool deep) |
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ConnectorImplP | Connect (const AtomImplPtr &first, const AtomImplPtr &second, Real len, Real theta, Real phi, unsigned char bond_order) |
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TorsionImplP | AddTorsion (const String &name, const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, const AtomImplPtr &a4) |
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void | TraceDirectionality () |
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TorsionImplP | FindTorsion (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, const AtomImplPtr &a4) const |
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void | RenameChain (ChainImplPtr chain, const String &new_name) |
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bool | SetAngle (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, Real angle) |
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Real | GetAngle (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const |
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Real | GetAngleXCS (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const |
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Real | GetAngleICS (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const |
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void | UpdateFromICS () |
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void | UpdateFromXCS () |
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void | Apply (EntityVisitor &v) |
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void | ApplyTransform (const geom::Transform &t) |
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void | SetTransform (const geom::Transform &t) |
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const geom::Transform & | GetTransform () const |
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bool | HasTransform () const |
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void | ClearTransform () |
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void | FixTransform () |
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void | AttachObserver (const EntityObserverPtr &o) |
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void | DetachObserver (const EntityObserverPtr &o) |
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void | NotifyObserver () |
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void | UpdateOrganizer () |
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AtomImplList | FindWithin (const geom::Vec3 &pos, Real radius) |
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EntityView | Select (const EntityHandle &h, const Query &q) const |
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EntityView | Select (const EntityHandle &h, const Query &q, QueryFlags flags) const |
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EntityView | CreateFullView (const EntityHandle &h) const |
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void | SetDefaultQueryFlags (QueryFlags f) |
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QueryFlags | GetDefaultQueryFlags () const |
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ChainImplPtr | FindChain (const String &name) const |
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ResidueImplPtr | FindResidue (const String &chain_name, const ResNum &residue) const |
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AtomImplPtr | FindAtom (const String &chain_name, const ResNum &residue, const String &atom_name) const |
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void | Swap (EntityImpl &impl) |
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int | GetAtomCount () const |
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int | GetBondCount () const |
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mol::BondHandleList | GetBondList () const |
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int | GetResidueCount () const |
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int | GetChainCount () const |
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const ChainImplList & | GetChainList () const |
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ChainImplList & | GetChainList () |
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void | DeleteFromConnMap (const ConnectorImplP &conn) |
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void | DeleteChain (const ChainImplPtr &chain) |
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void | DeleteAtom (const AtomImplPtr &atom) |
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void | IncXCSEditorCount () |
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void | DecXCSEditorCount () |
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void | IncICSEditorCount () |
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void | DecICSEditorCount () |
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TorsionImplMap & | GetTorsionMap () |
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void | UpdateXCSIfNeeded () |
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void | UpdateICSIfNeeded () |
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void | UpdateOrganizerIfNeeded () |
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void | EnableICS () |
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bool | HasICS () const |
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bool | IsXCSDirty () const |
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void | MarkXCSDirty () |
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void | MarkICSDirty () |
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void | MarkTraceDirty () |
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void | MarkOrganizerDirty () |
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void | UpdateTransformedPos () |
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const String & | GetName () const |
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impl::ChainImplList::iterator | GetChain (const String &name) |
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pointer_it< ChainImplPtr > | GetChainIter (const String &name) |
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void | SetName (const String &ent_name) |
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void | ReorderAllResidues () |
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void | RenumberAllResidues (int start, bool keep_spacing) |
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void | RenumberChain (const String &name, int start, bool keep_spacing) |
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| GenericPropContainerImpl () |
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| ~GenericPropContainerImpl () |
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| GenericPropContainerImpl (const GenericPropContainerImpl &rhs) |
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GenericPropContainerImpl & | operator= (const GenericPropContainerImpl &r) |
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GenericPropValue & | GenericProp (const String &key) |
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const GenericPropValue & | GenericProp (const String &key) const |
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bool | HasProp (const String &key) const |
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void | ClearProps () |
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void | RemoveProp (const String &key) |
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void | Assign (const GenericPropContainerImpl &impl) |
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PropertyMap | GetPropMap () const |
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std::vector< String > | GetPropList () const |
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Definition at line 82 of file entity_impl.hh.