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