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OpenStructure
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#include <atom_handle.hh>
Inherits AtomBase.
Public Member Functions | |
| AtomHandle () | |
| AtomHandle (const impl::AtomImplPtr &impl) | |
| ResidueHandle | GetResidue () const |
| EntityHandle | GetEntity () const |
| AtomHandle | GetHandle () const |
| unsigned long | GetHashCode () const |
| bool | operator== (const AtomHandle &ref) const |
| bool | operator!= (const AtomHandle &ref) const |
Bonds | |
| int | GetBondCount () const |
| BondHandleList | GetBondList () const |
| BondHandle | FindBondToAtom (const AtomHandle &handle) const |
| AtomHandleList | GetBondPartners () const |
Traversing the hierarchy | |
| void | Apply (EntityVisitor &) |
 Public Member Functions inherited from AtomBase | |
| AtomBase () | |
| AtomBase (const impl::AtomImplPtr &impl) | |
| const String & | GetName () const |
| void | SetName (const String &atom_name) |
| const geom::Vec3 & | GetPos () const |
| const geom::Vec3 & | GetOriginalPos () const |
| geom::Vec3 | GetAltPos (const String &alt_group) const |
| Real | GetAltBFactor (const String &alt_group) const |
| Real | GetAltOcc (const String &alt_group) const |
| std::vector< String > | GetAltGroupNames () const |
| String | GetQualifiedName () const |
| String | GetStringProperty (Prop::ID prop_id) const |
| Real | GetFloatProperty (Prop::ID prop_id) const |
| int | GetIntProperty (Prop::ID prop_id) const |
| unsigned long | GetIndex () const |
| Real | GetRadius () const |
| const String & | GetElement () const |
| bool | IsHetAtom () const |
| Real | GetBFactor () const |
| void | SetBFactor (Real factor) |
| void | SetOccupancy (Real occ) |
| void | SetCharge (Real charge) |
| void | SetMass (Real mass) |
| void | SetHetAtom (bool het) |
| void | SetRadius (Real radius) |
| void | SetIndex (const unsigned long index) |
| const geom::Mat3 & | GetAnisou () const |
| void | SetAnisou (const geom::Mat3 &anisou) |
| Real | GetMass () const |
| Real | GetCharge () const |
| Real | GetOccupancy () const |
| const impl::AtomImplPtr & | Impl () const |
| impl::AtomImplPtr & | Impl () |
| void | SetElement (const String &element) |
| operator bool () const | |
| bool | IsValid () const |
| Public Member Functions inherited from GenericPropContainer< AtomBase > | |
| void | ClearProps () |
| void | SetStringProp (const String &key, const String &value) |
| void | SetFloatProp (const String &key, Real value) |
| void | SetIntProp (const String &key, int value) |
| void | SetBoolProp (const String &key, bool value) |
| void | SetVec3Prop (const String &key, geom::Vec3 value) |
| void | RemoveProp (const String &key) |
| Public Member Functions inherited from ConstGenericPropContainer< AtomBase > | |
| bool | HasProp (const String &key) const |
| String | GetPropAsString (const String &key) const |
| String | GetStringProp (const String &key) const |
| String | GetStringProp (const String &key, const String &def) const |
| Real | GetFloatProp (const String &key) const |
| Real | GetFloatProp (const String &key, Real def) const |
| int | GetIntProp (const String &key) const |
| int | GetIntProp (const String &key, int def) const |
| bool | GetBoolProp (const String &key) const |
| bool | GetBoolProp (const String &key, bool def) const |
| geom::Vec3 | GetVec3Prop (const String &key) const |
| std::map< String, GenericPropValue > | GetPropMap () const |
| std::vector< String > | GetPropList () const |
Additional Inherited Members | |
| Protected Member Functions inherited from AtomBase | |
| GenericPropContainerImpl * | GpImpl () |
| const GenericPropContainerImpl * | GpImpl () const |
| void | CheckValidity () const |
| Protected Member Functions inherited from ConstGenericPropContainer< AtomBase > | |
| T | gp_get (const String &key) const |
| T | gp_get (const String &key, const T &def) const |
| GenericPropContainerImpl * | GetImpl () |
| const GenericPropContainerImpl * | GetImpl () const |
| Protected Attributes inherited from AtomBase | |
| impl::AtomImplPtr | impl_ |
Handle to atom datatype.
The bonds of an atom are accessible via GetBondList(). For a list of atoms that this atom is bonded to, use GetBondPartners().
New bonds are formed with one of the EditorBase::Connect() methods.
A valid atom handle is always part of a residue.
Definition at line 37 of file atom_handle.hh.
| AtomHandle | ( | ) |
| AtomHandle | ( | const impl::AtomImplPtr & | impl | ) |
| void Apply | ( | EntityVisitor & | ) |
Apply visitor.
This method is used by the EntityVisitor interface to traverse the entity - chain - residue -atom hierarchy.
| BondHandle FindBondToAtom | ( | const AtomHandle & | handle | ) | const |
Find bond to specific atom.
| int GetBondCount | ( | ) | const |
Get number of bonds this atom forms.
Count of all bonds where this atom is either the first or second atom.
| BondHandleList GetBondList | ( | ) | const |
get bond list
Returns all bonds where this atom is either the first or second atom.
| AtomHandleList GetBondPartners | ( | ) | const |
Get all atoms this atom is bonded to.
| EntityHandle GetEntity | ( | ) | const |
| AtomHandle GetHandle | ( | ) | const |
get this handle
Useful for duck-typing in Python and templated code.
| unsigned long GetHashCode | ( | ) | const |
Get unique identifier for atom.
Get hash code that uniquely identifies every atom. The hash code is identical for all atom views pointing to a given atom.
| ResidueHandle GetResidue | ( | ) | const |
| bool operator!= | ( | const AtomHandle & | ref | ) | const |
| bool operator== | ( | const AtomHandle & | ref | ) | const |
1.8.5