#include <residue_view.hh>
Inherits ResidueBase.
Protected Member Functions | |
| void | SetIndex (int index) |
 Protected Member Functions inherited from ResidueBase | |
| GenericPropContainerImpl * | GpImpl () |
| const GenericPropContainerImpl * | GpImpl () const |
| void | CheckValidity () const |
Friends | |
| class | ChainView |
Detailed Description
residue view
Atoms are added with ResidueView::AddAtom() and removed with ResidueView::RemoveAtom(). Like other view operations, these operations only affect the view and do not alter the structure and topology of the underlying residue.
Definition at line 39 of file residue_view.hh.
Constructor & Destructor Documentation
| ResidueView | ( | ) |
Create invalid ResidueView.
| ResidueView | ( | const ChainView & | chain, |
| const ResidueHandle & | residue | ||
| ) |
Create new residue view.
- Parameters:
-
chain is the parent chain view to insert into residue is residue handle this view points to.
- Note:
- For better readability consider using ChainView::AddResidue()
| ResidueView | ( | const ResidueViewDataPtr & | data, |
| const impl::ResidueImplPtr & | impl | ||
| ) |
construct new view from view data and impl.
This has the same effect as using the default copy constructor of the view.
Member Function Documentation
| AtomView AddAtom | ( | const AtomView & | atom_view, |
| ViewAddFlags | flags = 0 |
||
| ) |
Add atom to view.
If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the view is not already included in this view. This method is an alias for residue_view.AddAtom(atom_view.GetHandle())
- Parameters:
-
atom_view is the atom view to add flags can be a ORed together combination of ViewAddFlag
- Returns:
- The added atom view, or a reference to the existing atom view that points to the very same view.
| AtomView AddAtom | ( | const AtomHandle & | atom_handle, |
| ViewAddFlags | flags = 0 |
||
| ) |
Add atom to view.
If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the handle is not already included in the view.
- Parameters:
-
atom_handle the atom handle to add flags can be a ORed together combination of ViewAddFlag
- Returns:
- The added atom view, or a reference to the existing atom view that points to the very same handle.
| void Apply | ( | EntityVisitor & | visitor | ) |
Apply entity visitor to whole chain.
| void Apply | ( | EntityViewVisitor & | visitor | ) |
| AtomView FindAtom | ( | const AtomHandle & | handle | ) | const |
Find residue by residue handle.
| int GetAtomCount | ( | ) | const |
return number of atoms in this residue view.
| const AtomViewList& GetAtomList | ( | ) | const |
get list of atoms in this view
| geom::AlignedCuboid GetBounds | ( | ) | const |
Get entity's axis-aligned bounding box.
| geom::Vec3 GetCenterOfAtoms | ( | ) | const |
Get entity's center of atoms (not mass weighted)
Returns the center of all the atoms in an entity. This is similar to GetCenterOfMass(), but the atoms are not mass weighted
| geom::Vec3 GetCenterOfMass | ( | ) | const |
Get entity's center of mass (mass weighted)
| ChainView GetChain | ( | ) | const |
get parent chain view.
| EntityView GetEntity | ( | ) | const |
get entity
| ResidueHandle GetHandle | ( | ) | const |
get handle this view points to
| int GetIndex | ( | ) | const |
get index of residue view in chain
| double GetMass | ( | ) | const |
Get entity's mass.
| bool IsAtomIncluded | ( | const AtomHandle & | handle | ) | const |
Check whether the view includes the the given atom.
|
inline |
check validity of handle
- See also:
- operator bool()
Reimplemented from ResidueBase.
Definition at line 68 of file residue_view.hh.
|
inline |
check validity of view
check, whether the residue view points to a valid residue.
- Note:
- It is an error to use any method other than IsValid, Impl and operator bool() when the handle is invalid. An InvalidHandle exception will be thrown.
Reimplemented from ResidueBase.
Definition at line 65 of file residue_view.hh.
| bool operator!= | ( | const ResidueView & | rhs | ) | const |
| bool operator== | ( | const ResidueView & | rhs | ) | const |
| void RemoveAtom | ( | AtomView | view | ) |
remove given atom from view
all bonds involving this atom will be removed from the view as well.
| void RemoveAtoms | ( | ) |
remove all atoms
all bonds involving one of the atoms will be removed from the view as well.
| EntityView Select | ( | const Query & | q, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on a query object
- See also:
- Query
| EntityView Select | ( | const String & | query_string, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on query String.
- See also:
- Query
|
protected |
set the index of residiue view in chain should be called from chainview whenever indexes change
|
inline |
Get internal view data.
Definition at line 80 of file residue_view.hh.
|
inline |
Get internal view data.
Definition at line 84 of file residue_view.hh.
Friends And Related Function Documentation
|
friend |
Definition at line 41 of file residue_view.hh.
The documentation for this class was generated from the following file:
- stage/include/ost/mol/residue_view.hh
