OpenStructure
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#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 |
Protected Member Functions inherited from ConstGenericPropContainer< ResidueBase > | |
T | gp_get (const String &key) const |
T | gp_get (const String &key, const T &def) const |
GenericPropContainerImpl * | GetImpl () |
const GenericPropContainerImpl * | GetImpl () const |
Friends | |
class | ChainView |
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.
ResidueView | ( | ) |
Create invalid ResidueView.
ResidueView | ( | const ChainView & | chain, |
const ResidueHandle & | residue | ||
) |
Create new residue view.
chain | is the parent chain view to insert into |
residue | is residue handle this view points to. |
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.
AtomView AddAtom | ( | const AtomView & | atom_view, |
ViewAddFlags | flags = 0 |
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) |
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())
atom_view | is the atom view to add |
flags | can be a ORed together combination of ViewAddFlag |
AtomView AddAtom | ( | const AtomHandle & | atom_handle, |
ViewAddFlags | flags = 0 |
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) |
Add atom to view.
If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the handle is not already included in the view.
atom_handle | the atom handle to add |
flags | can be a ORed together combination of ViewAddFlag |
void Apply | ( | EntityVisitor & | visitor | ) |
Apply entity visitor to whole chain.
void Apply | ( | EntityViewVisitor & | visitor | ) |
AtomView FindAtom | ( | const AtomHandle & | handle | ) | const |
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 residue's axis-aligned bounding box.
geom::Vec3 GetCenterOfAtoms | ( | ) | const |
Get residue's center of atoms (not mass weighted)
Returns the center of all the atoms in this residue. This is similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfMass | ( | ) | const |
Get residue'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
unsigned long GetHashCode | ( | ) | const |
get unique id
The unique id is the same for all ResidueViews pointing to the same residue view data.
int GetIndex | ( | ) | const |
get index of residue view in chain
double GetMass | ( | ) | const |
Get residue's mass.
bool HasAtoms | ( | ) | const |
bool IsAtomIncluded | ( | const AtomHandle & | handle | ) | const |
Check whether the view includes the the given atom.
bool IsValid | ( | ) | const |
check validity of handle
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inline |
check validity of view
check, whether the residue view points to a valid residue.
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 |
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) | const |
return view based on a query object
EntityView Select | ( | const String & | query_string, |
QueryFlags | flags = 0 |
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) | const |
return view based on query String.
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protected |
set the index of residiue view in chain should be called from chainview whenever indexes change
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inline |
Get internal view data.
Definition at line 80 of file residue_view.hh.
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inline |
Get internal view data.
Definition at line 84 of file residue_view.hh.
AtomView ViewForHandle | ( | const AtomHandle & | handle | ) | const |
Find residue by residue handle.
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friend |
Definition at line 41 of file residue_view.hh.