#include <chain_view.hh>
Inherits ChainBase.
Internal | |
| ChainViewDataPtr & | ViewData () |
| const ChainViewDataPtr & | ViewData () const |
| bool | InSequence () const |
| EntityView | Select (const Query &q, QueryFlags flags=0) const |
| EntityView | Select (const String &query_string, QueryFlags flags=0) const |
| unsigned long | GetHashCode () const |
| bool | operator== (const ChainView &rhs) const |
| bool | operator!= (const ChainView &rhs) const |
| bool | HasAtoms () const |
Additional Inherited Members | |
 Protected Member Functions inherited from ChainBase | |
| GenericPropContainerImpl * | GpImpl () |
| const GenericPropContainerImpl * | GpImpl () const |
| void | CheckValidity () const |
| Protected Member Functions inherited from ConstGenericPropContainer< H > | |
| template<typename T > | |
| T | gp_get (const String &key) const |
| template<typename T > | |
| T | gp_get (const String &key, const T &def) const |
| GenericPropContainerImpl * | GetImpl () |
| const GenericPropContainerImpl * | GetImpl () const |
Detailed Description
definition of ChainView
Definition at line 37 of file chain_view.hh.
Constructor & Destructor Documentation
◆ ChainView() [1/3]
| ChainView | ( | ) |
◆ ChainView() [2/3]
| ChainView | ( | ChainViewDataPtr | data, |
| impl::ChainImplPtr | impl | ||
| ) |
◆ ChainView() [3/3]
| ChainView | ( | const EntityView & | entity, |
| const ChainHandle & | chain | ||
| ) |
Member Function Documentation
◆ AddAtom()
| AtomView AddAtom | ( | const AtomHandle & | atom_handle, |
| ViewAddFlags | flags = 0 |
||
| ) |
Add atom to view.
If the atoms's residue has not been added to the view it will be added.
- Parameters
-
atom_handle The atom 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.
◆ AddResidue() [1/2]
| ResidueView AddResidue | ( | const ResidueHandle & | residue_handle, |
| ViewAddFlags | flags = 0 |
||
| ) |
Add residue to view.
If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the handle is not already included in the view.
- Parameters
-
residue_handle The residue handle to add flags Can be a ORed together combination of ViewAddFlag. Flags that do not affect the operation are silently ignored.
- Returns
- the added residue view, or a reference to the existing residue view that points to the very same handle.
◆ AddResidue() [2/2]
| ResidueView AddResidue | ( | const ResidueView & | residue_view, |
| ViewAddFlags | flags = 0 |
||
| ) |
Add residue to view.
This method is identical to AddResidue(const ResidueHandle&) except that in case ViewAddFlag::INCLUDE_ATOMS is set only the atoms included in the residue view are considered.
If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the view is not already included in the view.
- Parameters
-
residue_view The residue view to add flags Can be a ORed together combination of ViewAddFlag. Flags that do not affect the operation are silently ignored.
- Returns
- The added residue view, or a reference to the existing residue view that points to the very same handle.
◆ Apply() [1/2]
| void Apply | ( | EntityViewVisitor & | visitor | ) |
◆ Apply() [2/2]
| void Apply | ( | EntityVisitor & | visitor | ) |
◆ FindAtom() [1/2]
| AtomView FindAtom | ( | const AtomHandle & | atom | ) | const |
Find view for given atom handle Deprecated: Use ViewForHandle instead.
◆ FindAtom() [2/2]
◆ FindResidue() [1/2]
| ResidueView FindResidue | ( | const ResidueHandle & | handle | ) | const |
◆ FindResidue() [2/2]
| ResidueView FindResidue | ( | const ResNum & | number | ) | const |
Find residue by number
◆ GetAtomCount()
| int GetAtomCount | ( | ) | const |
Get number of atoms in this chain view.
◆ GetBondCount()
| int GetBondCount | ( | ) | const |
Get number of all inclusive bonds of this chain.
- Warning
- For a bond between two different chains, it is not clearly defined to which chain it belongs. Therefore, this method will only return the number of bonds where both bonded atoms are within the same chain (all inclusive bonds).
◆ GetBounds()
| geom::AlignedCuboid GetBounds | ( | ) | const |
Get entity's axis aligned bounding box.
◆ GetCenterOfAtoms()
| 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
◆ GetCenterOfMass()
| geom::Vec3 GetCenterOfMass | ( | ) | const |
Get entity's center of mass (mass weighted)
◆ GetEntity()
| EntityView GetEntity | ( | ) | const |
Get parent entity view.
◆ GetHandle()
| ChainHandle GetHandle | ( | ) | const |
Get handle this view points to.
◆ GetHashCode()
| unsigned long GetHashCode | ( | ) | const |
get unique id
The unique id is the same for all ChainViews pointing to the same chain view data.
◆ GetMass()
| Real GetMass | ( | ) | const |
Get entity's mass.
◆ GetResidueByIndex()
| ResidueView GetResidueByIndex | ( | int | index | ) | const |
get residue by index
returns an invalid residue handle if the index is out of bounds
◆ GetResidueCount()
| int GetResidueCount | ( | ) | const |
Get number of residues in this chain view.
◆ GetResidueIndex()
| int GetResidueIndex | ( | const ResNum & | number | ) | const |
◆ GetResidueList()
| const ResidueViewList& GetResidueList | ( | ) | const |
Get residues of this chain view.
- Todo:
- Residue list may be unordered. Is it the responsibility of the method building the view to have them ordered or is it our job?
◆ HasAtoms()
| bool HasAtoms | ( | ) | const |
◆ InSequence()
| bool InSequence | ( | ) | const |
whether the residues form an ordered sequence with respect to their residue numbers.
◆ IsResidueIncluded()
| bool IsResidueIncluded | ( | const ResidueHandle & | handle | ) | const |
Check whether the view includes the given residue.
◆ IsValid()
| bool IsValid | ( | ) | const |
check validity of handle
- See also
- operator bool()
◆ operator bool()
|
inline |
check validity of handle
check, whether the chain handle points to a valid handle.
- 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.
Definition at line 56 of file chain_view.hh.
◆ operator!=()
| bool operator!= | ( | const ChainView & | rhs | ) | const |
◆ operator==()
| bool operator== | ( | const ChainView & | rhs | ) | const |
◆ RemoveResidue()
| void RemoveResidue | ( | ResidueView | view | ) |
remove given residue from the view
◆ RemoveResidues()
| void RemoveResidues | ( | ) |
///
remove all residues from the view
◆ Select() [1/2]
| EntityView Select | ( | const Query & | q, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on a query object
- See also
- Query
◆ Select() [2/2]
| EntityView Select | ( | const String & | query_string, |
| QueryFlags | flags = 0 |
||
| ) | const |
return view based on query String.
- See also
- Query
◆ ViewData() [1/2]
|
inline |
Get view data.
Definition at line 180 of file chain_view.hh.
◆ ViewData() [2/2]
|
inline |
Get view data.
Definition at line 185 of file chain_view.hh.
◆ ViewForHandle() [1/2]
| AtomView ViewForHandle | ( | const AtomHandle & | atom | ) | const |
◆ ViewForHandle() [2/2]
| ResidueView ViewForHandle | ( | const ResidueHandle & | handle | ) | const |
Find residue by residue handle.
The documentation for this class was generated from the following file:
- build-2.9.0-doc/stage/include/ost/mol/chain_view.hh
