OpenStructure
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#include <chain_view.hh>
Inherits ChainBase.
Public Member Functions | |
ChainView () | |
ChainView (ChainViewDataPtr data, impl::ChainImplPtr impl) | |
ChainView (const EntityView &entity, const ChainHandle &chain) | |
EntityView | GetEntity () const |
void | Apply (EntityVisitor &visitor) |
void | Apply (EntityViewVisitor &visitor) |
int | GetResidueCount () const |
int | GetAtomCount () const |
int | GetBondCount () const |
ResidueView | AddResidue (const ResidueHandle &residue_handle, ViewAddFlags flags=0) |
ResidueView | AddResidue (const ResidueView &residue_view, ViewAddFlags flags=0) |
AtomView | AddAtom (const AtomHandle &atom_handle, ViewAddFlags flags=0) |
ResidueView | FindResidue (const ResNum &number) const |
AtomView | FindAtom (const AtomHandle &atom) const |
AtomView | ViewForHandle (const AtomHandle &atom) const |
AtomView | FindAtom (const ResNum &num, const String &name) const |
ResidueView | ViewForHandle (const ResidueHandle &handle) const |
ResidueView | FindResidue (const ResidueHandle &handle) const |
bool | IsResidueIncluded (const ResidueHandle &handle) const |
ChainHandle | GetHandle () const |
const ResidueViewList & | GetResidueList () const |
void | RemoveResidue (ResidueView view) |
int | GetResidueIndex (const ResNum &number) const |
ResidueView | GetResidueByIndex (int index) const |
Real | GetMass () const |
geom::Vec3 | GetCenterOfMass () const |
geom::Vec3 | GetCenterOfAtoms () const |
geom::AlignedCuboid | GetBounds () const |
void | RemoveResidues () |
Handle validity | |
operator bool () const | |
bool | IsValid () const |
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 |
bool | operator== (const ChainView &rhs) const |
bool | operator!= (const ChainView &rhs) const |
bool | HasAtoms () const |
Public Member Functions inherited from ChainBase | |
ChainBase () | |
ChainBase (const impl::ChainImplPtr &impl) | |
String | GetName () const |
ChainType | GetType () const |
String | GetDescription () const |
const impl::ChainImplPtr & | Impl () const |
bool | IsPolymer () const |
bool | IsPolysaccharide () const |
bool | IsPolypeptide () const |
bool | IsPolynucleotide () const |
impl::ChainImplPtr & | Impl () |
operator bool () const | |
bool | IsValid () const |
Public Member Functions inherited from GenericPropContainer< ChainBase > | |
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< ChainBase > | |
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 ChainBase | |
GenericPropContainerImpl * | GpImpl () |
const GenericPropContainerImpl * | GpImpl () const |
void | CheckValidity () const |
Protected Member Functions inherited from ConstGenericPropContainer< ChainBase > | |
T | gp_get (const String &key) const |
T | gp_get (const String &key, const T &def) const |
GenericPropContainerImpl * | GetImpl () |
const GenericPropContainerImpl * | GetImpl () const |
definition of ChainView
Definition at line 37 of file chain_view.hh.
ChainView | ( | ) |
ChainView | ( | ChainViewDataPtr | data, |
impl::ChainImplPtr | impl | ||
) |
ChainView | ( | const EntityView & | entity, |
const ChainHandle & | chain | ||
) |
AtomView AddAtom | ( | const AtomHandle & | atom_handle, |
ViewAddFlags | flags = 0 |
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Add atom to view.
If the atoms's residue has not been added to the view it will be added.
atom_handle | The atom to add |
flags | Can be a ORed together combination of ViewAddFlag |
ResidueView AddResidue | ( | const ResidueHandle & | residue_handle, |
ViewAddFlags | flags = 0 |
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) |
Add residue to view.
If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the handle is not already included in the view.
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. |
ResidueView AddResidue | ( | const ResidueView & | residue_view, |
ViewAddFlags | flags = 0 |
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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.
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. |
void Apply | ( | EntityVisitor & | visitor | ) |
void Apply | ( | EntityViewVisitor & | visitor | ) |
AtomView FindAtom | ( | const AtomHandle & | atom | ) | const |
Find view for given atom handle Deprecated: Use ViewForHandle instead.
ResidueView FindResidue | ( | const ResNum & | number | ) | const |
Find residue by number.
ResidueView FindResidue | ( | const ResidueHandle & | handle | ) | const |
int GetAtomCount | ( | ) | const |
Get number of atoms in this chain view.
int GetBondCount | ( | ) | const |
Get number of all inclusive bonds of this chain.
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)
EntityView GetEntity | ( | ) | const |
Get parent entity view.
ChainHandle GetHandle | ( | ) | const |
Get handle this view points to.
Real GetMass | ( | ) | const |
Get entity's mass.
ResidueView GetResidueByIndex | ( | int | index | ) | const |
get residue by index
returns an invalid residue handle if the index is out of bounds
int GetResidueCount | ( | ) | const |
Get number of residues in this chain view.
int GetResidueIndex | ( | const ResNum & | number | ) | const |
const ResidueViewList& GetResidueList | ( | ) | const |
Get residues of this chain view.
bool HasAtoms | ( | ) | const |
bool InSequence | ( | ) | const |
whether the residues form an ordered sequence with respect to their residue numbers.
bool IsResidueIncluded | ( | const ResidueHandle & | handle | ) | const |
Check whether the view includes the given residue.
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check validity of handle
check, whether the chain handle points to a valid handle.
Definition at line 56 of file chain_view.hh.
bool operator!= | ( | const ChainView & | rhs | ) | const |
bool operator== | ( | const ChainView & | rhs | ) | const |
void RemoveResidue | ( | ResidueView | view | ) |
remove given residue from the view
void RemoveResidues | ( | ) |
///
remove all residues from the view
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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Get view data.
Definition at line 180 of file chain_view.hh.
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inline |
Get view data.
Definition at line 185 of file chain_view.hh.
AtomView ViewForHandle | ( | const AtomHandle & | atom | ) | const |
ResidueView ViewForHandle | ( | const ResidueHandle & | handle | ) | const |
Find residue by residue handle.