Protein or molecule. More...
#include <entity_handle.hh>
Inherits ost::mol::EntityBase.
Protein or molecule.
Molecules such as proteins and ligands are all represented as entities in OpenStructure. To work with subsets of atoms, residues, chains and bonds, refer to EntityView
Entities consist of zero or more chains of residues. The interface of entities is tailored to proteins, but is not limited to that. An entity may also represent a ligand or a collection of water molecules - hence the rather generic name. A new, empty entity is created with CreateEntity(). Atoms, residues, chains and bonds are added,removed or manipulated via editors.
Definition at line 54 of file entity_handle.hh.
| EntityHandle | ( | const impl::EntityImplPtr & | ) |
internally used ctor
| EntityHandle | ( | ) |
default ctor. creates invalid handle.
| void Apply | ( | EntityVisitor & | v | ) |
visitor interface
| void AttachObserver | ( | const EntityObserverPtr & | ) |
attach observer
| void ClearTransform | ( | ) |
remove transform
| EntityHandle Copy | ( | ) | const |
copy entity, effectively duplicating the whole data structure
Alternative atom positions are not handled at all!
| EntityView CreateEmptyView | ( | ) | const |
return a (new) empty view of this entity
| EntityView CreateFullView | ( | ) | const |
return a (new) full view of this entity
| void DeepSwap | ( | EntityHandle & | eh | ) |
deep swaps the implementations, effectively affecting _all_ entity handles that point to either
| void DetachObserver | ( | const EntityObserverPtr & | ) |
remove observer
Get editor for the internal coordinate system to manipulate torsions bond lengths and angles between bonds.
Get editor for external coordinate system to manipulate atom positions.
| AtomHandle FindAtom | ( | const String & | chain_name, | |
| const ResNum & | number, | |||
| const String & | atom_name | |||
| ) | const |
| ChainHandle FindChain | ( | const String & | name | ) | const |
Find chain by name.
Find chain within this entity with given name.
| ResidueHandle FindResidue | ( | const String & | chain_name, | |
| const ResNum & | number | |||
| ) | const |
| TorsionHandle FindTorsion | ( | const AtomHandle & | a1, | |
| const AtomHandle & | a2, | |||
| const AtomHandle & | a3, | |||
| const AtomHandle & | a4 | |||
| ) | const |
Search a specific torsion.
The order of atoms is important. For the torsion to exist, it must have been added before via AddTorsion.
| AtomHandleList FindWithin | ( | const geom::Vec3 & | pos, | |
| Real | radius | |||
| ) | const |
use atom hash to perform fast within lookup
| void FixTransform | ( | ) |
write transformed pos to orig, and the clear tf
Get angle in radians between bonds a1-a2 and a2-a3.
| Real GetAngle | ( | const AtomHandle & | a1, | |
| const AtomHandle & | a2, | |||
| const AtomHandle & | a3 | |||
| ) | const |
Get angle in radians between bonds a1-a2 and a2-a3.
| int GetAtomCount | ( | ) | const |
Get number of atoms of this entity.
To count the atoms of a specific chain or residue, use the respective method of ChainHandle and ResidueHandle.
| AtomHandleList GetAtomList | ( | ) | const |
get complete list of atoms
| geom::Vec3List GetAtomPosList | ( | bool | ordered_by_index = false |
) | const |
get complete list of atom positions
| int GetBondCount | ( | ) | const |
Get number of bonds.
| mol::BondHandleList GetBondList | ( | ) | const |
Get list of bonds.
| geom::AlignedCuboid GetBounds | ( | ) | const |
| 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).
| int GetChainCount | ( | ) | const |
Get number of chains of this entity.
| ChainHandleList GetChainList | ( | ) | const |
Get list of chains.
| QueryFlags GetDefaultQueryFlags | ( | ) | const |
return default query flags
| EntityHandle GetHandle | ( | ) | const |
get this handle
Useful for templated code and duck-typing in Python
| geom::Mat4 GetInvTransformationMatrix | ( | ) | const |
DEPRECATED.
| Real GetMass | ( | ) | const |
Get entity's mass.
| int GetResidueCount | ( | ) | const |
Get number of residues of this entity.
To count the atoms of a chain, use the GetResidueCount() of ChainHandle.
| ResidueHandleList GetResidueList | ( | ) | const |
get complete list of residues
| geom::Transform GetTransform | ( | ) | const |
retrieve transformation of this entity
| geom::Mat4 GetTransformationMatrix | ( | ) | const |
DEPRECATED.
| bool HasTransform | ( | ) | const |
checks whether a transform has been set
| bool IsTransformationIdentity | ( | ) | const |
DEPRECATED.
| bool operator!= | ( | const EntityHandle & | ref | ) | const |
| bool operator== | ( | const EntityHandle & | ref | ) | const |
| EntityView Select | ( | const String & | query_string, | |
| QueryFlags | flags | |||
| ) | const |
return view based on query String, specifying behavior flags
| EntityView Select | ( | const Query & | q, | |
| QueryFlags | flags | |||
| ) | const |
return view based on a query object, specifying behavior flags
| EntityView Select | ( | const String & | query_string | ) | const |
return view based on query String.
| EntityView Select | ( | const Query & | q | ) | const |
return view based on a query object
| void SetDefaultQueryFlags | ( | QueryFlags | flags | ) |
set default query flags these will be used if flags are not explicitely specified as a second argument to a Select call
| void SetTransform | ( | const geom::Transform & | t | ) |
set transformation that will affect this entity
| void Swap | ( | EntityHandle & | eh | ) |
swaps implementations on the entity handle level
| DLLEXPORT_OST_MOL EntityHandle CreateEntity | ( | ) | [related] |
create entity
friend class ICSEditor [friend] |
Definition at line 57 of file entity_handle.hh.
friend class XCSEditor [friend] |
Definition at line 56 of file entity_handle.hh.
1.6.1
