OpenStructure
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#include <residue_handle.hh>
Inherits ResidueBase.
Public Member Functions | |
ResidueHandle () | |
ResidueHandle (const impl::ResidueImplPtr &impl) | |
EntityHandle | GetEntity () const |
double | GetMass () const |
geom::Vec3 | GetCenterOfMass () const |
geom::Vec3 | GetCenterOfAtoms () const |
geom::AlignedCuboid | GetBounds () const |
ChainHandle | GetChain () const |
ResidueHandle | GetPrev () const |
ResidueHandle | GetNext () const |
AtomHandle | FindAtom (const String &aname) const |
void | Apply (EntityVisitor &visitor) |
AtomHandleList | GetAtomList () const |
int | GetAtomCount () const |
int | GetBondCount () const |
TorsionHandle | FindTorsion (const String &torsion_name) const |
TorsionHandleList | GetTorsionList () const |
int | GetIndex () const |
ResidueHandle | GetHandle () const |
unsigned long | GetHashCode () const |
EntityView | Select (const Query &q, QueryFlags flags=0) const |
EntityView | Select (const String &query_string, QueryFlags flags=0) const |
bool | operator== (const ResidueHandle &ref) const |
bool | operator!= (const ResidueHandle &ref) const |
Alternative atom positions | |
Alternative atom positions have traditionally been used to indicate that the position of an atom is not limited to one point, but that the atom may occur at more than one position. The following functions let you work with alternative atom locations on the level of residues. | |
bool | HasAltAtomGroup (const String &group) const |
const String & | GetCurrentAltGroupName () const |
std::vector< String > | GetAltAtomGroupNames () const |
bool | HasAltAtoms () const |
geom::Vec3 | GetAltAtomPos (const AtomHandle &atom, const String &group) const |
bool | SwitchAtomPos (const String &group) |
Public Member Functions inherited from ResidueBase | |
ResidueBase () | |
ResidueBase (const impl::ResidueImplPtr &impl) | |
ResidueBase (const ResidueBase &rhs) | |
operator bool () const | |
bool | IsValid () const |
const ResNum & | GetNumber () const |
const ResidueKey & | GetKey () const |
const String & | GetName () const |
String | GetQualifiedName () const |
AtomHandle | GetCentralAtom () const |
void | SetCentralAtom (const AtomHandle &a) |
geom::Vec3 | GetCentralNormal () const |
bool | IsPeptideLinking () const |
bool | IsNucleotideLinking () const |
ChemClass | GetChemClass () const |
void | SetChemClass (ChemClass cc) |
ChemType | GetChemType () const |
void | SetChemType (ChemType ct) |
SecStructure | GetSecStructure () const |
void | SetSecStructure (SecStructure ss) |
TorsionHandle | GetPhiTorsion () const |
TorsionHandle | GetPsiTorsion () const |
TorsionHandle | GetOmegaTorsion () const |
char | GetOneLetterCode () const |
void | SetOneLetterCode (char olc) |
String | GetStringProperty (Prop::ID prop_id) const |
Real | GetFloatProperty (Prop::ID prop_id) const |
int | GetIntProperty (Prop::ID prop_id) const |
bool | IsProtein () const |
void | SetIsProtein (bool protein) |
void | SetIsLigand (bool ligand) |
bool | IsLigand () const |
impl::ResidueImplPtr & | Impl () |
const impl::ResidueImplPtr & | Impl () const |
Public Member Functions inherited from GenericPropContainer< ResidueBase > | |
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< ResidueBase > | |
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 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 |
Residue handle.
In a polymer a residue is a single unit such as a nucleotide or an amino acid. In case of ligands, a residue ofter represents a completye molecule, such as a HEM group.
Every residue belongs to a chain and has a defined position (GetIndex) in that chain. In a peptide chain, the previous (towards N-terminus) and next (towards C-terminus) can be obtained with GetPrev() and GetNext() respectively.
A residue consist of one or more atoms. The list of atoms can be retrieved with GetAtomList(), wheras FindAtom() will locate a particular atom in the residue.
To add atoms to the residue, you have to request an editor and call EditorBase::InsertAtom() or EditorBase::InsertAltAtom()
Definition at line 54 of file residue_handle.hh.
ResidueHandle | ( | ) |
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inline |
Definition at line 59 of file residue_handle.hh.
void Apply | ( | EntityVisitor & | visitor | ) |
AtomHandle FindAtom | ( | const String & | aname | ) | const |
Find atom by name.
aname | is the atom name |
TorsionHandle FindTorsion | ( | const String & | torsion_name | ) | const |
Find torsion by name.
torsion_name | is the name of the torsion you are looking for. Torsions are named with uppercase letters. |
std::vector<String> GetAltAtomGroupNames | ( | ) | const |
Get names of alternative atom groups.
geom::Vec3 GetAltAtomPos | ( | const AtomHandle & | atom, |
const String & | group | ||
) | const |
Get alternative atom position for given atom.
If the atom is not in group
, an IntegrityError is thrown.
int GetAtomCount | ( | ) | const |
Get number of atoms of this residue.
AtomHandleList GetAtomList | ( | ) | const |
Get number of atoms of this residue.
int GetBondCount | ( | ) | const |
Get number of bonds of this residue. This method might NOT work as expected (see warning below).
geom::AlignedCuboid GetBounds | ( | ) | const |
get axis-aligned bounding box of residue
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)
ChainHandle GetChain | ( | ) | const |
The chain this residue is attached to.
const String& GetCurrentAltGroupName | ( | ) | const |
Name of active alternative atom group.
EntityHandle GetEntity | ( | ) | const |
ResidueHandle GetHandle | ( | ) | const |
get this handle
This method exists as a convenience duck-typing in Python.
unsigned long GetHashCode | ( | ) | const |
int GetIndex | ( | ) | const |
Get position of residue in chain.
double GetMass | ( | ) | const |
Get residue's mass.
ResidueHandle GetNext | ( | ) | const |
Get next residue in chain.
ResidueHandle GetPrev | ( | ) | const |
Get previous residue in chain.
TorsionHandleList GetTorsionList | ( | ) | const |
Get list of all torsion angles of this residue.
bool HasAltAtomGroup | ( | const String & | group | ) | const |
Test if residue has group of alternative atoms with a certain name.
bool HasAltAtoms | ( | ) | const |
Test if the residue has any alternative atom positions.
bool operator!= | ( | const ResidueHandle & | ref | ) | const |
bool operator== | ( | const ResidueHandle & | ref | ) | const |
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.
bool SwitchAtomPos | ( | const String & | group | ) |
switch atoms that have alternative positions to the position in the group. Atoms that do not have an alternative position are left untouched.
group | is the group name to switch to. |