Residue handle. More...
#include <residue_handle.hh>
Inherits ost::mol::ResidueBase.
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()
XCSEditor edi=residue.GetEntity().EditXCS();
edi.InsertAtom(residue, "CA", geom.Vec3(1.0, 0.0, 0.0));
Definition at line 54 of file residue_handle.hh.
| ResidueHandle | ( | ) |
| ResidueHandle | ( | const impl::ResidueImplPtr & | impl | ) | [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 String & | query_string, | |
| QueryFlags | flags = 0 | |||
| ) | const |
return view based on query String.
| EntityView Select | ( | const Query & | q, | |
| QueryFlags | flags = 0 | |||
| ) | const |
return view based on a query object
| 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. |
1.6.1