ResidueImpl Class Reference
#include <residue_impl.hh>
Inherits ost::GenericPropContainerImpl.
Public Member Functions |
| | ResidueImpl (const EntityImplPtr &ent, const ChainImplPtr &ch, const ResNum &num, const ResidueKey &key) |
| AtomImplPtr | InsertAtom (const String &name, const geom::Vec3 &pos, const String &ele) |
| AtomImplPtr | InsertAtom (const AtomImplPtr &atom) |
| AtomImplPtr | InsertAltAtom (const String &name, const String &alt_group, const geom::Vec3 &pos, const String &ele, Real occ, Real b_factor) |
| const ResNum & | GetNumber () const |
| void | SetNumber (const ResNum &num) |
| const ResidueKey & | GetKey () const |
| void | SetKey (const ResidueKey &key) |
| ChainImplPtr | GetChain () const |
| AtomImplPtr | GetCentralAtom () const |
| void | SetCentralAtom (const AtomImplPtr &a) |
| geom::Vec3 | GetCentralNormal () const |
| char | GetOneLetterCode () const |
| void | SetOneLetterCode (const char olc) |
| AtomImplPtr | FindAtom (const String &aname) const |
| void | Apply (EntityVisitor &v) |
| int | GetAtomCount () const |
| int | GetBondCount () const |
| EntityImplPtr | GetEntity () const |
| TorsionImplP | GetPhiTorsion () const |
| TorsionImplP | GetOmegaTorsion () const |
| TorsionImplP | GetPsiTorsion () const |
| SecStructure | GetSecStructure () const |
| void | SetSecStructure (SecStructure ss) |
| const AtomImplList & | GetAtomList () const |
| AtomImplList & | GetAtomList () |
| Real | GetMass () const |
| geom::Vec3 | GetCenterOfMass () const |
| geom::Vec3 | GetCenterOfAtoms () const |
| geom::AlignedCuboid | GetBounds () const |
| void | DeleteAtom (const AtomImplPtr &atom) |
| void | DeleteAtoms (const String &atom_name) |
| void | DeleteAllAtoms () |
| void | AddTorsion (const TorsionImplP &torsion) |
| const TorsionImplList & | GetTorsionList () const |
| bool | HasAltAtomGroup (const String &group) const |
| std::vector< String > | GetAltAtomGroupNames () const |
| std::vector< String > | GetAltAtomGroupNames (const AtomImplPtr &atom) const |
| bool | HasAltAtoms () const |
| Real | GetAverageBFactor () const |
| bool | SwitchAtomPos (const String &group) |
| void | AddAltAtomPos (const String &group, const AtomImplPtr &atom, const geom::Vec3 &position, Real occ, Real b_factor) |
| geom::Vec3 | GetAltAtomPos (const AtomImplPtr &atom, const String &group) const |
| Real | GetAltAtomOcc (const AtomImplPtr &atom, const String &group) const |
| Real | GetAltAtomBFactor (const AtomImplPtr &atom, const String &group) const |
| const String & | GetCurrentAltGroupName () const |
| int | GetIndex () const |
| String | GetQualifiedName () const |
| const String & | GetName () const |
| TorsionImplList & | GetTorsionList () |
| void | SetChemClass (ChemClass cc) |
| ChemClass | GetChemClass () const |
| ChemType | GetChemType () const |
| void | SetChemType (ChemType ct) |
| TorsionImplP | FindTorsion (const String &torsion_name) const |
| String | GetStringProperty (Prop::ID prop_id) const |
| Real | GetFloatProperty (Prop::ID prop_id) const |
| int | GetIntProperty (Prop::ID prop_id) const |
| void | SetProtein (bool protein) |
| bool | IsProtein () const |
| bool | IsLigand () const |
| void | SetIsLigand (bool flag) |
| void | UpdateTransformedPos () |
Detailed Description
Definition at line 47 of file residue_impl.hh.
Constructor & Destructor Documentation
Member Function Documentation
| void DeleteAtoms |
( |
const String & |
atom_name |
) |
|
Find atom by name.
- Todo:
- make the return type a AtomImplList, since there may be several atoms with the given name.
- Returns:
- The first atom matchin the name, or an invalid AtomImplPtr if there is no such atom.
| std::vector<String> GetAltAtomGroupNames |
( |
|
) |
const |
| int GetAtomCount |
( |
|
) |
const |
Get number of atoms of this residue.
| Real GetAverageBFactor |
( |
|
) |
const |
retrieve average temperature factor of residue.
| int GetBondCount |
( |
|
) |
const |
Get number of bonds of this residue.
| const String& GetCurrentAltGroupName |
( |
|
) |
const [inline] |
| int GetIntProperty |
( |
Prop::ID |
prop_id |
) |
const |
| const String& GetName |
( |
|
) |
const [inline] |
Get name of residue. At the moment an alias for GetKey.
Definition at line 189 of file residue_impl.hh.
| const ResNum& GetNumber |
( |
|
) |
const [inline] |
Retrieve omega torsion between this and the previous residue.
If no omega torsion has been assigned to this residue an invalid TorsionImplP will be returned.
| char GetOneLetterCode |
( |
|
) |
const |
Get phi torsion.
If no phi torsion has been assigned to this residue an invalid TorsionImplP will be returned.
Get psi torsion.
If no psi torsion has been assigned to this residue an invalid TorsionImplP will be returned.
| String GetQualifiedName |
( |
|
) |
const |
Get secondary structure type. By default, the residue is in COIL conformation.
Get all torsions this residue is involved in.
Definition at line 194 of file residue_impl.hh.
| bool HasAltAtomGroup |
( |
const String & |
group |
) |
const |
Test if residue has alternative atoms with a certain name.
| bool HasAltAtoms |
( |
|
) |
const |
insert new residue with exactly the same parameters as atom, but no bonds
| bool IsLigand |
( |
|
) |
const [inline] |
| bool IsProtein |
( |
|
) |
const [inline] |
explicitely set central atom
if this is set, it will override the heuristic encoded in GetCentralAtom; pass an invalid ptr to deactivate again
| void SetChemType |
( |
ChemType |
ct |
) |
[inline] |
| void SetIsLigand |
( |
bool |
flag |
) |
[inline] |
| void SetNumber |
( |
const ResNum & |
num |
) |
[inline] |
| void SetOneLetterCode |
( |
const char |
olc |
) |
|
| void SetProtein |
( |
bool |
protein |
) |
[inline] |
Set secondary structure type.
| bool SwitchAtomPos |
( |
const String & |
group |
) |
|
| void UpdateTransformedPos |
( |
|
) |
|
The documentation for this class was generated from the following file:
1.6.1
