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OpenStructure
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OpenStructure
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#include <residue_base.hh>
Inherits GenericPropContainer< ResidueBase >.
Inherited by ResidueHandle, and ResidueView.
Public Member Functions | |
| ResidueBase () | |
| ResidueBase (const impl::ResidueImplPtr &impl) | |
| ResidueBase (const ResidueBase &rhs) | |
 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 | 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 |
| std::map< String, GenericPropValue > | GetPropMap () const |
| std::vector< String > | GetPropList () const |
base class for ResidueHandle and ResidueView
This class implements the common functionality for both ResidueHandle and ResidueView.
Like atoms and chains, residues are generic property containers and as such can store user-defined properties.
Each residue has a residue number that uniquely identifies the residue in a chain. This number consists of a numeric part and an optional alphanumeric insertion code.
Residues have names that are usually 3 characters long. The most common residue types such as the 20 standard amino acids and nucleotides also have a defined one-letter code. For other residues, the one-letter code is set to ?.
Residues have a chemical class. For standard amino acids this class is ChemClass::L_PEPTIDE_LINKING, indicating that the residue is capable to participate in a peptide bond. For nucleotides, the chemical class is either ChemClass::RNA_LINKING or ChemClass::DNA_LINKING. For unknown compounds the chemical class is ChemClass::UNKNOWN.
In addition, residues have a ChemType. A classification of all components into nine categories (ions, non-canonical molecules, saccharised, nucleotides, amino acids, co-enzymes, water coordinated ions, drugs, solvents) as obtained from the PDB.
When loading an entity from file, the one-letter and chemical class of a residue are assigned by the default builder.
Definition at line 67 of file residue_base.hh.
| ResidueBase | ( | ) |
| ResidueBase | ( | const impl::ResidueImplPtr & | impl | ) |
| ResidueBase | ( | const ResidueBase & | rhs | ) |
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protected |
| AtomHandle GetCentralAtom | ( | ) | const |
returns main atom, ie CA for amino acids
| geom::Vec3 GetCentralNormal | ( | ) | const |
| ChemClass GetChemClass | ( | ) | const |
| ChemType GetChemType | ( | ) | const |
PDB ligand classification from component dictionary.
| int GetIntProperty | ( | Prop::ID | prop_id | ) | const |
Get int property by id.
| const ResidueKey& GetKey | ( | ) | const |
return the residue key.
| const ResNum& GetNumber | ( | ) | const |
return residue number
| TorsionHandle GetOmegaTorsion | ( | ) | const |
Get omega torsion.
If no omega torsion has been assigned to this residue an invalid TorsionHandle will be returned.
| char GetOneLetterCode | ( | ) | const |
| TorsionHandle GetPhiTorsion | ( | ) | const |
Get phi torsion.
If no phi torsion has been assigned to this residue an invalid TorsionHandle will be returned.
| TorsionHandle GetPsiTorsion | ( | ) | const |
Get psi torsion.
If no psi torsion has been assigned to this residue an invalid TorsionHandle will be returned.
| String GetQualifiedName | ( | ) | const |
get fully qualified name of residue, including the chain name, residue name and residue number
| SecStructure GetSecStructure | ( | ) | const |
Get secondary structure type. By default, the residue is in COIL conformation.
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protected |
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protected |
| impl::ResidueImplPtr& Impl | ( | ) |
| const impl::ResidueImplPtr& Impl | ( | ) | const |
| bool IsLigand | ( | ) | const |
| bool IsNucleotideLinking | ( | ) | const |
whether the residue can be part of a polynucleotide
| bool IsPeptideLinking | ( | ) | const |
whether the residue can form peptide bonds
| bool IsProtein | ( | ) | const |
whether the residue is part of the protein.
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inline |
check validity of handle
Reimplemented in ResidueView.
Definition at line 86 of file residue_base.hh.
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inline |
check validity of handle
check, whether the residue handle points to a valid residue.
Reimplemented in ResidueView.
Definition at line 83 of file residue_base.hh.
| void SetCentralAtom | ( | const AtomHandle & | a | ) |
set explicit central atom
overrides the heuristic of GetCentralAtom to explicitely use the given one as the central atom; passing in an invalid handle reverts back to the heurstic determination
| void SetChemClass | ( | ChemClass | cc | ) |
| void SetChemType | ( | ChemType | ct | ) |
| void SetIsLigand | ( | bool | ligand | ) |
| void SetIsProtein | ( | bool | protein | ) |
| void SetOneLetterCode | ( | char | olc | ) |
| void SetSecStructure | ( | SecStructure | ss | ) |
Set secondary structure type.
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friend |
Definition at line 87 of file residue_base.hh.
1.8.1.1