#include <residue_base.hh>
Inherits GenericPropContainer< ResidueBase >.
Inherited by 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::LPeptideLinking, indicating that the residue is capable to participate in a peptide bond. For nucleotides, the chemical class is either ChemClass::RNALinking or ChemClass::DNALinking. For unknown compounds the chemical class is ChemClass::Unknown.
When loading an entity from file, the one-letter and chemical class of a residue are assigned by the default builder.
Definition at line 59 of file residue_base.hh.
| ResidueBase | ( | ) |
| ResidueBase | ( | const impl::ResidueImplPtr & | impl | ) |
| ResidueBase | ( | const ResidueBase & | rhs | ) |
| void CheckValidity | ( | ) | const [protected] |
| ChemClass GetChemClass | ( | ) | const |
| 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.
| const GenericPropContainerImpl* GpImpl | ( | ) | const [protected] |
| GenericPropContainerImpl* GpImpl | ( | ) | [protected] |
| const impl::ResidueImplPtr& Impl | ( | ) | const |
| impl::ResidueImplPtr& Impl | ( | ) |
| bool IsNucleotideLinking | ( | ) | const |
whether the residue can be part of a polynucleotide
| bool IsPeptideLinking | ( | ) | const |
whether the residue can form peptide bonds
| bool IsValid | ( | ) | const |
| operator bool | ( | ) | const |
check validity of handle
check, whether the residue handle points to a valid residue.
| void SetChemClass | ( | ChemClass | cc | ) |
| void SetOneLetterCode | ( | char | olc | ) |
| void SetSecStructure | ( | SecStructure | ss | ) |
friend class ConstGenericPropContainer< ResidueBase > [friend] |
Definition at line 66 of file residue_base.hh.
1.5.8