Biopolymer Class Reference
The base class for DNA, RNA, and Protein molecules. More...
#include <Compound.h>
Public Types | |
| typedef String | Sequence |
| String representing the sequence of a Protein or nucleic acid (DNA or RNA). | |
Public Member Functions | |
| Biopolymer () | |
| Default constructore for Biopolymer. | |
| int | getNumResidues () const |
| const ResidueInfo & | getResidue (ResidueInfo::Index residueIndex) const |
| ResidueInfo & | updResidue (ResidueInfo::Index residueIndex) |
| const ResidueInfo & | getResidue (Compound::Name residueName) const |
| ResidueInfo & | updResidue (Compound::Name residueName) |
| const Compound::Name & | getResidueName (ResidueInfo::Index residueIndex) const |
| Biopolymer & | renumberPdbResidues (int firstPdbResidueNumber) |
| This method renumbers the PDB Residue Numbers of the biopolymer chain to start at the supplied integer and increase consecutively. | |
| bool | assignResidueBiotypes (ResidueInfo::Index, Ordinality::Residue) |
| void | assignBiotypes () |
| Attempt to automatically assign a Biotype to each atom. | |
| ResidueInfo::Index | appendResidue (const Compound::Name &resName, const BiopolymerResidue &residue) |
| Attach a new residue onto the end of the current Biopolymer chain. | |
| ResidueInfo::Index | appendResidue (const Compound::Name &resName, const BiopolymerResidue &residue, BondMobility::Mobility mobility) |
| Attach a new residue onto the end of the current Biopolymer chain. | |
| Biopolymer & | setResidueBondMobility (ResidueInfo::Index, BondMobility::Mobility) |
| MobilizedBodyIndex | getResidueAtomMobilizedBodyIndex (ResidueInfo::Index res, ResidueInfo::AtomIndex a) const |
| Vec3 | getResidueAtomLocationInMobilizedBodyFrame (ResidueInfo::Index res, ResidueInfo::AtomIndex a) const |
| virtual AtomTargetLocations | createAtomTargets (const class PdbStructure &targetStructure) const |
| Create a mapping between this Compound and atom locations in a PdbStructure. | |
| virtual AtomTargetLocations | createAtomTargets (const class PdbChain &targetChain) const |
| Compute atom location in local Compound frame. | |
| SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS (Biopolymer, BiopolymerRep, Molecule) | |
| int | getNResidues () const |
Detailed Description
The base class for DNA, RNA, and Protein molecules.
Contains an ordered list of BiopolymerResidue subcompounds. Derives from Molecule. (though that may not be obvious in the automatically generated API documentation).
Member Typedef Documentation
String representing the sequence of a Protein or nucleic acid (DNA or RNA).
For use in Biopolymer constructor.
Constructor & Destructor Documentation
| Biopolymer | ( | ) |
Default constructore for Biopolymer.
Produces a Biopolymer with no atoms nor residues.
Member Function Documentation
| ResidueInfo::Index appendResidue | ( | const Compound::Name & | resName, | |
| const BiopolymerResidue & | residue, | |||
| BondMobility::Mobility | mobility | |||
| ) |
Attach a new residue onto the end of the current Biopolymer chain.
- Parameters:
-
resName new residue name, from the viewpoint of this parent Biopolymer residue template residue to copy onto the end of the chain. The residue will be copied, not incorporated. mobility allowed motion of the new bond connecting the new residue to the rest of the chain
| ResidueInfo::Index appendResidue | ( | const Compound::Name & | resName, | |
| const BiopolymerResidue & | residue | |||
| ) |
Attach a new residue onto the end of the current Biopolymer chain.
- Parameters:
-
resName new name for the new residue, local to this parent Biopolymer. residue template residue to copy onto the end of the chain. The residue will be copied, not incorporated.
Referenced by RNA::RNA().
| void assignBiotypes | ( | ) |
Attempt to automatically assign a Biotype to each atom.
Biotype assignments for each atom in a compound are required to match atoms to force field parameters. Residue name and atom name, including synonyms, are used to identify Biotypes. Previous loading of relevant Biotypes from a force field definition may be required for the assignBiotypes() method to work.
| bool assignResidueBiotypes | ( | ResidueInfo::Index | , | |
| Ordinality::Residue | ||||
| ) |
| virtual AtomTargetLocations createAtomTargets | ( | const class PdbChain & | targetChain | ) | const [virtual] |
| virtual AtomTargetLocations createAtomTargets | ( | const class PdbStructure & | targetStructure | ) | const [virtual] |
Create a mapping between this Compound and atom locations in a PdbStructure.
For use in the process of importing a configuration from a PDB file
Reimplemented from Compound.
| int getNResidues | ( | ) | const [inline] |
| int getNumResidues | ( | ) | const |
- Returns:
- The number of residues in the polymer chain.
| const ResidueInfo& getResidue | ( | Compound::Name | residueName | ) | const |
- Returns:
- A read-only reference to a BiopolymerResidue subcompound of this Biopolymer molecule
- Parameters:
-
residueName a Compound::Name for the BiopolymerResidue from the viewpoint of this Biopolymer.
| const ResidueInfo& getResidue | ( | ResidueInfo::Index | residueIndex | ) | const |
- Warning:
- The residueIndex is ordinarily NOT the same as the PdbResidueNumber of the BiopolymerResidue.
- Returns:
- A read-only reference to a BiopolymerResidue subcompound of this Biopolymer molecule
- Parameters:
-
residueIndex integer index of residue in context of this Biopolymer, in the range zero (0) to (getNumResidues() - 1).
Referenced by RNA::calcRNABaseNormal().
| Vec3 getResidueAtomLocationInMobilizedBodyFrame | ( | ResidueInfo::Index | res, | |
| ResidueInfo::AtomIndex | a | |||
| ) | const [inline] |
| MobilizedBodyIndex getResidueAtomMobilizedBodyIndex | ( | ResidueInfo::Index | res, | |
| ResidueInfo::AtomIndex | a | |||
| ) | const [inline] |
| const Compound::Name& getResidueName | ( | ResidueInfo::Index | residueIndex | ) | const |
- Warning:
- The residueIndex is ordinarily NOT the same as the PdbResidueNumber of the BiopolymerResidue.
- Returns:
- A Compound::Name for a BiopolymerResidue from the viewpoint of this containing Biopolymer.
- Parameters:
-
residueIndex integer index of residue in context of this Biopolymer, in the range zero (0) to (getNumResidues() - 1).
| Biopolymer& renumberPdbResidues | ( | int | firstPdbResidueNumber | ) |
This method renumbers the PDB Residue Numbers of the biopolymer chain to start at the supplied integer and increase consecutively.
- Returns:
- A reference to this Biopolymer.
| Biopolymer& setResidueBondMobility | ( | ResidueInfo::Index | , | |
| BondMobility::Mobility | ||||
| ) |
Referenced by RNA::setRNABondMobility().
| SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS | ( | Biopolymer | , | |
| BiopolymerRep | , | |||
| Molecule | ||||
| ) |
| ResidueInfo& updResidue | ( | Compound::Name | residueName | ) |
- Returns:
- A mutable reference to a BiopolymerResidue subcompound of this Biopolymer molecule
- Parameters:
-
residueName a Compound::Name for the BiopolymerResidue from the viewpoint of this Biopolymer.
| ResidueInfo& updResidue | ( | ResidueInfo::Index | residueIndex | ) |
- Warning:
- The residueIndex is ordinarily NOT the same as the PdbResidueNumber of the BiopolymerResidue.
- Returns:
- A mutable reference to a BiopolymerResidue subcompound of this Biopolymer molecule
- Parameters:
-
residueIndex integer index of residue in context of this Biopolymer, in the range zero (0) to (getNumResidues() - 1).
The documentation for this class was generated from the following file:
