RNA Class Reference
#include <RNA.h>
Public Member Functions | |
| RNA (const PdbStructure &pdbStructure) | |
| RNA (const PdbChain &pdbChain) | |
| RNA (const Sequence &seq, int useCappingHydroxyls=1) | |
| /brief First parameter is just the RNA sequence in single-letter code. | |
| RNA | setRNABondMobility (BondMobility::Mobility mobility, int startResidue, int endResidue) |
| /brief This method sets the BondMobility::Mobility for each residue in a stretch of polynucleotide spanning residues startResidue to endResidue. | |
Constructor & Destructor Documentation
| RNA | ( | const PdbStructure & | pdbStructure | ) | [inline] |
References PdbModel::getChain(), and PdbStructure::getModel().
/brief First parameter is just the RNA sequence in single-letter code.
AUGC are the only residue types supported at this time. Second parameter, when set to zero, results in an RNA with no capping hydroxyls at the termini. Instead the terminal residues have the same complement of atoms as residues in the interior of the chain.
References Biopolymer::appendResidue(), BiopolymerResidue::assignBiotypes(), Compound::bondCompound(), Compound::convertInboardBondCenterToOutboard(), RibonucleotideResidue::create(), Compound::defineDihedralAngle(), Biotype::exists(), SimTK::Ordinality::Final, Biotype::get(), Compound::getPdbResidueName(), Compound::hasAtom(), Compound::inheritAtomNames(), SimTK::Ordinality::Initial, Biotype::initializePopularBiotypes(), Compound::setBiotypeIndex(), Compound::setDefaultDihedralAngle(), and Compound::setPdbResidueNumber().
Member Function Documentation
| RNA setRNABondMobility | ( | BondMobility::Mobility | mobility, | |
| int | startResidue, | |||
| int | endResidue | |||
| ) | [inline] |
/brief This method sets the BondMobility::Mobility for each residue in a stretch of polynucleotide spanning residues startResidue to endResidue.
It also sets the BondMobility::Mobility for bonds connecting the included residues to the same value.
Added by Samuel Flores /brief This method sets the BondMobility for all bonds in a certain stretch of residues of a polynucleotide chain added by scf
References Compound::setBondMobility(), Compound::setCompoundBondMobility(), and Biopolymer::updResidue().
The documentation for this class was generated from the following file:
