RNA Class Reference

#include <RNA.h>

Inheritance diagram for RNA:

List of all members.

Public Member Functions
	RNA (const PdbStructure &pdbStructure)
	RNA (const PdbChain &pdbChain)
	RNA (const Sequence &seq, bool useCappingHydroxyls=true)
	/brief First parameter is just the RNA sequence in single-letter code.
RNA &	setRNABondMobility (BondMobility::Mobility mobility, ResidueInfo::Index startResidue, ResidueInfo::Index endResidue)
	/brief This method sets the BondMobility::Mobility for each residue in a stretch of polynucleotide spanning residues startResidue to endResidue.
Vec3	calcRNABaseNormal (const State &state, int residueNumber, int bodyOrGroundFrame, const SimbodyMatterSubsystem &matter) const
	/brief This method returns the base normal of a given residue.

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Constructor & Destructor Documentation

RNA

(

const PdbStructure &

pdbStructure

)

[inline, explicit]

References PdbModel::getChain(), and PdbStructure::getModel().

RNA

(

const PdbChain &

pdbChain

)

[inline, explicit]

RNA	(	const Sequence &	seq,
		bool	useCappingHydroxyls = true
	)			[inline, explicit]

/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(), Compound::setPdbResidueNumber(), String::size(), and RibonucleosideResidue::withPhosphodiester().

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Member Function Documentation

Vec3 calcRNABaseNormal	(	const State &	state,
		int	residueNumber,
		int	bodyOrGroundFrame,
		const SimbodyMatterSubsystem &	matter
	)			const [inline]

/brief This method returns the base normal of a given residue.

the direction of the normal follows the "curl" of the atoms in the cycle of which the glycosidic nitrogen is a part, following the numbering convention in use here. added by scf

/param residueNumber starts at 0. bodyOrGroundFrame = 0 if the normal is desired in the frame of the glycosidic nitrogen, = 1 if in the frame of Ground.

References ResidueInfo::getAtomIndex(), Compound::getAtomLocationInMobilizedBodyFrame(), Compound::getAtomMobilizedBodyIndex(), MobilizedBody::getBodyTransform(), SimbodyMatterSubsystem::getMobilizedBody(), ResidueInfo::getPdbResidueName(), Biopolymer::getResidue(), and Vec< M, ELT, STRIDE >::norm().

RNA& setRNABondMobility	(	BondMobility::Mobility	mobility,
		ResidueInfo::Index	startResidue,
		ResidueInfo::Index	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(), and Biopolymer::setResidueBondMobility().

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The documentation for this class was generated from the following file:

• RNA.h