SimTK::Biopolymer Class Reference

The base class for DNA, RNA, and Protein molecules. More...

#include <Compound.h>

Inheritance diagram for SimTK::Biopolymer:

List of all members.

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

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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).

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Member Typedef Documentation

typedef String SimTK::Biopolymer::Sequence

String representing the sequence of a Protein or nucleic acid (DNA or RNA).

For use in Biopolymer constructor.

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Constructor & Destructor Documentation

SimTK::Biopolymer::Biopolymer

(

)

Default constructore for Biopolymer.

Produces a Biopolymer with no atoms nor residues.

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Member Function Documentation

int SimTK::Biopolymer::getNumResidues

(

)

const

Returns:

The number of residues in the polymer chain.

const ResidueInfo& SimTK::Biopolymer::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).

ResidueInfo& SimTK::Biopolymer::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).

const ResidueInfo& SimTK::Biopolymer::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.

ResidueInfo& SimTK::Biopolymer::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.

const Compound::Name& SimTK::Biopolymer::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& SimTK::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.

bool SimTK::Biopolymer::assignResidueBiotypes	(	ResidueInfo::Index	,
		Ordinality::Residue
	)

void SimTK::Biopolymer::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.

ResidueInfo::Index SimTK::Biopolymer::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.

ResidueInfo::Index SimTK::Biopolymer::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

Biopolymer& SimTK::Biopolymer::setResidueBondMobility	(	ResidueInfo::Index	,
		BondMobility::Mobility
	)

MobilizedBodyIndex SimTK::Biopolymer::getResidueAtomMobilizedBodyIndex	(	ResidueInfo::Index	res,
		ResidueInfo::AtomIndex	a
	)		const [inline]

Vec3 SimTK::Biopolymer::getResidueAtomLocationInMobilizedBodyFrame	(	ResidueInfo::Index	res,
		ResidueInfo::AtomIndex	a
	)		const [inline]

virtual AtomTargetLocations SimTK::Biopolymer::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 SimTK::Compound.

virtual AtomTargetLocations SimTK::Biopolymer::createAtomTargets

(

const class PdbChain &

targetChain

)

const [virtual]

Compute atom location in local Compound frame.

Returns:

default (initial) location of atom in orthogonal nanometers with respect to Ground frame

Reimplemented from SimTK::Compound.

SimTK::Biopolymer::SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS	(	Biopolymer	,
		BiopolymerRep	,
		Molecule
	)

int SimTK::Biopolymer::getNResidues

(

)

const [inline]

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

• Compound.h