PProtein Class Reference

#include <PProtein.h>

Inheritance diagram for PProtein:

List of all members.

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Detailed Description

A subclass of PChain which makes strong assumptions about the properties the loop should have. Specifically, convenience methods are provided to selectively manipulate the backbone and sidechain or to retrieve anchor/end effector atoms at the amino or carboxy terminus. This class should be used when using the builtin resources with LoopTK.

Usage of a PProtein must follow the following sequence of steps:

1. Construction - all residues are added to chain. Use the PProtein::AddResidue() methods to do this.
2. Finalization - finishes construction of the protein and prepares it for manipulation. Use PProtein::finalize() to do this.
3. Analysis - the full range of functionality of PProtein can be used at this point. However, no more residues can be added.

Creating a PProtein using PDBIO automatically completes the first two steps.

Public Member Functions
	PProtein ()
	PProtein (const string &firstResidueName)
	PProtein (const string &firstResidueName, PResidueSpec &firstResidueSpec)
	PProtein (PProtein *protein, int resStartIndex, int resEndIndex)
	PProtein (int numResidues)
PProtein *	getParent ()
PProtein *	getTopLevelProtein ()
PProteinResidue *	getResidue (int localIndex)
PProteinResidue *	getResidueByPdbIndex (int pdbIndex)
PProtein *	getSubchainByPdbIndices (int startPdbIndex, int endPdbIndex)
int	NumBackboneDOFs () const
int	NumSidechainDOFs () const
void	RandomizeSidechainAtRes (int resIndex)
void	RandomizeAllSidechains ()
void	GetEndEffectors (ProteinSide side, PAtom *&endAtom, PAtom *&endPriorAtom)
void	GetAnchors (ProteinSide side, PAtom *&endAnchor, PAtom *&endPriorAnchor)
void	DisableSidechains ()
void	DisableSidechains (int resIndex1, int resIndex2)
void	EnableSidechains ()
void	EnableSidechains (int resIndex1, int resIndex2)
void	RotateBackbone (int DOF_index, BondDirection dir, Real numDegrees)
void	RotateSidechain (int DOF_index, float numDegrees)
PProtein *	Clone ()
void	RandomizeBackbone ()
Protected Member Functions
virtual PResidue *	CreateResidue (const string &name)
virtual PResidue *	CreateResidue (const string &name, PResidueSpec &spec)
virtual PResidue *	CreateResidue (const string &name, PResidue *res)
virtual PResidue *	CreateResidue (const string &name, PResidueSpec &spec, PResidue *res)

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Constructor & Destructor Documentation

PProtein::PProtein

(

)

Constructs a new PProtein with no residues.

PProtein::PProtein

(

const string &

firstResidueName

)

Constructs a new PProtein with one residue, using the default positions for its atoms.

PProtein::PProtein	(	const string &	firstResidueName,
		PResidueSpec &	firstResidueSpec
	)

Constructs a new PProtein with one residue, using the specified positions for its atoms.

PProtein::PProtein	(	PProtein *	protein,
		int	resStartIndex,
		int	resEndIndex
	)

Constructs a new PProtein as a subchain of protein, from residue resStartIndex to residue resEndIndex.

PProtein::PProtein

(

int

numResidues

)

Constructs a new PProtein with numResidues random residues.

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Member Function Documentation

PProtein* PProtein::getParent

(

)

[inline]

Returns the parent PProtein of this PProtein, or NULL if this is the top level protein.

PProtein * PProtein::getTopLevelProtein

(

)

Returns the top level protein in the hierarchy this protein belongs to.

PProteinResidue* PProtein::getResidue

(

int

localIndex

)

[inline, virtual]

Returns the residue at the given index. Residues are indexed from 0 to size()-1 inclusive.

Reimplemented from PChain.

PProteinResidue * PProtein::getResidueByPdbIndex

(

int

pdbIndex

)

Returns the residue with the specified PDB index, or NULL if no such residue exists in the PProtein.

PProtein * PProtein::getSubchainByPdbIndices	(	int	startPdbIndex,
		int	endPdbIndex
	)

Returns a subchain of this PProtein in which the first residue has PDB index startPdbIndex, the second residue has PDB index startPdbIndex + 1, ..., and the last residue has PDB index endPdbIndex.

int PProtein::NumBackboneDOFs

(

)

const

Returns the number of degrees of freedom in this PProtein's backbone.

int PProtein::NumSidechainDOFs

(

)

const

Returns the number of degrees of freedom in this PProtein's side chains.

void PProtein::RandomizeSidechainAtRes

(

int

resIndex

)

Randomizes the DOFs of the side-chain at the given residue index.

void PProtein::RandomizeAllSidechains

(

)

Randomizes all side-chains in this protein.

void PProtein::GetEndEffectors	(	ProteinSide	side,
		PAtom *&	endAtom,
		PAtom *&	endPriorAtom
	)

Returns the loop closure end effectors on the specified side of this PProtein (front or back).

void PProtein::GetAnchors	(	ProteinSide	side,
		PAtom *&	endAnchor,
		PAtom *&	endPriorAnchor
	)

Returns the loop closure anchors on the specified side of the protein (front or back).

void PProtein::DisableSidechains

(

)

Disables all side chain blocks in the protein.

void PProtein::DisableSidechains	(	int	resIndex1,
		int	resIndex2
	)

Disables all side chain blocks between the specified start and end residues.

void PProtein::EnableSidechains

(

)

Enables all side chain blocks in the protein.

void PProtein::EnableSidechains	(	int	resIndex1,
		int	resIndex2
	)

Enables all side chain blocks between the specified start and end residues.

void PProtein::RotateBackbone	(	int	DOF_index,
		BondDirection	dir,
		Real	numDegrees
	)

Rotates the backbone numDegrees degrees, starting from the degree of freedom DOF_index in the direction dir.

void PProtein::RotateSidechain	(	int	DOF_index,
		float	numDegrees
	)

Rotates the sidechain at index DOF_index by numDegrees degrees.

PProtein * PProtein::Clone

(

)

Creates an exact copy of the protein. If a sub-chain is being copied, it creates a top-level protein as well. So, to free the memory of the sub-chain, Obliterate() must be called.

Reimplemented from PChain.

void PProtein::RandomizeBackbone

(

)

Randomize backbone DOFs, but does not check collision

virtual PResidue* PProtein::CreateResidue

(

const string &

name

)

[inline, protected, virtual]

Reimplemented from PChain.

virtual PResidue* PProtein::CreateResidue	(	const string &	name,
		PResidueSpec &	spec
	)			[inline, protected, virtual]

Reimplemented from PChain.

virtual PResidue* PProtein::CreateResidue	(	const string &	name,
		PResidue *	res
	)			[inline, protected, virtual]

Reimplemented from PChain.

virtual PResidue* PProtein::CreateResidue	(	const string &	name,
		PResidueSpec &	spec,
		PResidue *	res
	)			[inline, protected, virtual]

Reimplemented from PChain.

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

• src/core/PProtein.h
• src/core/PProtein.cc

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