PResidue Class Reference

#include <PResidue.h>

Inheritance diagram for PResidue:

List of all members.

---

Detailed Description

Encapsulates a single residue in a chain as a set of connected blocks. It is assumed that PBlock are not connected cyclically residues have a head and a tail and they connect together head to tail.

Public Member Functions
	PResidue (PChain *loop, const string &shellName)
	PResidue (PChain *loop, const string &shellName, PResidueSpec &spec)
	PResidue (PChain *loop, const string &shellName, PResidue *toConnect)
	PResidue (PChain *loop, const string &shellName, PResidueSpec &spec, PResidue *toConnect)
	~PResidue ()
PResidue *	NextResidue () const
PResidue *	PreviousResidue () const
PBond *	getDOF (const string &blockType, const string &atomId1, const string &atomId2)
const ID_To_DOF_Map *	getDOFsForBlock (const string &blockType)
void	RandomizeDOFs (const string &blockType, PChain *rootChain)
void	RandomizeDOFs (const string &blockType)
void	DetachBlocks (const string &blockType, const string &blockToDetachFrom)
void	ReattachBlocks (const string &blockType)
void	ReattachAllBlocks ()
PBond *	getBond (const string &id1, const string &id2)
PChain *	getChain () const
string	getResourceName () const
string	getName () const
void	setName (string name)
PBlock *	getHeadBlock ()
PBlock *	getTailBlock ()
vector< PAtom * > *	getAtoms ()
	HASH_MAP_STR (PAtom *)*getAtomMap()
PAtom *	getAtom (const string &id)
Vector3	getAtomPosition (const string &id)
bool	InStaticCollision () const
bool	InSelfCollision () const
bool	InAnyCollision () const
pair< PAtom *, PAtom * >	FindStaticCollision () const
pair< PAtom *, PAtom * >	FindSelfCollision () const
pair< PAtom *, PAtom * >	FindAnyCollision () const
AtomCollisions *	getAllCollidingStatic () const
AtomCollisions *	getAllCollidingSelf () const
AtomCollisions *	getAllCollidingEither () const
const PSpaceManager *	getSpaceManager () const
PResidueSpec	getSpec ()
void	setPositions (const PAtomPositionsSpec &spec)
int	getPdbId () const
void	inactivate ()
void	activate ()
Friends
class	PChain
struct	DOFCacher

---

Constructor & Destructor Documentation

PResidue::PResidue	(	PChain *	loop,
		const string &	shellName
	)

Constructs a new PResidue as a member of the specified PChain loop. This constructor uses default positions for all blocks in the residue shell specified by shellName, starting with default positions for the head block. After construction, the new PResidue is "isolated", i.e. it is not connected to any other residues

PResidue::PResidue	(	PChain *	loop,
		const string &	shellName,
		PResidueSpec &	spec
	)

Constructs a new PResidue as a member of the specified PChain loop. This constructor specifies the residue shell (shellName) for the new residue but also uses the atom positions defined in spec. After construction, the new PResidue is "isolated", i.e. it is not connected to any other residues.

PResidue::PResidue	(	PChain *	loop,
		const string &	shellName,
		PResidue *	toConnect
	)

Constructs a new PResidue as a member of the specified PChain loop. This constructor uses default positions for all blocks in the residue shell specified by shellName, starting with default positions for the head block. After construction, the new PResidue's "head" is connected to the tail of toConnect.

PResidue::PResidue	(	PChain *	loop,
		const string &	shellName,
		PResidueSpec &	spec,
		PResidue *	toConnect
	)

Constructs a new PResidue as a member of the specified PChain loop. This constructor specifies the residue shell (shellName) for the new residue but also uses the atom positions defined in spec. After construction, the new PResidue's "head" is connected to the tail of toConnect.

PResidue::~PResidue

(

)

---

Member Function Documentation

PResidue* PResidue::NextResidue

(

)

const [inline]

Returns the next residue in the chain following this PResidue, or NULL if this residue is not part of a chain.

PResidue* PResidue::PreviousResidue

(

)

const [inline]

Returns the previous residue in the chain before this PResidue, or NULL if this residue is not part of a chain.

PBond * PResidue::getDOF	(	const string &	blockType,
		const string &	atomId1,
		const string &	atomId2
	)

Returns the DOF between the two given atom ID's in the specified block type.

const ID_To_DOF_Map * PResidue::getDOFsForBlock

(

const string &

blockType

)

Returns a pointer to a mapping of atom Id's to bonds for all DOF's associated with the given block. Use an iterator to iterate through all the bonds.

Returns NULL if it can't find the blockType. Return should NOT be deleted.

void PResidue::RandomizeDOFs	(	const string &	blockType,
		PChain *	rootChain
	)

Randomizes the DOFs associated with the given blockType.

void PResidue::RandomizeDOFs

(

const string &

blockType

)

void PResidue::DetachBlocks	(	const string &	blockType,
		const string &	blockToDetachFrom
	)

void PResidue::ReattachBlocks

(

const string &

blockType

)

void PResidue::ReattachAllBlocks

(

)

PBond * PResidue::getBond	(	const string &	id1,
		const string &	id2
	)

Returns bond between given atoms, or NULL if bond or either atom does not exist.

PChain * PResidue::getChain

(

)

const

Returns a pointer to this residue's parent chain.

string PResidue::getResourceName

(

)

const [inline]

Returns this residue's name, currently just the name of its underlying PResidueShell.

string PResidue::getName

(

)

const [inline]

Returns this residue's name which can be custom set

void PResidue::setName

(

string

name

)

[inline]

Sets the name of the residue

PBlock* PResidue::getHeadBlock

(

)

[inline]

Returns a pointer to this residue's head block.

PBlock* PResidue::getTailBlock

(

)

[inline]

Returns a pointer to this residue's tail block.

vector<PAtom *>* PResidue::getAtoms

(

)

[inline]

Returns a pointer to a vector of all atoms in this residue.

PResidue::HASH_MAP_STR

(

PAtom *

)

[inline]

Returns a pointer to a hash_map mapping all atom IDs to atom pointers in this residue.

PAtom* PResidue::getAtom

(

const string &

id

)

[inline]

Returns a pointer to the PAtom in this residue with the specified ID, or NULL if no atom with this ID exists in the residue.

Vector3 PResidue::getAtomPosition

(

const string &

id

)

[inline]

Returns the Vector3 position of the atom in this residue with the specified ID.

bool PResidue::InStaticCollision

(

)

const

Returns true if any atom in this PResidue is in static collision, false otherwise.

bool PResidue::InSelfCollision

(

)

const

Returns true if any atom in this PResidue is in self collision, false otherwise.

bool PResidue::InAnyCollision

(

)

const

Returns true if any atom in this PResidue is in either static or self collision, false otherwise.

pair< PAtom *, PAtom * > PResidue::FindStaticCollision

(

)

const

Returns a pair of atoms in static collision within this PResidue, or (NULL, NULL) if no such atoms exist.

pair< PAtom *, PAtom * > PResidue::FindSelfCollision

(

)

const

Returns a pair of atoms in self collision within this PResidue, or (NULL, NULL) if no such atoms exist.

pair< PAtom *, PAtom * > PResidue::FindAnyCollision

(

)

const

Returns a pair of atoms in either static or self collision within this PResidue, or (NULL, NULL) if no such atoms exist.

AtomCollisions * PResidue::getAllCollidingStatic

(

)

const

Returns a set of all atoms in static collision in this PResidue.

AtomCollisions * PResidue::getAllCollidingSelf

(

)

const

Returns a set of all atoms in self collision in this PResidue.

AtomCollisions * PResidue::getAllCollidingEither

(

)

const

Returns a set of all atoms in either static or self collision in this PResidue.

const PSpaceManager * PResidue::getSpaceManager

(

)

const

Returns the space manager of the chain this residue is in.

PResidueSpec PResidue::getSpec

(

)

Gets a PResidueSpec with the information about this residue's atom positions.

void PResidue::setPositions

(

const PAtomPositionsSpec &

spec

)

Sets the residue's atom positions from the PAtomPositionsSpec spec. Atoms in the residue that are not found in spec are ignored.

int PResidue::getPdbId

(

)

const [inline]

Returns the index of this residue in a PDB file.

void PResidue::inactivate

(

)

Inactivate the residue so that it won't be considered in collision

void PResidue::activate

(

)

Activate the residue so that it will be considered in collision

---

Friends And Related Function Documentation

friend class PChain [friend]

friend struct DOFCacher [friend]

---

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

• src/core/PResidue.h
• src/core/PResidue.cc

---