PBlock Class Reference

#include <PBlock.h>

List of all members.

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Detailed Description

Encapsulates a set of atoms and bonds between them. Blocks may be connected together to form residues.

Public Member Functions
	PBlock (PResidue *myRes, const string &shellName)
	PBlock (PResidue *myRes, const string &shellName, const PAtomPositionsSpec &spec)
	PBlock (PResidue *myRes, const string &shellName, const PAtomPositionsSpec &spec, PBlock *toConnect)
	PBlock (PResidue *myRes, const string &shellName, PBlock *toConnect)
	~PBlock ()
string	getName () const
string	getType () const
bool	isOn () const
PResidue *	getParentResidue ()
int	size ()
PChain *	getChain () const
void	Detach (const string &blockType)
void	Reattach ()
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
void	AddAtomsToMap (HASH_MAP_STR(PAtom *)&atomCache) const
const PSpaceManager *	getSpaceManager () const
Friends
class	PBlockConnection
class	PBlockReconnector

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Constructor & Destructor Documentation

PBlock::PBlock	(	PResidue *	myRes,
		const string &	shellName
	)

Constructs a new PBlock as a member of the residue myRes and with a block shell specified by shellName. This constructor uses relative coordinates as global positions.

PBlock::PBlock	(	PResidue *	myRes,
		const string &	shellName,
		const PAtomPositionsSpec &	spec
	)

Constructs a new PBlock as a member of the residue myRes and with a block shell specified by shellName. This constructor uses the atom positions specified by spec and should be called when the PBlock is created "in isolation" (not connected to other blocks).

PBlock::PBlock	(	PResidue *	myRes,
		const string &	shellName,
		const PAtomPositionsSpec &	spec,
		PBlock *	toConnect
	)

Constructs a new PBlock as a member of the residue myRes and with a block shell specified by shellName. This constructor uses the atom positions specified by spec and connects the new PBlock to the block toConnect; it should be called when the block's positions are known, e.g. from a PDB file, but the block must also be connected to an existing block.

PBlock::PBlock	(	PResidue *	myRes,
		const string &	shellName,
		PBlock *	toConnect
	)

Constructs a new PBlock as a member of the residue myRes and with a block shell specified by shellName. This constructor uses the block's default atom positions and connects the new PBlock to the block toConnect; it should be called when the block's positions are not known (and thus should be determined randomly) but the block must still be connected to an existing block.

PBlock::~PBlock

(

)

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Member Function Documentation

string PBlock::getName

(

)

const [inline]

Returns the block's name, e.g. "TRP".

string PBlock::getType

(

)

const [inline]

Returns the block's type, e.g. "backbone" or "sidechain".

bool PBlock::isOn

(

)

const [inline]

Returns true if this block is active, false otherwise.

PResidue* PBlock::getParentResidue

(

)

[inline]

Returns this block's parent residue.

int PBlock::size

(

)

[inline]

Returns the number of atoms within this block.

PChain * PBlock::getChain

(

)

const

Returns this block's parent chain.

void PBlock::Detach

(

const string &

blockType

)

Detaches this block from the parent PChain. The PBlock "remembers" the relative coordinates to the first block it can find of type blockType, so the Detach method can only be called once.

void PBlock::Reattach

(

)

Reattaches this block to its parent chain.

bool PBlock::InStaticCollision

(

)

const

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

bool PBlock::InSelfCollision

(

)

const

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

bool PBlock::InAnyCollision

(

)

const

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

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

(

)

const

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

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

(

)

const

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

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

(

)

const

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

AtomCollisions * PBlock::getAllCollidingStatic

(

)

const

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

AtomCollisions * PBlock::getAllCollidingSelf

(

)

const

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

AtomCollisions * PBlock::getAllCollidingEither

(

)

const

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

void PBlock::AddAtomsToMap

(

HASH_MAP_STR(PAtom *)&

atomCache

)

const

Adds all atoms in this PBlock to the map atomCache.

const PSpaceManager * PBlock::getSpaceManager

(

)

const

Returns the space manager for the chain this block is in.

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Friends And Related Function Documentation

friend class PBlockConnection [friend]

friend class PBlockReconnector [friend]

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

• src/core/PBlock.h
• src/core/PBlock.cc

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