ENM::BoundSuperBlock Class Reference

Decorator for switching spring functions based on a matrix of flags. More...

#include <hessian.hpp>

Inheritance diagram for ENM::BoundSuperBlock:

Collaboration diagram for ENM::BoundSuperBlock:

Public Member Functions
	BoundSuperBlock (SuperBlock *b, SpringFunction *bs, loos::Math::Matrix< int > &cm)
loos::DoubleMatrix	block (const uint j, const uint i)
	Returns a 3x3 matrix representing a superblock in the Hessian for the two nodes.
SpringFunction::Params	setParams (const SpringFunction::Params &v)
	Assign parameters and propagate to the decorated superblock.
bool	validParams () const
	Both the alternate and all decorated parameters are valid.
uint	paramSize () const
	Returns the aggregate parameter size.
Public Member Functions inherited from ENM::SuperBlockDecorator
	SuperBlockDecorator (SuperBlock *b)
	Constructor that takes a SuperBlock to decorate.
Public Member Functions inherited from ENM::SuperBlock
	SuperBlock (SpringFunction *func, const loos::AtomicGroup &nodelist)
	Constructor taking a spring function and a list of nodes.
	SuperBlock (const SuperBlock &b)
uint	size () const

Additional Inherited Members
Protected Member Functions inherited from ENM::SuperBlock
loos::DoubleMatrix	blockImpl (const uint j, const uint i, SpringFunction *fptr)
	Implementation of the superblock calculation.
Protected Attributes inherited from ENM::SuperBlockDecorator
SuperBlock *	decorated
Protected Attributes inherited from ENM::SuperBlock
SpringFunction *	springs
loos::AtomicGroup	nodes

Detailed Description

Decorator for switching spring functions based on a matrix of flags.

The following is a decorator for SuperBlock that implements an alternative set of spring constants for nodes that are "bound" together. The constructor takes a SuperBlock to decorate, along with a pointer to the alternative SpringFunction and a matrix of ints representing the connectivity (i.e. 1 if two nodes are connected, 0 otherwise).

A few notes about using decorators... The idea behind a decorator is that you add layers (or decorate) to a class by combining multiple decorators. For example, suppose you have two different kinds of connectivity you want to represent in a Hessian. You would set-up your SuperBlock like,

SuperBlock* unbound = new SuperBlock(unbound_spring, nodes);
BoundSuperBlock* backboned = new BoundSuperBlock(unbound, backbone_springs, backbone_bonds);
BoundSuperBlock* side_chained = new BoundSuperBlock(backboned, side_chain_springs, side_chain_bonds);

You now always work with the last decorated object, i.e. side_chained. When side_chained->block() is called, it first checks to see if the nodes represent a side-chain bond. If so, that spring function is used. If not, then it passes control to the object it decorates, i.e. backboned. Backboned now checks to see if the nodes represent a backbone bond. If so, it uses that spring function. If not, then control is passed to the inner unbound SuperBlock which uses its spring function.

This method has two important caveats. First, the calculation is now order-dependent. If, for some reason, you have nodes that are listed as both side-chains and backbones (for a contrived example), then the one used will depend on the order in which the SuperBlock was decorated. The second caveat is that we are using real, raw pointers here, so be careful about cleaning up to avoid memory leaks and also keep in mind that the intermediate pointers (i.e. backboned) are contained within the higher-level decorators. So, do NOT delete any of the intermediate steps until you are sure you are done with everything.

Member Function Documentation

block()

loos::DoubleMatrix ENM::BoundSuperBlock::block ( const uint j, const uint i )

inlinevirtual

Returns a 3x3 matrix representing a superblock in the Hessian for the two nodes.

Reimplemented from ENM::SuperBlock.

paramSize()

uint ENM::BoundSuperBlock::paramSize ( ) const

inlinevirtual

Returns the aggregate parameter size.

Reimplemented from ENM::SuperBlock.

setParams()

SpringFunction::Params ENM::BoundSuperBlock::setParams ( const SpringFunction::Params & v )

inlinevirtual

Assign parameters and propagate to the decorated superblock.

Reimplemented from ENM::SuperBlock.

validParams()

bool ENM::BoundSuperBlock::validParams ( ) const

inlinevirtual

Both the alternate and all decorated parameters are valid.

Reimplemented from ENM::SuperBlock.

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

• Packages/ElasticNetworks/hessian.hpp