stormm::chemistry::MaskComponent Class Reference

A mask is a series of operators and more primitive masks. This struct comprises both things, with an indicator as to what it contains. A complete mask for a given scope is composed by stepping through a list of these objects. More...

#include <atommask.h>

Public Member Functions
MaskComponentKind	getKind () const
	Get the kind of component.
MaskOperator	getOperator () const
	Get the operator, if relevant.
std::vector< uint >	getMask () const
	Get the bitmask, if relevant.
std::string	getText () const
	Get the textual basis of this mask component.
int2	getTextLimits () const
	Get the indices from within the original mask string where this component's textual basis is to be found.
void	applyNotOperator ()
	Apply the NOT operator to a primitive mask.
void	applyAndOperator (const std::vector< uint > &other)
	Apply the AND operator to a primitive mask, given another primitive mask.
void	applyOrOperator (const std::vector< uint > &other)
	Apply the OR operator to a primitive mask, given another primitive mask.
MaskComponent	applyRangeOperator (const std::vector< uint > &other, const AtomGraph *ag, const CoordinateFrameReader &cfr)
	Apply one of the ranged operators. This will produce a new MASK-kind MaskComponent. Ranged operators are expected to occur last in their scopes. Once the scope is broken into MaskComponents of operators and other masks, the list is processed by applying operators to eliminate MaskComponents until there is a single MASK-kind MaskComponent left. With range operators, the list whittles down to a MASK-kind followed by an OPERATOR MaskComponent. Both of these will be eliminated after the output of this function is tacked onto the end of the list, where it will then become the only element.
	MaskComponent (MaskOperator op_in, const std::string &basis_in, int start_idx, int end_idx)
	Constructor takes either an operator designation or a series of atoms or residues.
	MaskComponent (MaskOperator op_in, double range, const std::string &basis_in, int start_idx, int end_idx)
	MaskComponent (const std::vector< SelectionItem > &parts_in, const AtomGraph *ag, const ChemicalFeatures &chemfe, const std::string &basis_in, int start_idx, int end_idx)
	MaskComponent (const std::vector< uint > &primitive_mask_in, const std::string &basis_in, int start_idx, int end_idx)

Detailed Description

A mask is a series of operators and more primitive masks. This struct comprises both things, with an indicator as to what it contains. A complete mask for a given scope is composed by stepping through a list of these objects.

Constructor & Destructor Documentation

MaskComponent()

stormm::chemistry::MaskComponent::MaskComponent	(	MaskOperator	op_in,
		const std::string &	basis_in,
		int	start_idx,
		int	end_idx )

Constructor takes either an operator designation or a series of atoms or residues.

Overloaded:

• Build a basic "&", "|", or "!" operator component
• Build a ranged operator component
• Build a primitive mask component from a list of named or numbered atoms or residues
• Take a primitive mask component output by a recursive call to parseMask and store it

Parameters

op_in	Operator designation
parts_in	A series of atom or residue names and indices to find
ag	System topology containing atom and residue names and indices
primitive_mask_in	Bit mask for all atoms, as output by parseMask (see below)

Member Function Documentation

applyAndOperator()

void stormm::chemistry::MaskComponent::applyAndOperator

(

const std::vector< uint > &

other

)

Apply the AND operator to a primitive mask, given another primitive mask.

Parameters

other

Pre-determined primitive mask of atoms

applyOrOperator()

void stormm::chemistry::MaskComponent::applyOrOperator

(

const std::vector< uint > &

other

)

Apply the OR operator to a primitive mask, given another primitive mask.

Parameters

other

Pre-determined primitive mask of atoms

applyRangeOperator()

MaskComponent stormm::chemistry::MaskComponent::applyRangeOperator	(	const std::vector< uint > &	other,
		const AtomGraph *	ag,
		const CoordinateFrameReader &	cfr )

Apply one of the ranged operators. This will produce a new MASK-kind MaskComponent. Ranged operators are expected to occur last in their scopes. Once the scope is broken into MaskComponents of operators and other masks, the list is processed by applying operators to eliminate MaskComponents until there is a single MASK-kind MaskComponent left. With range operators, the list whittles down to a MASK-kind followed by an OPERATOR MaskComponent. Both of these will be eliminated after the output of this function is tacked onto the end of the list, where it will then become the only element.

Parameters

other	Pre-determined primitive mask of atoms
ag	Pointer to the original topology
cfr	Coordinates of the system

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

• src/Chemistry/atommask.h
• src/Chemistry/atommask.cpp