stormm::chemistry::AtomMask Class Reference

An atom selection within a system. Internally, this stores a bitmask, one bit for every particle, to denote whether it is in the mask. The object also stores the original string upon which the mask was constructed and a description of the mask, as it is a significant computation to build. More...

#include <atommask.h>

Public Member Functions
MaskTraversalMode	getRecommendation () const
	Get the recommendation for scanning this mask.
const std::vector< uint > &	getRawMask () const
	Get the raw mask as a vector of unsigned long integers (bit strings storing whether each atom is masked at one atom per bit)
int	getMaskedAtomCount () const
	Get a count of the number of masked atoms.
std::vector< bool >	getMask () const
	Get the mask as a vector of boolean values (not just a bit mask as the object stores privately)
std::vector< int >	getMaskedAtomList () const
std::vector< int2 >	getSegments () const
	Get the segments of atoms over which the mask applies (only filled out if the recommended scanning method is by segment)
std::string	getInputText () const
	Get the input text used to generate this atom mask.
MaskInputMode	getInputKind () const
	Get the input text mode, e.g. AMBMASK to indicate that an Amber-style atom mask string was used to make this mask.
std::string	getDescription () const
	Get the description of the mask, if provided.
const AtomGraph *	getTopologyPointer () const
	Get a pointer to the topology that this mask describes.
	AtomMask (const AtomGraph *ag_in=nullptr)
	Constructor takes a mask string, topology, and coordinates.
	AtomMask (const std::string &input_text_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, MaskInputMode mode=MaskInputMode::AMBMASK, const std::string &description_in=std::string("No description provided"))
	AtomMask (const std::string &input_text_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const CoordinateFrame &cf, MaskInputMode mode=MaskInputMode::AMBMASK, const std::string &description_in=std::string("No description provided"))
	AtomMask (const std::string &input_text_in, const AtomGraph *ag_in, const ChemicalFeatures &chemfe, const PhaseSpace &ps, MaskInputMode mode=MaskInputMode::AMBMASK, const std::string &description_in=std::string("No description provided"))
	AtomMask (const AtomMask &original)=default
	AtomMask (AtomMask &&original)=default
bool	isAtomInMask (const char4 atom_name) const
	Answer whether an atom is in the mask.
bool	isAtomInMask (const char4 res_name, const char4 atom_name) const
bool	isAtomInMask (int atom_index) const
void	addAtoms (const std::vector< int > &new_indices, ExceptionResponse policy=ExceptionResponse::DIE)
	Add atoms to the atom mask.
void	addAtoms (const std::vector< char4 > &new_names)
void	addAtoms (const AtomMask &new_mask, const CoordinateFrame &cf, const ChemicalFeatures &chemfe)
void	addAtoms (const std::string &new_mask, const CoordinateFrame &cf, const ChemicalFeatures &chemfe)
void	addAtoms (const AtomMask &new_mask, const CoordinateFrame &cf)
void	addAtoms (const std::string &new_mask, const CoordinateFrame &cf)

Detailed Description

An atom selection within a system. Internally, this stores a bitmask, one bit for every particle, to denote whether it is in the mask. The object also stores the original string upon which the mask was constructed and a description of the mask, as it is a significant computation to build.

Constructor & Destructor Documentation

AtomMask() [1/2]

stormm::chemistry::AtomMask::AtomMask

(

const AtomGraph *

ag_in = nullptr

)

Constructor takes a mask string, topology, and coordinates.

Overloaded:

• Blank constructor (build later from a provided topology and optional coordinates)
• Require no coordinates (only valid if the mask has no range operators)
• Take coordinates as a PhaseSpace object
• Take coordinates as a CoordinateFrame object
• Take coordinates as three std::vectors for Cartesian X, Y, and Z positions, with or without unit cell transforms (if the transform vectors do not exist, the system is assumed to have isolated boundary conditions)
• Take coordinates as three C-style arrays, with unit cell transforms (if the transform arrays are nullptr, the system is assumed to exist in isolated boundary conditions)

Parameters

input_text_in	The mask string
ag_in	System topology
chemfe	Chemical features computed for the topology
crd	Coordinates obtained from a CoordinateFrame object
xcrd	Cartesian X coordinates of all atoms
ycrd	Cartesian Y coordinates of all atoms
zcrd	Cartesian Z coordinates of all atoms
description	[Optional] description of the mask and its purpose

AtomMask() [2/2]

stormm::chemistry::AtomMask::AtomMask ( const AtomMask & original )

default

The standard copy and move constructors will be effective for this object, which has no pointers to repair. Because there is a const member, the copy and move assignment operators will be implicitly deleted.

Member Function Documentation

addAtoms()

void stormm::chemistry::AtomMask::addAtoms	(	const std::vector< int > &	new_indices,
		ExceptionResponse	policy = ExceptionResponse::DIE )

Add atoms to the atom mask.

Overloaded:

• Add a series of atom indices, with indexing beginning at 0.
• Add a series of atom names. All examples of any supplied name will be matched and added to the mask (an O(NM) operation for N atom names and a topology of M atoms)
• Add the atoms of another mask (the topologies will be checked for a reasonable degree of congruity)
• Add atoms implied by another mask string.
• Supply the system's pre-computed chemical features, or have it constructed temporarily.

Parameters

new_indices	The atom indices to add to the current mask
new_names	The names of atoms to add to the current mask
new_mask	Another atom mask (or mask string) to add to the current mask
policy	The policy to take in the event that an error is encountered

isAtomInMask()

bool stormm::chemistry::AtomMask::isAtomInMask

(

const char4

atom_name

)

const

Answer whether an atom is in the mask.

Overloaded:

• Provide the atom name only (any instance of the atom name found in the mask will suffice to say that an atom with the specified name is present in the mask)
• Provide the atom residue name and atom name (any instance of an atom conforming to this pair of names will result in the function returning TRUE)
• Provide the atom index number (indexing starting at zero)

Parameters

atom_name	Name of the atom of interest
res_name	Name of the residue of interest
atom_index	Topological index number of the atom of interest

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

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