Encapsulate the data extracted from a &receptor namelist to define a grid-mapped representation of a rigid macromolecular structure. More...

#include <nml_mesh.h>

Public Member Functions
double	getAlpha () const
	Get the mesh alpha angle, between the b and c unit cell axes. The value is returned in units of radians.

double	getBeta () const
	Get the mesh beta angle, between the a and c unit cell axes, in units of radians.

double	getGamma () const
	Get the mesh gamma angle, between the a and b unit cell axes, in units of radians.

double	getOrigin (CartesianDimension dim) const
	Get the origin of the mesh in one Cartesian dimension.

GridDetail	getDetail () const
	Get the type of content (potential energy field) that the mesh will represent. In general, programs that use meshes will have specific applications for them, and therefore have a concept of what their content should be. This keyword will often be specified to associate its parameters with one of the meshes that a given program intends to make, e.g. "the dimensions in this namelist apply to the clash grid, whereas the electrostatic non-bonded field uses parameters specified in a separate &mesh namelist.".

NonbondedPotential	getPotential () const
	Get the type of potential to be expressed on the mesh. This complements the getContent() function and its associated "kind" keyword to specify a particular non-bonded potential in situations where programs utilize separate meshes for electrostatics and van-der Waals potentials.

BoundaryCondition	getBoundaries () const
	Get the boundary conditions of the mesh.

MeshPosition	getPosition () const
	Get the manner in which the mesh is aligned to the rigid molecule it represents.

int	getScalingBits () const
	Get the number of bits after the decimal to be used in composing the mesh-based field as well as the positions of its vertices.

double	getElecClashDistance () const
	Get the switching range for softcore electrostatic potentials. This will only apply to meshes representing an electrostatic potential.

double	getVdwClashRatio () const
	Get the switching ratio for softcore van-der Waals potentials. This will only apply to meshes representing a Lennard-Jones (or, perhaps other) van-der Waals potential.

const NamelistEmulator &	getTranscript () const
	Get the original namelist emulator object as a transcript of the user input.

void	setAlphaAngle (double alpha_in)
	Set the mesh alpha angle.

void	setBetaAngle (double beta_in)
	Set the mesh beta angle.

void	setGammaAngle (double gamma_in)
	Set the mesh gamma angle.

void	setOrigin (double mesh_origin_in, CartesianDimension dim)
	Set the mesh origin along one Cartesian axis.

void	setScalingBits (int mesh_scaling_bits_in)
	Set the number of bits after the decimal to be used in mesh calculations.

void	setElecClashDistance (double clash_distance_in)
	Set the electrostatic clash distance.

void	setVdwClashRatio (double clash_ratio_in)
	Set the van-der Waals clash ratio.


	MeshControls (ExceptionResponse policy_in=ExceptionResponse::DIE)
	The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.

	MeshControls (const TextFile &tf, int start_line, bool found_nml, ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO)


	MeshControls (const MeshControls &original)=default
	As with other control objects, copy and move constructors, plus copy and move assignment operators, can all take their default forms.

	MeshControls (MeshControls &&original)=default

MeshControls &	operator= (const MeshControls &original)=default

MeshControls &	operator= (MeshControls &&original)=default


int	getAxisElementCount (UnitCellAxis dim) const
	Get the number of grid points in a particular dimension. This can serve to query a particular piece of information without invoking the more complex but comprehensive MeshParameters object.

int	getAxisElementCount (CartesianDimension dim) const


double	getSpacing (UnitCellAxis dim) const
	Get the mesh spacing along a particular axis. Overloads and input parameters to this function follow from getAxisElementCount() above.

double	getSpacing (CartesianDimension dim) const


double	getBufferWidth (UnitCellAxis dim) const
	Get buffer widths between mesh boundaries and the receptor structure or structures.

double	getBufferWidth (CartesianDimension dim) const


void	setElementCount (int mesh_points_in, UnitCellAxis dim)
	Set the number of mesh points along a particular axis.

void	setElementCount (int mesh_points_in, CartesianDimension dim)


void	setSpacing (double mesh_spacing_in, UnitCellAxis dim)
	Set the mesh spacing along a particular axis. Overloading of this function follows from setElementCount() above.

void	setSpacing (double mesh_spacing_in, CartesianDimension dim)


void	setBufferWidth (double buffer_width_in)
	Set the buffer distance between the mesh boundary and the nearest van-der Waals sphere.

void	setBufferWidth (double buffer_width_in, UnitCellAxis dim)

void	setBufferWidth (double buffer_width_in, CartesianDimension dim)


void	setDetail (const std::string &kind_in)
	Set the type of mesh that this namelist will be assumed to describe.

void	setDetail (GridDetail kind_in)


void	setPotential (const std::string &potential_in)
	Set the potential energy field that the mesh will represent.

void	setPotential (NonbondedPotential potential_in)


void	setBoundaries (const std::string &boundaries_in)
	Set the boundary conditions for the mesh. Overloading in this function follows from setPotential() above.

void	setBoundaries (BoundaryCondition boundaries_in)

Detailed Description

Encapsulate the data extracted from a &receptor namelist to define a grid-mapped representation of a rigid macromolecular structure.

Constructor & Destructor Documentation

◆ MeshControls()

stormm::namelist::MeshControls::MeshControls ( ExceptionResponse policy_in = ExceptionResponse::DIE )

The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.

Parameters

tf	Input file translated into RAM
start_line	Line of the input file to begin searching for the &solvent namelist
found_nml	Indication of whether the namelist was found in the input file
policy_in	Requested error handling behavior
wrap	Indicate that the search for a &conformer namelist should carry on from the beginning of an input file if no such namelist is found starting from the original starting point

Member Function Documentation

◆ getAxisElementCount()

int stormm::namelist::MeshControls::getAxisElementCount ( UnitCellAxis dim ) const

Get the number of grid points in a particular dimension. This can serve to query a particular piece of information without invoking the more complex but comprehensive MeshParameters object.

Overloaded:

Technically more correct, specify the unit cell axis
Specify the axis by analogy to Cartesian axes (X -> a, Y -> b, Z -> c)

Parameters

dim	The axis along which to measure the number of mesh points

◆ getBufferWidth()

double stormm::namelist::MeshControls::getBufferWidth ( UnitCellAxis dim ) const

Get buffer widths between mesh boundaries and the receptor structure or structures.

Overloaded:

Technically more correct, specify the unit cell axis
Specify the axis by analogy to Cartesian axes (X -> a, Y -> b, Z -> c)

Parameters

dim	The Cartesian or unit cell axis normal to the face of interest (along which the width is relevant)

◆ setAlphaAngle()

void stormm::namelist::MeshControls::setAlphaAngle ( double alpha_in )

Set the mesh alpha angle.

Parameters

alpha_in The angle to set, in units of radians.

◆ setBetaAngle()

void stormm::namelist::MeshControls::setBetaAngle ( double beta_in )

Set the mesh beta angle.

Parameters

beta_in The angle to set, in units of radians.

◆ setBoundaries()

void stormm::namelist::MeshControls::setBoundaries ( const std::string & boundaries_in )

Set the boundary conditions for the mesh. Overloading in this function follows from setPotential() above.

Parameters

boundaries_in The chosen boundary conditions

◆ setBufferWidth()

void stormm::namelist::MeshControls::setBufferWidth ( double buffer_width_in )

Set the buffer distance between the mesh boundary and the nearest van-der Waals sphere.

Overloaded:

Set a single parameter for all three unit cell or Cartesian axes
Set separate parameters for secific unit cell or Cartesian axes

Parameters

buffer_width_in	The buffer width to set, in units of Angstroms
dim	The unit cell or Cartesian axis normal to the face of interest

◆ setDetail()

void stormm::namelist::MeshControls::setDetail ( const std::string & kind_in )

Set the type of mesh that this namelist will be assumed to describe.

Overloaded:

Provide the enumerated value explicitly
Translate a string into the appropriate enumeration

Parameters

kind_in The type of energetic field

◆ setElecClashDistance()

void stormm::namelist::MeshControls::setElecClashDistance ( double clash_distance_in )

Set the electrostatic clash distance.

Parameters

clash_distance_in The point at which electrostatic interactions switch over to a softcore potential (inverted parabola, with a maximum at r = -1.0)

◆ setElementCount()

void stormm::namelist::MeshControls::setElementCount	(	int	mesh_points_in,
		UnitCellAxis	dim )

Set the number of mesh points along a particular axis.

Overloaded:

Technically more correct, specify the unit cell axis
Specify the axis by analogy to Cartesian axes (X -> a, Y -> b, Z -> c)

Parameters

mesh_points_in	The desired number of mesh points
dim	The unit cell axis in question

◆ setGammaAngle()

void stormm::namelist::MeshControls::setGammaAngle ( double gamma_in )

Set the mesh gamma angle.

Parameters

gamma_in The angle to set, in units of radians.

◆ setOrigin()

void stormm::namelist::MeshControls::setOrigin	(	double	mesh_origin_in,
		CartesianDimension	dim )

Set the mesh origin along one Cartesian axis.

Parameters

mesh_origin_in	The desired mesh origin coordinate
dim	The Cartesian axis of interest

◆ setPotential()

void stormm::namelist::MeshControls::setPotential ( const std::string & potential_in )

Set the potential energy field that the mesh will represent.

Overloaded:

Provide the enumerated value explicitly
Translate a string into the appropriate enumeration

Parameters

potential_in The type of energetic field

◆ setScalingBits()

void stormm::namelist::MeshControls::setScalingBits ( int mesh_scaling_bits_in )

Set the number of bits after the decimal to be used in mesh calculations.

Parameters

scaling_bits_in The bit count

◆ setSpacing()

void stormm::namelist::MeshControls::setSpacing	(	double	mesh_spacing_in,
		UnitCellAxis	dim )

Set the mesh spacing along a particular axis. Overloading of this function follows from setElementCount() above.

Parameters

mesh_spacing_in	The desired distance between mesh points, in Angstroms
dim	The unit cell axis in question

◆ setVdwClashRatio()

void stormm::namelist::MeshControls::setVdwClashRatio ( double clash_ratio_in )

Set the van-der Waals clash ratio.

Parameters

clash_ratio_in The proportion of the van-der Waals (Lennard-Jones) sigma parameter at which interactions for a given pair switch over to a softcore potential (inverted quartic function, with a maximum at r = -1.0)

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

src/Namelists/nml_mesh.h
src/Namelists/nml_mesh.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MeshControls()

Member Function Documentation

◆ getAxisElementCount()

◆ getBufferWidth()

◆ setAlphaAngle()

◆ setBetaAngle()

◆ setBoundaries()

◆ setBufferWidth()

◆ setDetail()

◆ setElecClashDistance()

◆ setElementCount()

◆ setGammaAngle()

◆ setOrigin()

◆ setPotential()

◆ setScalingBits()

◆ setSpacing()

◆ setVdwClashRatio()