stormm::namelist::SolventControls Class Reference

Object to encapsulate the data that can be extracted from a &solvent namelist. Typical C++ construction. Having this object, like others accompanying their respective namelists, makes the transition between namelists and custom-formatted control objects much simpler. More...

#include <nml_solvent.h>

Public Member Functions
ImplicitSolventModel	getImplicitSolventModel () const
	Get the type of implicit solvent (some flavor of Generalized Born).
double	getBornRadiiCutoff () const
	Get the Born radius calculation cutoff.
double	getInternalDielectric () const
	Get the internal dielectric constant.
double	getExternalDielectric () const
	Get the external dielectric constant.
double	getSaltConcentration () const
	Get the salt concentration.
AtomicRadiusSet	getPBRadiiSet () const
	Get the Poisson-Boltzmann radii set.
double	getSurfaceAreaScalingFactor () const
	Get the surface area scaling factor, in units of kcal/mol per square Angstrom.
const NamelistEmulator &	getTranscript () const
	Get the original namelist emulator object as a transcript of the user input.
void	setBornRadiiCutoff (double rgbmax_in)
	Set the Born radius calculation cutoff.
void	setInternalDielectric (double idiel_in)
	Set the internal dielectric.
void	setExternalDielectric (double ediel_in)
	Set the external dielectric.
void	setSaltConcentration (double saltcon_in)
	Set the salt concentration, the concentration of 1:1 monovalent ion pairs in the implicit solvent.
void	setSurfaceAreaScalingFactor (double sa_scaling_in)
	Set the surface area scaling factor. Any value is accepted, even negative values, as it may be favorable, in some solvents, for a molecule to have more surface area.
	SolventControls (ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO)
	The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.
	SolventControls (const TextFile &tf, int *start_line, bool *found_nml, ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO)
	SolventControls (const SolventControls &original)=default
	As with other control objects, copy and move constructors, plus copy and move assignment operators, can all take their default forms.
	SolventControls (SolventControls &&original)=default
SolventControls &	operator= (const SolventControls &original)=default
SolventControls &	operator= (SolventControls &&original)=default
void	setImplicitSolventModel (int ism_in)
	Set the implicit solvent model.
void	setImplicitSolventModel (ImplicitSolventModel ism_in)
void	choosePBRadiiSet (const std::string &pbrad_in)
	Choose the Poisson-Boltzmann radii set.
void	choosePBRadiiSet (AtomicRadiusSet pbrad_in)

Detailed Description

Object to encapsulate the data that can be extracted from a &solvent namelist. Typical C++ construction. Having this object, like others accompanying their respective namelists, makes the transition between namelists and custom-formatted control objects much simpler.

Constructor & Destructor Documentation

SolventControls()

stormm::namelist::SolventControls::SolventControls	(	ExceptionResponse	policy_in = ExceptionResponse::DIE,
		WrapTextSearch	wrap = WrapTextSearch::NO )

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 that the namelist was found
policy_in	Requested error handling behavior
wrap	Indicate that the search for a &solvent 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

choosePBRadiiSet()

void stormm::namelist::SolventControls::choosePBRadiiSet

(

const std::string &

pbrad_in

)

Choose the Poisson-Boltzmann radii set.

Overloaded:

• Use string input (and translate the string, checking for validity)
• Use enumeration input

Parameters

pbrad_in

The radii set to select (will be checked for validity)

setBornRadiiCutoff()

void stormm::namelist::SolventControls::setBornRadiiCutoff

(

double

rgbmax_in

)

Set the Born radius calculation cutoff.

Parameters

rgbmax_in

The Born radius calculation cutoff of choice

setExternalDielectric()

void stormm::namelist::SolventControls::setExternalDielectric

(

double

ediel_in

)

Set the external dielectric.

Parameters

ediel_in

The external dielectric to apply

setImplicitSolventModel()

void stormm::namelist::SolventControls::setImplicitSolventModel

(

int

ism_in

)

Set the implicit solvent model.

Overloaded:

• Take the integer code for the implicit solvent model (and apply validation)
• Take the enumeration for the implicit solvent model

Parameters

ism_in

Implicit solvent model of choice

setInternalDielectric()

void stormm::namelist::SolventControls::setInternalDielectric

(

double

idiel_in

)

Set the internal dielectric.

Parameters

idiel_in

The internal dielectric to apply

setSaltConcentration()

void stormm::namelist::SolventControls::setSaltConcentration

(

double

saltcon_in

)

Set the salt concentration, the concentration of 1:1 monovalent ion pairs in the implicit solvent.

Parameters

saltcon_in

The concentration to set

setSurfaceAreaScalingFactor()

void stormm::namelist::SolventControls::setSurfaceAreaScalingFactor

(

double

sa_scaling_in

)

Set the surface area scaling factor. Any value is accepted, even negative values, as it may be favorable, in some solvents, for a molecule to have more surface area.

Parameters

sa_scaling_in

The scaling factor, in units of kcal/mol per square Angstrom

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

• src/Namelists/nml_solvent.h
• src/Namelists/nml_solvent.cpp