Class to encapsulate the data that can be extracted from the &conformer namelist. More...

#include <nml_conformer.h>

Public Member Functions
const std::string &	getCoreAtomMask () const
	Get the core atom mask string.

const std::string &	getCoreDataItemName () const
	Get the name of the data item expected to contain core atoms.

double	getCoreRK2Value () const
	Get the core restraint r2 penalty (near-repulsive potential) stiffness.

double	getCoreRK3Value () const
	Get the core restraint r3 penalty (position-keeping potential) stiffness.

double	getCoreR2Value () const
	Get the core restraint r2 displacement.

double	getCoreR3Value () const
	Get the core restraint r3 displacement.

bool	sampleChirality () const
	Get an indicator of whether to sample chirality.

bool	sampleCisTrans () const
	Get an indicator of whether to sample cis- and trans- isomers.

bool	preventHydrogenBonding () const
	Get an indicator as to whether to apply restraints that will prevent hydrogen bond formation in the resulting conformers.

int	getRunningStateCount () const
	Get the total number of states to attempt minimizing at one time. This will put a limit on the expanded population of conformer systems that the program will attempt to model and minimize on the GPU, which takes a significant amount of memory. If there are more systems, the program will expand each and attempt minimizations as this limit (a safeguard against overrunning available resources) permits.

int	getFinalStateCount () const
	Get the number of final states to produce for each initial system.

int	getRotationSampleCount () const
	Get the number of samples to apply to each explicitly sampled rotatable bond.

int	getCisTransSampleCount () const
	Get the number of samples to apply to each explicitly sampled cis-trans isomeric bond.

const std::vector< double > &	getRotationSampleValues () const
	Get the list of rotational angle values to sample about each rotatable bond.

const std::vector< double > &	getCisTransSampleValues () const
	Get the list of rotational angle values to sample about each cis-trans isomeric bond.

int	getRotatableBondLimit () const
	Get the maximum number of rotatable bonds to sample.

int	getMaxSeedingAttempts () const
	Get the maximum number of conformer seeding attempts.

int	getClashPairTolerance () const
	Get the number of clashing pairs of atoms that can be seen in a structure before it is declared to contain too much internal conflict and a clash is reported.

int	getSamplingTrialLimit () const
	Get the maximum number of sampling trials that will be permitted across the various systems when attempting to sample the viable rotameric states of each bond and other possible isomerizations of each compound. This applies on a per-system basis.

int	getMaximumTrialLimit () const
	Get the maximum number of minimizations to attempt with any one molecule. Each initial state provided by the user will be subject to this limit, so if the limit is 5000 and one molecule has two initial states listed in the input deck, the total number of conformations sampled will be no greater than 10000.

double	getRMSDTolerance () const
	Get the positional root mean squared deviation that will distinguish each reported confomer.

SystemGrouping	getGroupingMethod () const
	Get the output grouping strategy, indicating whether to take the specified number of final states for each system entered by the user, for each label group spanning one or more systems, or for each unique topology spanning one or more systems.

SamplingIntensity	getSamplingIntensity () const
	Get a general sampling strategy from the user.

double	getRotatableBondSnapThreshold () const
	Get the tolerance for snapping rotatable bond settings to consensus values.

double	getCisTransBondSnapThreshold () const
	Get the tolerance for snapping cis-trans isomeric bond settings to consensus values.

VariableTorsionAdjustment	getTorsionAdjustmentProtocol () const
	Get the torsion angle adjustment strategy (applies to rotatable and cis-trans isomeric bonds) used in reconciling general settings to the known values emerging from a collection of structures for each molecule.

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


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

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


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

	ConformerControls (ConformerControls &&original)=default

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

ConformerControls &	operator= (ConformerControls &&original)=default

Detailed Description

Class to encapsulate the data that can be extracted from the &conformer namelist.

Constructor & Destructor Documentation

◆ ConformerControls()

stormm::namelist::ConformerControls::ConformerControls ( 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

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

src/Namelists/nml_conformer.h
src/Namelists/nml_conformer.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ConformerControls()