An object for tracking the states and The object itself stores a series of permutor maps, detailing the atoms that move as a consequence of rotating about some bond or inverting a chiral center. One such map is kept for each unique topology, and the atom indices of a particular system are then obtained by adding the atom offset from the PhaseSpaceSynthesis, Condensate, or AtomGraphSynthesis. More...

#include <synthesis_permutor.h>

Public Member Functions
int	getSystemCount () const
	Get the total number of systems tracked in the synthesis.

int	getPermutorSetCount () const
	Get the number of unique permutor sets (the number of unique topologies served by the object).

int	getRotatableBondSampleCount () const
	Get the default number of rotatable bond angle samples.

int	getCisTransBondSampleCount () const
	Get the default number of cis-trans isomeric bond angle samples.

int	getVariableElementCount (int system_index) const
	Get the total number of variable elements in one of the systems: rotatable bonds, cis-trans bonds, and chiral centers (even centers that cannot invert are counted).

int	getSystemRotatableBondCount (int system_index) const
	Get the number of rotatable groups in one of the systems of the attached synthesis.

int	getSystemCisTransBondCount (int system_index) const
	Get the number of cis-trans isomeric groups in one of the systems of the attached synthesis.

int	getSystemChiralCenterCount (int system_index) const
	Get the number of chiral centers in one of the systems of the attached synthesis.

const IsomerPlan &	getRotatableGroup (int system_index, int group_index) const
	Get one of the rotatable groups.

const IsomerPlan &	getCisTransGroup (int system_index, int group_index) const
	Get one of the cis-trans isomeric groups.

const IsomerPlan &	getInvertibleGroup (int system_index, int group_index) const
	Get one of the invertible chiral centers.

const PhaseSpaceSynthesis *	getSynthesisPointer () const
	Get the a pointer to the coordinate synthesis for the collection of permutor maps.

const SyPermutorKit< double >	dpData (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the double-precision read-only abstract for the object.

const SyPermutorKit< float >	spData (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the single-precision read-only abstract for the object.

void	defineRotatableBondSettings (int map_index, const std::vector< std::vector< double > > &settings)
	Load specific settings into the available states of rotatable bonds for a particular system. If the vectors differ from the originally stated rotatable bond sample counts, the specific system will be updated.

void	defineCisTransBondSettings (int system_index, const std::vector< std::vector< double > > &settings)
	Load specific settings into the available states of cis-trans bonds for a particular system. If the vectors are not of length 2 (the assumption for the number of choices in a cis-trans rotatable bond), the number of states will be updated to accommodate the provided choices.

void	defineChiralCenterSettings (int system_index, const std::vector< std::vector< int > > &settings)
	Load specific settings into the available states of an invertible chiral center for a particular system.

void	setVariableRanges (const std::vector< double > &general_rot_settings_in, const std::vector< double > &general_ctx_settings_in, bool sample_cis_trans_states=false, bool sample_chiral_states=false)
	Set the ranges of variables (rotatable bonds, cis-trans bonds, chiral centers) for each permutor map.

void	impartControlData (const ConformerControls &confcon)
	Transfer control data from a &conformer namelist to the object. This will include vectors of torsion angle settings as well as information on how to adjust the settings based on a set of supplied structures.


	SynthesisPermutor ()
	The constructor accepts an array of pointers to existing chemical features objects, in which case a pointer to the original object for each system will be retained. The constructor also accepts an array of topologies, in which case the chemical features object will be temporarily created for the purpose of extracting critical arrays of atoms used in manipulations while the pointer to the chemical features object itself will go on to read null.

	SynthesisPermutor (const AtomGraphSynthesis poly_ag, StopWatch timer=nullptr)

	SynthesisPermutor (const AtomGraphSynthesis &poly_ag, StopWatch *timer=nullptr)

	SynthesisPermutor (const AtomGraphSynthesis poly_ag, const ConformerControls &confcon, StopWatch timer=nullptr)

	SynthesisPermutor (const AtomGraphSynthesis &poly_ag, const ConformerControls &confcon, StopWatch *timer=nullptr)

	SynthesisPermutor (const PhaseSpaceSynthesis poly_ps, StopWatch timer=nullptr)

	SynthesisPermutor (const PhaseSpaceSynthesis &poly_ps, StopWatch *timer=nullptr)

	SynthesisPermutor (const PhaseSpaceSynthesis poly_ps, const ConformerControls &confcon, StopWatch timer=nullptr)

	SynthesisPermutor (const PhaseSpaceSynthesis &poly_ps, const ConformerControls &confcon, StopWatch *timer=nullptr)

	SynthesisPermutor (const std::vector< ChemicalFeatures * > &chemfe_in, bool retain_pointers=true, StopWatch *timer=nullptr)

	SynthesisPermutor (const std::vector< ChemicalFeatures > &chemfe_in, bool retain_pointers=true, StopWatch *timer=nullptr)

	SynthesisPermutor (const std::vector< ChemicalFeatures * > &chemfe_in, const PhaseSpaceSynthesis poly_ps, const ConformerControls &confcon, const bool retain_pointers=true, StopWatch timer=nullptr)

	SynthesisPermutor (const std::vector< ChemicalFeatures * > &chemfe_in, const PhaseSpaceSynthesis &poly_ps, const ConformerControls &confcon, const bool retain_pointers=true, StopWatch *timer=nullptr)

	SynthesisPermutor (const std::vector< ChemicalFeatures > &chemfe_in, const PhaseSpaceSynthesis &poly_ps, const ConformerControls &confcon, const bool retain_pointers=true, StopWatch *timer=nullptr)


	SynthesisPermutor (const SynthesisPermutor &original)
	The presence of POINTER-kind Hybrid objects and multiple ARRAY-kind members means that the copy and move constructors as well as assignment operators must be written out explicitly.

	SynthesisPermutor (SynthesisPermutor &&original)

SynthesisPermutor &	operator= (const SynthesisPermutor &other)

SynthesisPermutor &	operator= (SynthesisPermutor &&other)


int	getPermutorMapIndex (const AtomGraph *query_ag) const
	Match a topology to the permutor map index, or a system in a synthesis to its permutor map index.

int	getPermutorMapIndex (const AtomGraph &query_ag) const

int	getPermutorMapIndex (const PhaseSpaceSynthesis *poly_ps, int system_index) const

int	getPermutorMapIndex (const PhaseSpaceSynthesis &poly_ps, int system_index) const


int	getRotatableBondCount (const int permutor_map_index) const
	Get the number of relevant rotatable bonds.

int	getRotatableBondCount () const


int	getCisTransBondCount (const int permutor_map_index) const
	Get the number of relevant cis-trans isomeric bonds.

int	getCisTransBondCount () const


int	getChiralCenterCount (const int permutor_map_index) const
	Get the number of relevant chiral centers.

int	getChiralCenterCount () const


const std::vector< int > &	getElementSampleCounts (int system_index) const
	Get the numbers of options for each mutable element in a specific system.

const std::vector< int > &	getElementSampleCounts (const AtomGraph *query_ag) const

const std::vector< int > &	getElementSampleCounts (const AtomGraph &query_ag) const


int	getElementSampleCount (ConformationEdit element_kind, int index) const
	Get the number of settings to be sampled in one element, of a particular kind, from the concatenated list spanning all systems.

int	getElementSampleCount (CoupledEdit ce) const


const TickCounter< double > &	getStateTracker (int system_index) const
	Get a const reference to the state tracker for the molecule. Also useable to get a copy of the state tracker which is then mutable.

const TickCounter< double > &	getStateTracker (const AtomGraph *ag) const

const TickCounter< double > &	getStateTracker (const AtomGraph &ag) const


llint	getReplicaCount (int query_index, SamplingIntensity effort) const
	Get the number of replicas needed to fulfill a given level of sampling in one of the permutor maps.

llint	getReplicaCount (const AtomGraph *query_ag, SamplingIntensity effort) const

llint	getReplicaCount (const AtomGraph &query_ag, SamplingIntensity effort) const

std::vector< llint >	getReplicaCount (SamplingIntensity effort) const


const ChemicalFeatures *	getChemicalFeaturesPointer (int map_index) const
	Get the pointer to the chemical features object for one of the permutor maps, which can in turn reveal the original topology governing the map. This function will apply a check to ensure that the ChemicalFeatures pointers are valid.

const std::vector< ChemicalFeatures * >	getChemicalFeaturesPointer () const


void	applySynthesis (const PhaseSpaceSynthesis *poly_ps_in, VariableTorsionAdjustment adj=VariableTorsionAdjustment::DO_NOT_CHANGE)
	Apply a synthesis to the permutor maps, which will be used as the starting point for defining new conformations of each molecule. If cis-trans or chirality sampling are shut off, the synthesis will be used to define the settings available for sampling.

void	applySynthesis (const PhaseSpaceSynthesis &poly_ps_in, VariableTorsionAdjustment adj=VariableTorsionAdjustment::DO_NOT_CHANGE)


void	permuteSystem (PhaseSpaceSynthesis *psynth, int system_index, int map_index, const CoupledEdit ce, int setting_index, PrecisionModel prec=PrecisionModel::SINGLE) const
	Manipulate one of the systems inside a synthesis, based on the internal permutor maps. The type of manipulation will be interpreted so that the appropriate group of atoms can be set to the internal coordinates selected from the array of settings. See randomizeSystem() below for a discussion on the limited advantages of batching these operations to work on a single, real-valued coordinate set and then converting all of the coordinates back to the split fixed-precision format.

void	permuteSystem (int system_index, const CoupledEdit ce, int setting_index, PrecisionModel prec=PrecisionModel::SINGLE)


void	randomizeSystem (PhaseSpaceSynthesis psynth, int system_index, int map_index, Xoshiro256ppGenerator xrs, PrecisionModel prec=PrecisionModel::SINGLE, const CoupledEdit mask_a={ ConformationEdit::BOND_ROTATION, -1 }, const CoupledEdit mask_b={ ConformationEdit::BOND_ROTATION, -1 }, const CoupledEdit mask_c={ ConformationEdit::BOND_ROTATION, -1 }) const
	Randomize the system's degrees of freedom. Up to three degrees of freedom can be masked against any changes. This function inherently converts the (possibly split) fixed-precision coordinate arrays of the synthesis to real numbers for manipulation, then converts the real numbers back. However, due to the limited extent to which this happens, it is not of much performance advantage to perform the full conversion of all coordinates to real values, batch the manipulations, and then convert the results back (primarily because of the reverse conversion). Such an optimization would also require additional code, and not be replicable on the GPU.

void	randomizeSystem (int system_index, Xoshiro256ppGenerator *xrs, PrecisionModel prec=PrecisionModel::SINGLE, const CoupledEdit mask_a={ ConformationEdit::BOND_ROTATION, -1 }, const CoupledEdit mask_b={ ConformationEdit::BOND_ROTATION, -1 }, const CoupledEdit mask_c={ ConformationEdit::BOND_ROTATION, -1 })


PhaseSpaceSynthesis	buildSynthesis (SamplingIntensity effort, Xoshiro256ppGenerator xrs, std::vector< int > correspondence, int system_limit, int globalpos_scale_bits=default_globalpos_scale_bits, int localpos_scale_bits=default_localpos_scale_bits, int velocity_scale_bits=default_velocity_scale_bits, int force_scale_bits=default_force_scale_bits, PrecisionModel prec=PrecisionModel::SINGLE, ClashReport *clrep=nullptr, int iteration_limit=default_conf_max_seeding_attempts, int max_clashes=default_conf_clash_pairs) const
	Produce a new synthesis containing permutations of each structure in the current synthesis linked to the object.

PhaseSpaceSynthesis	buildSynthesis (SamplingIntensity effort, Xoshiro256ppGenerator xrs, std::vector< int > correspondence, PrecisionModel prec, int system_limit, ClashReport *clrep=nullptr, int iteration_limit=default_conf_max_seeding_attempts, int max_clashes=default_conf_clash_pairs) const

PhaseSpaceSynthesis	buildSynthesis (SamplingIntensity effort, Xoshiro256ppGenerator xrs, int system_limit, int globalpos_scale_bits=default_globalpos_scale_bits, int localpos_scale_bits=default_localpos_scale_bits, int velocity_scale_bits=default_velocity_scale_bits, int force_scale_bits=default_force_scale_bits, PrecisionModel prec=PrecisionModel::SINGLE, ClashReport clrep=nullptr, int iteration_limit=default_conf_max_seeding_attempts, int max_clashes=default_conf_clash_pairs) const

PhaseSpaceSynthesis	buildSynthesis (SamplingIntensity effort, Xoshiro256ppGenerator xrs, PrecisionModel prec, int system_limit, ClashReport clrep=nullptr, int iteration_limit=default_conf_max_seeding_attempts, int max_clashes=default_conf_clash_pairs) const

Detailed Description

An object for tracking the states and The object itself stores a series of permutor maps, detailing the atoms that move as a consequence of rotating about some bond or inverting a chiral center. One such map is kept for each unique topology, and the atom indices of a particular system are then obtained by adding the atom offset from the PhaseSpaceSynthesis, Condensate, or AtomGraphSynthesis.

Constructor & Destructor Documentation

◆ SynthesisPermutor() [1/2]

stormm::synthesis::SynthesisPermutor::SynthesisPermutor ( )

The constructor accepts an array of pointers to existing chemical features objects, in which case a pointer to the original object for each system will be retained. The constructor also accepts an array of topologies, in which case the chemical features object will be temporarily created for the purpose of extracting critical arrays of atoms used in manipulations while the pointer to the chemical features object itself will go on to read null.

Parameters

poly_ag	Topology synthesis (sufficient for generating the object, but will calculate and discard chemical features for all individual topologies)
poly_ps	Coordinate synthesis (also sufficient for generating the object, but will again imply creating and discarding chemical features)
chemfe_in	A series of pointers to chemical features objects for each system
retain_pointers	Indicate whether a pointer to the provided chemical features object should be retained. This has a default value of true to make it transparent to future development, with any SynthesisPermutor created based on a topology passing a value of false.
timer	Wall time tracking object, passed down to ChemicalFeatures computations

◆ SynthesisPermutor() [2/2]

stormm::synthesis::SynthesisPermutor::SynthesisPermutor ( const SynthesisPermutor & original )

The presence of POINTER-kind Hybrid objects and multiple ARRAY-kind members means that the copy and move constructors as well as assignment operators must be written out explicitly.

Parameters

original	The object to copy or move
other	Another object sitting on the right hand side of the assignment operator

Member Function Documentation

◆ applySynthesis()

void stormm::synthesis::SynthesisPermutor::applySynthesis	(	const PhaseSpaceSynthesis *	poly_ps_in,
		VariableTorsionAdjustment	adj = VariableTorsionAdjustment::DO_NOT_CHANGE )

Apply a synthesis to the permutor maps, which will be used as the starting point for defining new conformations of each molecule. If cis-trans or chirality sampling are shut off, the synthesis will be used to define the settings available for sampling.

Overloaded:

Provide the synthesis by const pointer
Provide the synthesis by const reference

Parameters

poly_ps_in	The input synthesis of coordinates
adj	The manner in which to adjust settings for the permutation of molecular geometric variables (e.g. rotatable bonds, chiral centers) in response to the initial state of the synthesis

◆ buildSynthesis()

PhaseSpaceSynthesis stormm::synthesis::SynthesisPermutor::buildSynthesis	(	SamplingIntensity	effort,
		Xoshiro256ppGenerator *	xrs,
		std::vector< int > *	correspondence,
		int	system_limit,
		int	globalpos_scale_bits = default_globalpos_scale_bits,
		int	localpos_scale_bits = default_localpos_scale_bits,
		int	velocity_scale_bits = default_velocity_scale_bits,
		int	force_scale_bits = default_force_scale_bits,
		PrecisionModel	prec = PrecisionModel::SINGLE,
		ClashReport *	clrep = nullptr,
		int	iteration_limit = default_conf_max_seeding_attempts,
		int	max_clashes = default_conf_clash_pairs ) const

Produce a new synthesis containing permutations of each structure in the current synthesis linked to the object.

Overloaded:

Build the synthesis with or without specifying precision metrics for positions, velocities, and force accumulators
Provide an option to return the vector indicating which systems in the result originated in each system of the synthesis attached to this SynthesisPermutor object.

Parameters

effort	The degree of sampling to be carried out on the structures of the current synthesis.
xrs	Random number generator to use in randomizing degrees of freedom not explicitly sampled
system_limit	The maximum number of systems that the resulting synthesis can contain. If this limit would be exceeded, structures in the current synthesis will have their respective permutation efforts dialed down until the result falls within the system limits.
globalpos_scale_bits	Global position coordinate bits after the decimal
localpos_scale_bits	Local position coordinate bits after the decimal
velocity_scale_bits	Velocity coordinate bits after the decimal
force_scale_bits	Force component bits after the decimal
prec	Precision model in whcih to do calculations for structural manipulations
clrep	Object to collect reports on clashes in each structure as it is produced. A nullptr value will skip clash detection. If clashes are detected during EXHAUSTIVE permutation evaluations, the clashing structures will not be included in the output. In other contexts, if clash-free structures cannot be found within the allowed iterations, the structures will be removed from the output.
iteration_limit	The maximum number of iterations for randomizing variable groups before the sturcture is declared a loss
max_clashes	The maximum number of clashes between atoms before a structure is declared to clash

◆ defineChiralCenterSettings()

void stormm::synthesis::SynthesisPermutor::defineChiralCenterSettings	(	int	system_index,
		const std::vector< std::vector< int > > &	settings )

Load specific settings into the available states of an invertible chiral center for a particular system.

Parameters

system_index	Index of the system of interest
settings	A vector of vectors containing the acceptable settings as 0 or 1

◆ defineCisTransBondSettings()

void stormm::synthesis::SynthesisPermutor::defineCisTransBondSettings	(	int	system_index,
		const std::vector< std::vector< double > > &	settings )

Load specific settings into the available states of cis-trans bonds for a particular system. If the vectors are not of length 2 (the assumption for the number of choices in a cis-trans rotatable bond), the number of states will be updated to accommodate the provided choices.

Parameters

system_index	Index of the system of interest
settings	A vector of vectors containing the acceptable settings as real numbers, in units of radians

◆ defineRotatableBondSettings()

void stormm::synthesis::SynthesisPermutor::defineRotatableBondSettings	(	int	map_index,
		const std::vector< std::vector< double > > &	settings )

Load specific settings into the available states of rotatable bonds for a particular system. If the vectors differ from the originally stated rotatable bond sample counts, the specific system will be updated.

Parameters

system_index	Index of the system of interest
settings	A vector of vectors containing the acceptable settings as real numbers, in units of radians

◆ dpData()

const SyPermutorKit< double > stormm::synthesis::SynthesisPermutor::dpData ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get the double-precision read-only abstract for the object.

Parameters

tier	Get data pointers relevant to the CPU, or to the GPU.

◆ getChemicalFeaturesPointer()

const ChemicalFeatures * stormm::synthesis::SynthesisPermutor::getChemicalFeaturesPointer ( int map_index ) const

Get the pointer to the chemical features object for one of the permutor maps, which can in turn reveal the original topology governing the map. This function will apply a check to ensure that the ChemicalFeatures pointers are valid.

Overloaded:

Get the pointer to one map's underlying features
Get a const reference to the array of all such pointers

Parameters

map_index Index of the map of interest (this will also be checked for validity)

◆ getChiralCenterCount()

int stormm::synthesis::SynthesisPermutor::getChiralCenterCount ( const int permutor_map_index ) const

Get the number of relevant chiral centers.

Overloaded:

Get the number of chiral centers for a specific map
Get the number of chiral centers across all maps

Parameters

permutor_map_index Index of the map / topology of interest

◆ getCisTransBondCount()

int stormm::synthesis::SynthesisPermutor::getCisTransBondCount ( const int permutor_map_index ) const

Get the number of relevant cis-trans isomeric bonds.

Overloaded:

Get the number of cis-trans isomeric bonds for a specific map
Get the number of cis-trans isomeric bonds across all maps

Parameters

permutor_map_index Index of the map / topology of interest

◆ getCisTransGroup()

const IsomerPlan & stormm::synthesis::SynthesisPermutor::getCisTransGroup	(	int	system_index,
		int	group_index ) const

Get one of the cis-trans isomeric groups.

Parameters

system_index	Index of the system of interest within the attached synthesis
group_index	The cis-trans isomeric group of interest

◆ getElementSampleCount()

int stormm::synthesis::SynthesisPermutor::getElementSampleCount	(	ConformationEdit	element_kind,
		int	index ) const

Get the number of settings to be sampled in one element, of a particular kind, from the concatenated list spanning all systems.

Overloaded:

Provide the type and index of the element separately
Provide a tuple of the two pieces of information

element_kind The type of element, e.g. a rotatable bond

index Index of the variable element from within the concatenated list

◆ getElementSampleCounts()

const std::vector< int > & stormm::synthesis::SynthesisPermutor::getElementSampleCounts ( int system_index ) const

Get the numbers of options for each mutable element in a specific system.

Overloaded:

Search by system index
Search by topology

Parameters

system_index	Index of the system of interest
query_ag	Topology of interest (must match one of the topology pointers guiding a map, or the function will return an error)

◆ getInvertibleGroup()

const IsomerPlan & stormm::synthesis::SynthesisPermutor::getInvertibleGroup	(	int	system_index,
		int	group_index ) const

Get one of the invertible chiral centers.

Parameters

system_index	Index of the system of interest within the attached synthesis
group_index	The chiral center of interest

◆ getPermutorMapIndex()

int stormm::synthesis::SynthesisPermutor::getPermutorMapIndex ( const AtomGraph * query_ag ) const

Match a topology to the permutor map index, or a system in a synthesis to its permutor map index.

Overloaded:

Provide the topology by pointer or by const reference
Provide a coordinate synthesis by pointer or const reference with a system index indicating a topology to search for

Parameters

query_ag	The topology to search for
poly_ps	Coordinate synthesis containing many systems with topology pointers
system_index	Index of system within the coordinate synthesis

◆ getReplicaCount()

llint stormm::synthesis::SynthesisPermutor::getReplicaCount	(	int	query_index,
		SamplingIntensity	effort ) const

Get the number of replicas needed to fulfill a given level of sampling in one of the permutor maps.

Overloaded:

Identify the map of interest by system index from the attached synthesis
Identify the map of interest by topology pointer
Obtain a list of replicas needed for all permutor maps

Parameters

query_index	Index of the system of interest within the attached synthesis
query_ag	Pointer to the topology of interest
effort	The requested level of sampling effort

◆ getRotatableBondCount()

int stormm::synthesis::SynthesisPermutor::getRotatableBondCount ( const int permutor_map_index ) const

Get the number of relevant rotatable bonds.

Overloaded:

Get the number of rotatable bonds for a specific map
Get the number of rotatable bonds across all maps

Parameters

permutor_map_index Index of the map / topology of interest

◆ getRotatableGroup()

const IsomerPlan & stormm::synthesis::SynthesisPermutor::getRotatableGroup	(	int	system_index,
		int	group_index ) const

Get one of the rotatable groups.

Parameters

system_index	Index of the system of interest
group_index	The rotatable group of interest

◆ getStateTracker()

const TickCounter< double > & stormm::synthesis::SynthesisPermutor::getStateTracker ( int system_index ) const

Get a const reference to the state tracker for the molecule. Also useable to get a copy of the state tracker which is then mutable.

Overloaded:

Get the state tracker based on an index in the permutor
Get the state tracker based on a system's topology (this will raise an exception if the search fails)

Parameters

system_index	Index of the system of interest
ag	System topology

◆ getSystemChiralCenterCount()

int stormm::synthesis::SynthesisPermutor::getSystemChiralCenterCount ( int system_index ) const

Get the number of chiral centers in one of the systems of the attached synthesis.

Parameters

system_index Index of the system of interest

◆ getSystemCisTransBondCount()

int stormm::synthesis::SynthesisPermutor::getSystemCisTransBondCount ( int system_index ) const

Get the number of cis-trans isomeric groups in one of the systems of the attached synthesis.

Parameters

system_index Index of the system of interest

◆ getSystemRotatableBondCount()

int stormm::synthesis::SynthesisPermutor::getSystemRotatableBondCount ( int system_index ) const

Get the number of rotatable groups in one of the systems of the attached synthesis.

Parameters

system_index Index of the system of interest

◆ getVariableElementCount()

int stormm::synthesis::SynthesisPermutor::getVariableElementCount ( int system_index ) const

Get the total number of variable elements in one of the systems: rotatable bonds, cis-trans bonds, and chiral centers (even centers that cannot invert are counted).

Overloaded:

Search by system index
Search by topology

Parameters

system_index Index of the system of interest

◆ impartControlData()

void stormm::synthesis::SynthesisPermutor::impartControlData ( const ConformerControls & confcon )

Transfer control data from a &conformer namelist to the object. This will include vectors of torsion angle settings as well as information on how to adjust the settings based on a set of supplied structures.

Parameters

confcon User input derived from a &conformer namelist

◆ permuteSystem()

void stormm::synthesis::SynthesisPermutor::permuteSystem	(	PhaseSpaceSynthesis *	psynth,
		int	system_index,
		int	map_index,
		const CoupledEdit	ce,
		int	setting_index,
		PrecisionModel	prec = PrecisionModel::SINGLE ) const

Manipulate one of the systems inside a synthesis, based on the internal permutor maps. The type of manipulation will be interpreted so that the appropriate group of atoms can be set to the internal coordinates selected from the array of settings. See randomizeSystem() below for a discussion on the limited advantages of batching these operations to work on a single, real-valued coordinate set and then converting all of the coordinates back to the split fixed-precision format.

Overloaded:

Manipulate a structure in an arbitrary synthesis, such as one created by the object by replicating structures in the synthesis it references internally.
Manipulate a structure in the synthesis that this object references internally.

Parameters

psynth	The collection of systems to operate upon
system_index	Index of the system to manipulate within synth
map_index	Index of the permutor map (this can be inferred if the attached synthesis is the one being altered)
ce	A tuple of the manipulation to perform and its index from within the concatenated lists spanning all permutor maps
setting_index	Index of the setting to use, numbered 0, 1, ... N for a choice of N possible options

◆ randomizeSystem()

void stormm::synthesis::SynthesisPermutor::randomizeSystem	(	PhaseSpaceSynthesis *	psynth,
		int	system_index,
		int	map_index,
		Xoshiro256ppGenerator *	xrs,
		PrecisionModel	prec = PrecisionModel::SINGLE,
		const CoupledEdit	mask_a = { ConformationEdit::BOND_ROTATION, -1 },
		const CoupledEdit	mask_b = { ConformationEdit::BOND_ROTATION, -1 },
		const CoupledEdit	mask_c = { ConformationEdit::BOND_ROTATION, -1 } ) const

Randomize the system's degrees of freedom. Up to three degrees of freedom can be masked against any changes. This function inherently converts the (possibly split) fixed-precision coordinate arrays of the synthesis to real numbers for manipulation, then converts the real numbers back. However, due to the limited extent to which this happens, it is not of much performance advantage to perform the full conversion of all coordinates to real values, batch the manipulations, and then convert the results back (primarily because of the reverse conversion). Such an optimization would also require additional code, and not be replicable on the GPU.

Overloaded:

Manipulate a structure in an arbitrary synthesis, such as one created by the object by replicating structures in the synthesis it references internally.
Manipulate a structure in the synthesis that this object references internally.

Parameters

psynth	The collection of systems to operate upon
system_index	Index of the system to manipulate within synth
map_index	Index of the permutor map to which the system corresponds (if the synthesis to manipulate differs from the one referenced in the object)
xrs	Psuedo-random number generator for selecting random settings of each mutable element
prec	Precision model under which to perform the structural operations
mask_a	First of up to three features that will be left as they are found
mask_c	Second of up to three features that will be left as they are found
mask_b	Third of up to three features that will be left as they are found

◆ setVariableRanges()

void stormm::synthesis::SynthesisPermutor::setVariableRanges	(	const std::vector< double > &	general_rot_settings_in,
		const std::vector< double > &	general_ctx_settings_in,
		bool	sample_cis_trans_states = false,
		bool	sample_chiral_states = false )

Set the ranges of variables (rotatable bonds, cis-trans bonds, chiral centers) for each permutor map.

Parameters

general_rot_settings_in	General-purpose settings for any rotatable bond
general_ctx_settings_in	General-purpose settings for any cis-trans bond
sample_cis_trans_states	Directive to sample cis- and trans-isomeric forms of double bonds (likely passed down from a &conformer namelist, which carries the same default value of FALSE)
sample_chiral_states	Directive to sample D- and L-chiral states of invertible atom centers (likely passed down from a &conformer namelist, which carries the same default value of FALSE)

◆ spData()

const SyPermutorKit< float > stormm::synthesis::SynthesisPermutor::spData ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get the single-precision read-only abstract for the object.

Parameters

tier	Get data pointers relevant to the CPU, or to the GPU.

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

src/Synthesis/synthesis_permutor.h
src/Synthesis/synthesis_permutor.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SynthesisPermutor() [1/2]

◆ SynthesisPermutor() [2/2]

Member Function Documentation

◆ applySynthesis()

◆ buildSynthesis()

◆ defineChiralCenterSettings()

◆ defineCisTransBondSettings()

◆ defineRotatableBondSettings()

◆ dpData()

◆ getChemicalFeaturesPointer()

◆ getChiralCenterCount()

◆ getCisTransBondCount()

◆ getCisTransGroup()

◆ getElementSampleCount()

◆ getElementSampleCounts()

◆ getInvertibleGroup()

◆ getPermutorMapIndex()

◆ getReplicaCount()

◆ getRotatableBondCount()

◆ getRotatableGroup()

◆ getStateTracker()

◆ getSystemChiralCenterCount()

◆ getSystemCisTransBondCount()

◆ getSystemRotatableBondCount()

◆ getVariableElementCount()

◆ impartControlData()

◆ permuteSystem()

◆ randomizeSystem()

◆ setVariableRanges()

◆ spData()