stormm::synthesis::ClashReport Class Reference

An object for listing the clashes between atoms of a system. More...

#include <clash_detection.h>

Public Member Functions
int	getClashCount () const
	Get the number of detected clashes.
double	getMinimumDistance () const
	Get the minimum clash distance.
double	getMinimumSigmaRatio () const
	Get the minimum ratio of inter-particle distance to the pairwise sigma parameter.
const AtomGraph *	getTopologyPointer () const
	Get a const pointer to the topology describing the system.
int2	getClashingPair (int index) const
	Get one of the clashing pairs of atoms.
double	getClashDistance (int index) const
	Get the distance at which two particles clash.
ClashKind	getClashKind (int index) const
	Get the type of clash made by two particles.
void	addClash (int atom_i, int atom_j, double distance_in)
	Add notes about a clash between two particles.
void	clear ()
	Clear the clashes to recompile the report.
void	setMinimumDistance (double clash_distance_in)
	Set the minimum absolute distance for two particles' separation before a clash is declared.
void	setMinimumSigmaRatio (double clash_ratio_in)
	Set the minimum ratio of interparticle distance to the pairwise sigma value, below which a clash is declared.
	ClashReport (double clash_distance_in=default_minimize_clash_r0, double clash_ratio_in=default_minimize_clash_ratio, const AtomGraph *ag_pointer_in=nullptr)
	The constructor accepts optional parameters for the clash parameters, or just a pointer to the desired topology.
	ClashReport (const AtomGraph *ag_pointer_in)
	ClashReport (const ClashReport &original)=default
	Copy and move constructors, as well as copy and move assignment operators, can all take their default forms for this object with no POINTER-kind Hybrids or other pointers needing repair.
	ClashReport (ClashReport &&original)=default
ClashReport &	operator= (const ClashReport &original)=default
ClashReport &	operator= (ClashReport &&original)=default
std::string	getClashDescription (int clash_index) const
	Produce a string describing the atoms, indices, and relevant names of one of the clashes catalogged in this object.
std::string	getClashDescription (int clash_index, const CoordinateFrameReader &crd_object) const
std::string	getClashDescription (int clash_index, const CoordinateFrame &crd_object) const
std::string	getClashDescription (int clash_index, const CoordinateFrame *crd_object) const
std::string	getClashDescription (int clash_index, const PhaseSpaceReader &crd_object) const
std::string	getClashDescription (int clash_index, const PhaseSpace &crd_object) const
std::string	getClashDescription (int clash_index, const PhaseSpace *crd_object) const
template<typename T>
std::string	getClashDescription (int clash_index, const CoordinateSeriesReader< T > &crd_object, int frame) const
template<typename T>
std::string	getClashDescription (int clash_index, const CoordinateSeries< T > &crd_object, int frame) const
template<typename T>
std::string	getClashDescription (int clash_index, const CoordinateSeries< T > *crd_object, int frame) const
std::string	getClashDescription (int clash_index, const PsSynthesisReader &crd_object, int system_index) const
std::string	getClashDescription (int clash_index, const PhaseSpaceSynthesis &crd_object, int system_index) const
std::string	getClashDescription (int clash_index, const PhaseSpaceSynthesis *crd_object, int system_index) const
std::string	getClashDescription (int clash_index, const CondensateReader &crd_object, int system_index) const
std::string	getClashDescription (int clash_index, const Condensate &crd_object, int system_index) const
std::string	getClashDescription (int clash_index, const Condensate *crd_object, int system_index) const
void	setTopologyPointer (const AtomGraph *ag_pointer_in)
	Set the topology that the clash report shall use.
void	setTopologyPointer (const AtomGraph &ag_in)

Detailed Description

An object for listing the clashes between atoms of a system.

Constructor & Destructor Documentation

ClashReport()

stormm::structure::ClashReport::ClashReport ( const ClashReport & original )

default

Copy and move constructors, as well as copy and move assignment operators, can all take their default forms for this object with no POINTER-kind Hybrids or other pointers needing repair.

Parameters

original	Some other object to base the construction upon
other	Some other object to use in assignment

Member Function Documentation

addClash()

void stormm::structure::ClashReport::addClash	(	int	atom_i,
		int	atom_j,
		double	distance_in )

Add notes about a clash between two particles.

Parameters

atom_i	The first atom of the clashing pair
atom_j	The second atom of the clashing pair
distance_in	Distance between the two particles in the clashing pair

getClashDescription()

std::string stormm::structure::ClashReport::getClashDescription

(

int

clash_index

)

const

Produce a string describing the atoms, indices, and relevant names of one of the clashes catalogged in this object.

Overloaded:

• Get a string with just the atoms and the inter-particle distance
• Get a string with the atoms, inter-particle distance, and current coordinates of each particle

Parameters

clash_index	The index of the clashing pair
crd_object	Object containing the exact coordinates within which the clash occurs
frame	Index of the frame within a series
system_index	Index of the system within a synthesis

getClashDistance()

double stormm::structure::ClashReport::getClashDistance

(

int

index

)

const

Get the distance at which two particles clash.

Parameters

index

The index of the clashing pair

getClashingPair()

int2 stormm::structure::ClashReport::getClashingPair

(

int

index

)

const

Get one of the clashing pairs of atoms.

Parameters

index

The index of the clashing pair

getClashKind()

ClashKind stormm::structure::ClashReport::getClashKind

(

int

index

)

const

Get the type of clash made by two particles.

Parameters

index

The index of the clashing pair

setMinimumDistance()

void stormm::structure::ClashReport::setMinimumDistance

(

double

clash_distance_in

)

Set the minimum absolute distance for two particles' separation before a clash is declared.

Parameters

clash_distance_in

setMinimumSigmaRatio()

void stormm::structure::ClashReport::setMinimumSigmaRatio

(

double

clash_ratio_in

)

Set the minimum ratio of interparticle distance to the pairwise sigma value, below which a clash is declared.

Parameters

clash_ratio_in

setTopologyPointer()

void stormm::structure::ClashReport::setTopologyPointer

(

const AtomGraph *

ag_pointer_in

)

Set the topology that the clash report shall use.

Overloaded:

• Supply a pointer to the topology of interest
• Pass the topology of interest by reference

Parameters

ag_pointer_in	Pointer to the desired topology
ag_in	Reference to the desired topology

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

• src/Structure/clash_detection.h
• src/Structure/clash_detection.cpp