Collect the set of symmetry-related and interchangeable groups for one or more molecules within a topology. More...

#include <atom_equivalence.h>

Public Member Functions
int	getGroupCount () const
	Get the number of atom equivalence groups.

int	getSymmetryDepth () const
	Get the number of levels of symmetry-related groups. This is essential for mapping identity swaps that an atom might undergo in a symmetry-corrected RMSD calculation.

std::vector< int >	getGroup (int group_index) const
	Get the atoms of one group as an independent Standard Template Library vector.

int	getSymmetryRelatedAtom (int group_index, int domain_index, int atom_index) const
	Get one atom index from within a symmetry-equivalent atom group.

const int *	getGroupPointer (int group_index) const
	Get a pointer to the atom indices of a particular group.

int	getGroupSize (int group_index) const
	Get the size of a particular group.

int	getGroupOrder (int group_index) const
	Get the order of a particular group.

int	getGroupLevel (int group_index) const
	Get the depth of the group of interest in terms of its dependence on (containment within) other groups of symmetry-related atoms.

EquivalenceSwap	getGroupRule (int group_index) const
	Get the manner by which combinations of the group's interchangeable subunits should be laid out in order to search for the best RMSD fit.

std::vector< int >	getGroupDependencies (int group_index) const
	Get a list of a group's dependencies (other groups that the group in question contains completely). Chained dependencies are handled implicitly by the complete containment criterion.

int	getAsymmetricAtomCount () const
	Get the number of asymmetric core atoms.

const std::vector< int > &	getAsymmetricAtoms () const
	Get a const reference to the list of atoms outside any symmetry group.

const AtomGraph *	getTopologyPointer () const
	Get a const pointer to the topology for which these equivalencies apply.


	AtomEquivalence ()
	The constructor relies on a topology pointer plus arrays of formal charges, bond orders, and ring inclusion as will have been derived by a ChemicalFeatures object.

	AtomEquivalence (const AtomGraph ag_in, const std::vector< double > &formal_charges, const std::vector< double > &free_electrons, const std::vector< ullint > &ring_inclusion, const std::vector< ChiralOrientation > &chiralities, StopWatch timer=nullptr, int low_molecule_index=0, int high_molecule_index=-1)

	AtomEquivalence (const AtomGraph &ag_in, const std::vector< double > &formal_charges, const std::vector< double > &free_electrons, const std::vector< ullint > &ring_inclusion, const std::vector< ChiralOrientation > &chiralities, StopWatch *timer=nullptr, int low_molecule_index=0, int high_molecule_index=-1)

	AtomEquivalence (const ChemicalFeatures &chemfe_in, StopWatch *timer=nullptr, int low_molecule_index=0, int high_molecule_index=-1)

	AtomEquivalence (const AtomGraph &ag_in, const CoordinateFrame &cf, StopWatch *timer=nullptr, int low_molecule_index=0, int high_molecule_index=-1)


	AtomEquivalence (const AtomEquivalence &original)=default

	AtomEquivalence (AtomEquivalence &&original)=default

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

AtomEquivalence &	operator= (AtomEquivalence &&original)=default

Detailed Description

Collect the set of symmetry-related and interchangeable groups for one or more molecules within a topology.

Constructor & Destructor Documentation

◆ AtomEquivalence() [1/2]

stormm::chemistry::AtomEquivalence::AtomEquivalence ( )

The constructor relies on a topology pointer plus arrays of formal charges, bond orders, and ring inclusion as will have been derived by a ChemicalFeatures object.

Parameters

ag_in	Topology for the system of interest (a pointer will be retained by the object)
formal_charges	Array of formal charges for all atoms in the entire topology
free_electrons	Array of free electron content for all atoms in the topology
ring_inclusion	Array of ring inclusion marks for all atoms in the topology
chiralities	Array of chiral statuses for all atoms in the entire topology
chemfe_in	Chemical features of the molecular system in question, from which the previous four arrays as well as the original topology pointer can be obtained
timer	Wall time tracker to monitor time spent in various stages of the calculation
low_molecule_index	Index of the first molecule in the topology for which to draw atom equivalence groups
high_molecule_index	Upper index limit of molecules in the topology for which to draw atom equivalence groups. The default of -1 triggers the upper limit to be set as one beyond the lower limit.

◆ AtomEquivalence() [2/2]

stormm::chemistry::AtomEquivalence::AtomEquivalence ( const AtomEquivalence & original )

default

The default copy and move constructors, as well as copy and move assignment operators, will be adequate for this object which contains only Standard Template Library components and no const member variables.

Parameters

original	The original object to copy or move
other	Another object to which the current one shall be assigned

Member Function Documentation