stormm::structure::ChemicalFeaturesReader Struct Reference

Abstract of the chemical features object: this is about as complex as an object with a single abstract should get. More...

#include <chemical_features.h>

Collaboration diagram for stormm::structure::ChemicalFeaturesReader:

Public Member Functions
	ChemicalFeaturesReader (int atom_count_in, int planar_atom_count_in, int ring_count_in, int fused_ring_count_in, int twistable_ring_count_in, int conjugated_group_count_in, int aromatic_group_count_in, int polar_hydrogen_count_in, int hbond_donor_count_in, int hbond_acceptor_count_in, int chiral_center_count_in, int rotatable_bond_count_in, int cis_trans_bond_count_in, int double_bond_count_in, int triple_bond_count_in, int max_ring_size_in, double temperature_in, bool rotating_groups_mapped_in, bool chiralities_computed_in, const int *planar_centers_in, const int *ring_atoms_in, const int *ring_atom_bounds_in, const int *aromatic_pi_electrons_in, const int *aromatic_groups_in, const int *aromatic_group_bounds_in, const int *polar_hydrogens_in, const int *hydrogen_bond_donors_in, const int *hydrogen_bond_acceptors_in, const int *chiral_centers_in, const int *chiral_inversion_methods_in, const int *rotatable_groups_in, const int *rotatable_group_bounds_in, const int *cis_trans_groups_in, const int *cis_trans_group_bounds_in, const int *invertible_groups_in, const int *invertible_group_bounds_in, const int4 *chiral_arm_atoms_in, const double *formal_charges_in, const double *bond_orders_in, const double *free_electrons_in, const ullint *ring_inclusion_in, const AtomGraph *ag_pointer_in)
	The constructor takes a straight list of critical constants and pointers.
	ChemicalFeaturesReader (const ChemicalFeaturesReader &original)=default
	The default copy and move constructors are acceptable, but assignment operators are implicitly deleted due to the presence of const elements.
	ChemicalFeaturesReader (ChemicalFeaturesReader &&original)=default

Public Attributes
const int	atom_count
	Total number of atoms in the system.
const int	planar_atom_count
	Number of atoms with enforced planarity.
const int	ring_count
	Number of rings.
const int	fused_ring_count
	Number of fused rings.
const int	twistable_ring_count
	Number of twistable (i.e. boat-chair) rings.
const int	conjugated_group_count
	Number of separate conjugated pi-systems.
const int	aromatic_group_count
	Number of distinct aromatic groups.
const int	polar_hydrogen_count
	Number of polar hydrogens.
const int	hbond_donor_count
	Number of hydrogen bond donors.
const int	hbond_acceptor_count
	Number of hydrogen bond acceptors.
const int	chiral_center_count
	Number of chiral centers.
const int	rotatable_bond_count
	Number of rotatable single bonds.
const int	cis_trans_bond_count
	Number of cis-trans flippable bonds.
const int	double_bond_count
	Number of double bonds.
const int	triple_bond_count
	Number of triple bonds.
const int	max_ring_size
	The maximum ring size found.
const double	temperature
	Temperature at which resonance structures were computed.
const bool	rotating_groups_mapped
const bool	chiralities_computed
const int *	planar_centers
	Topological indices of atoms with enforced planarity.
const int *	ring_atoms
const int *	ring_atom_bounds
	Bounds array for ring_atoms.
const int *	aromatic_pi_electrons
const int *	aromatic_groups
const int *	aromatic_group_bounds
	Bounds array for aromatic_groups.
const int *	polar_hydrogens
	List of topological indices for polar hydrogen atoms.
const int *	hydrogen_bond_donors
const int *	hydrogen_bond_acceptors
	List of topological indices for H-bond acceptors.
const int *	chiral_centers
	List of topological indices for chiral centers.
const int *	chiral_inversion_methods
const int *	rotatable_groups
const int *	rotatable_group_bounds
	Bounds array for rotatable groups.
const int *	cis_trans_groups
const int *	cis_trans_group_bounds
	Bounds array for cis_trans_groups.
const int *	invertible_groups
const int *	invertible_group_bounds
	Bounds array for invertible_groups.
const int4 *	chiral_arm_atoms
const double *	formal_charges
const double *	bond_orders
const double *	free_electrons
	Free electron content of each atom.
const ullint *	ring_inclusion
const AtomGraph *	ag_pointer

Detailed Description

Abstract of the chemical features object: this is about as complex as an object with a single abstract should get.

Constructor & Destructor Documentation

ChemicalFeaturesReader()

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

default

The default copy and move constructors are acceptable, but assignment operators are implicitly deleted due to the presence of const elements.

Parameters

original

The original object to copy or move

Member Data Documentation

ag_pointer

const AtomGraph* stormm::chemistry::ChemicalFeaturesReader::ag_pointer

Pointer to the associated topology (only useable in the HOST version of the abstract)

aromatic_groups

const int* stormm::chemistry::ChemicalFeaturesReader::aromatic_groups

Lists of atoms involved in distinct aromatic groups, arranged back-to-back

aromatic_pi_electrons

const int* stormm::chemistry::ChemicalFeaturesReader::aromatic_pi_electrons

Numbers of pi electrons in each aromatic group (not a per-atom quantity, and not associated with limits in the aromatic_group_bounds array)

bond_orders

const double* stormm::chemistry::ChemicalFeaturesReader::bond_orders

The order of each bond (real numbers which frequently fall between 1.0 and 2.0)

chiral_arm_atoms

const int4* stormm::chemistry::ChemicalFeaturesReader::chiral_arm_atoms

Topological indices of the base atoms for all four arms around each chiral center (the y and z members are identical to entries in the anchor_a_branches and anchor_b_branches arrays)

chiral_inversion_methods

const int* stormm::chemistry::ChemicalFeaturesReader::chiral_inversion_methods

Integer translations of the ChiralInversionProtocol data types instructing

chiralities_computed

const bool stormm::chemistry::ChemicalFeaturesReader::chiralities_computed

Indicate whether the chiral centers of the system have been determined

cis_trans_groups

const int* stormm::chemistry::ChemicalFeaturesReader::cis_trans_groups

Lists of atoms that move when creating cis-trans isomers, arranged back-to-back

formal_charges

const double* stormm::chemistry::ChemicalFeaturesReader::formal_charges

Formal charges of each atom (real numbers taken from the resonance structure, often between 0.0 and 1.0)

hydrogen_bond_donors

const int* stormm::chemistry::ChemicalFeaturesReader::hydrogen_bond_donors

List of topological indices for H-bond donors (atoms bearin gpolar hydrogens)

invertible_groups

const int* stormm::chemistry::ChemicalFeaturesReader::invertible_groups

Lists of atoms that move based on inversion of a particular chiral center (various groups are arranged back-to-back in this array)

ring_atoms

const int* stormm::chemistry::ChemicalFeaturesReader::ring_atoms

Lists of topological indices for atoms involved in rings, arranged back-to-back

ring_inclusion

const ullint* stormm::chemistry::ChemicalFeaturesReader::ring_inclusion

Bitmask indicating the various sizes of rings that each atom is found in

rotatable_groups

const int* stormm::chemistry::ChemicalFeaturesReader::rotatable_groups

Lists of atoms that move when rotating about single bonds, arranged back-to-back

rotating_groups_mapped

const bool stormm::chemistry::ChemicalFeaturesReader::rotating_groups_mapped

Indicate whether the rotatable groups of the system (as well as chiral inversion groups) have been mapped

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

• src/Chemistry/chemical_features.h
• src/Chemistry/chemical_features.cpp