stormm::synthesis::SyPermutorKit< T > Struct Template Reference

Read-only abstract for the SynthesisPermutor. Access to all of the atom groups, critical measurements, and settings for mutable components is contained herein. More...

#include <synthesis_permutor.h>

Collaboration diagram for stormm::synthesis::SyPermutorKit< T >:

Public Member Functions
	SyPermutorKit (int system_count_in, int perm_map_count_in, const int *perm_map_idx_in, const int2 *perm_elements_in, const int *perm_element_bounds_in, const int *system_settings_in, const int *system_settings_limits_in, const int *rot_grp_atoms_in, const int *rot_grp_bounds_in, const int *prm_rot_grp_bounds_in, const int *ctx_grp_atoms_in, const int *ctx_grp_bounds_in, const int *prm_ctx_grp_bounds_in, const int *inv_grp_atoms_in, const int *inv_grp_bounds_in, const int *prm_inv_grp_bounds_in, const int *chiral_atoms_in, const int *chiral_protocols_in, const int4 *rot_bond_markers_in, const int4 *ctx_bond_markers_in, const int4 *chiral_markers_in, const T *rot_bond_settings_in, const T *ctx_bond_settings_in, const int *rot_bond_settings_bounds_in, const int *ctx_bond_settings_bounds_in, const int *chiral_settings_in, const int *chiral_settings_bounds_in)
	As with other abstracts, the constructor takes input arguments for every member variable.

Public Attributes
int	system_count
	Number of systems in the synthesis.
int	perm_map_count
const int *	perm_map_idx
const int2 *	perm_elements
const int *	perm_element_bounds
	Bounds array for perm_elements.
const int *	system_settings
const int *	system_settings_limits
const int *	rot_grp_atoms
	Rotatable bond group associated atoms.
const int *	rot_grp_bounds
	Bounds array for rot_grp_atoms.
const int *	prm_rot_grp_bounds
const int *	ctx_grp_atoms
	Cis-trans isomeric bond group atoms.
const int *	ctx_grp_bounds
	Bounds array for ctx_grp_atoms.
const int *	prm_ctx_grp_bounds
const int *	inv_grp_atoms
	Chiral center inversion group atoms.
const int *	inv_grp_bounds
	Bounds array for inv_grp_atoms.
const int *	prm_inv_grp_bounds
const int *	chiral_atoms
const int *	chiral_protocols
const int4 *	rot_bond_markers
const int4 *	ctx_bond_markers
const int4 *	chiral_markers
const T *	rot_bond_settings
	Specific values that each rotatable bond can take on.
const T *	ctx_bond_settings
const int *	chiral_settings
	Specific values that each chiral center can take on.
const int *	rot_bond_settings_bounds
	Bounds array for rot_bond_settings.
const int *	ctx_bond_settings_bounds
	Bounds array for ctx_bond_settings.
const int *	chiral_settings_bounds
	Bounds array for chiral_settings.

Detailed Description

template<typename T>
struct stormm::synthesis::SyPermutorKit< T >

Read-only abstract for the SynthesisPermutor. Access to all of the atom groups, critical measurements, and settings for mutable components is contained herein.

Member Data Documentation

chiral_atoms

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::chiral_atoms

Concatenated lists of chiral atoms in all systems, also bounded by prm_inv_grp_bounds

chiral_markers

template<typename T>

const int4* stormm::synthesis::SyPermutorKit< T >::chiral_markers

Marker atoms for each chiral center, giving chiral arm priorities in the order .x = 0, .y = 3, .z = 2, and .w = 1. See the ChemicalFeatures object documentation for more details.

chiral_protocols

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::chiral_protocols

Protocols for inverting each chiral center in each system, also bounded by prm_inv_grp_bounds

ctx_bond_markers

template<typename T>

const int4* stormm::synthesis::SyPermutorKit< T >::ctx_bond_markers

Marker atoms for each cis-trans isomeric bond, used to define the angle about that bond

ctx_bond_settings

template<typename T>

const T* stormm::synthesis::SyPermutorKit< T >::ctx_bond_settings

Specific values that each cis-trans isomeric bond can take on

perm_elements

template<typename T>

const int2* stormm::synthesis::SyPermutorKit< T >::perm_elements

Array identities and array indices of each element in each permutor map. This information directs threads on where to search in rot_bond_settings, ctx_bond_settings, or chiral_settings after reading limits set forth in those arrays' bounds.

perm_map_count

template<typename T>

int stormm::synthesis::SyPermutorKit< T >::perm_map_count

Number of permutation maps (unique topologies in the synthesis)

perm_map_idx

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::perm_map_idx

Permutation map indices for every system in the synthesis

prm_ctx_grp_bounds

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::prm_ctx_grp_bounds

Bounds array for ctx_grp_bounds–giving the limits of ctx_grp_atoms limits within each permutor map

prm_inv_grp_bounds

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::prm_inv_grp_bounds

Bounds array for inv_grp_bounds–giving the limits of inv_grp_atoms limits within each permutor map

prm_rot_grp_bounds

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::prm_rot_grp_bounds

Bounds array for rot_grp_bounds–giving the limits of rot_grp_atoms limits within each permutor map

rot_bond_markers

template<typename T>

const int4* stormm::synthesis::SyPermutorKit< T >::rot_bond_markers

Marker atoms for each rotatable bond, used to define the angle about that bond

system_settings

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::system_settings

Array of settings indices for all elements of all systems in the synthesis.

system_settings_limits

template<typename T>

const int* stormm::synthesis::SyPermutorKit< T >::system_settings_limits

Array of limits for system_settings–the ith element of system_settings must always fall within the range [ 0, system_settings_limits[i] ).

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

• src/Synthesis/synthesis_permutor.h