A shorthand form of a conformational degree of freedom, which could be a rotable bond, cis-trans invertible bond, or chiral center. More...

#include <chemical_features.h>

Public Member Functions
ConformationEdit	getMotion () const
	Get the isomerizing motion.

ChiralInversionProtocol	getChiralPlan () const
	Get the plan for inverting a chiral center.

int	getRootAtom () const
	Get the root atom for the motion.

int	getPivotAtom () const
	Get the pivot atom for the motion.

int	getRootHandle () const
	Get the root atom handle (for a rotatable bond J-K, this might be I of the sequence I-J-K-L).

int	getPivotHandle () const
	Get the pivot atom handle (for a rotatable bond J-K, this might be L of the sequence I-J-K-L).

int	getMovingAtomCount () const
	Get the number of moving atoms.

int	getRealMovingAtomCount () const
	Get the number of real moving atoms.

double	getMovingAtomWeight () const
	Get the total mass of moving atoms.

int	getMovingAtom (const size_t index) const
	Get the index of an individual moving atom from within this plan.

const std::vector< int > &	getMovingAtoms () const
	Get a const reference to the stored list of atoms that move as a consequence of the isomerization.

void	addMovingAtoms (const std::vector< int > &new_atom_idx)
	Add atoms to the moving atoms list.

void	eraseMovingAtoms ()
	Erase the list of moving atoms to start over. This will resize the vector to zero.


	IsomerPlan (ConformationEdit motion_in, ChiralInversionProtocol chiral_plan_in, int root_atom_in, int pivot_atom_in, const std::vector< int > &moving_atoms_in, const AtomGraph *ag_pointer_in)
	The constructor takes all applicable arguments. Different overloads check the value of the ConformationEdit parameter to determine whether they have all of the necessary information.

	IsomerPlan (ConformationEdit motion_in, int root_atom_in, int pivot_atom_in, const std::vector< int > &moving_atoms_in, const AtomGraph *ag_pointer_in)

	IsomerPlan (ConformationEdit motion_in, ChiralInversionProtocol chiral_plan_in, int root_atom_in, int pivot_atom_in, const AtomGraph *ag_pointer_in)

	IsomerPlan (ConformationEdit motion_in, int root_atom_in, int pivot_atom_in, const AtomGraph *ag_pointer_in)


	IsomerPlan (const IsomerPlan &original)=default
	The default copy and move constructors will suffice, and with no const members the copy and move assignment operators can also take on their default forms.

	IsomerPlan (IsomerPlan &&original)=default

IsomerPlan &	operator= (const IsomerPlan &other)=default

IsomerPlan &	operator= (IsomerPlan &&other)=default

Detailed Description

A shorthand form of a conformational degree of freedom, which could be a rotable bond, cis-trans invertible bond, or chiral center.

Constructor & Destructor Documentation

◆ IsomerPlan()

stormm::chemistry::IsomerPlan::IsomerPlan	(	ConformationEdit	motion_in,
		ChiralInversionProtocol	chiral_plan_in,
		int	root_atom_in,
		int	pivot_atom_in,
		const std::vector< int > &	moving_atoms_in,
		const AtomGraph *	ag_pointer_in )

The constructor takes all applicable arguments. Different overloads check the value of the ConformationEdit parameter to determine whether they have all of the necessary information.

Overloaded:

Accept a list of moving atoms
Leave the field blank to be filled later
Specify the chiral inversion protocol (used only in the case of motion_in being CHIRAL_INVERSION)

Member Function Documentation

◆ addMovingAtoms()

void stormm::chemistry::IsomerPlan::addMovingAtoms ( const std::vector< int > & new_atom_idx )

Add atoms to the moving atoms list.

Parameters

new_atom_idx The list of new atoms

◆ getMovingAtom()

int stormm::chemistry::IsomerPlan::getMovingAtom ( const size_t index ) const

Get the index of an individual moving atom from within this plan.