The temporary AoS interface to modify cvm::atom_group. More...

Collaboration diagram for cvm::atom_group::atom_modifier:

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Public Types
using	atom_iter = decltype(m_atoms)::iterator

using	const_atom_iter = decltype(m_atoms)::const_iterator

Public Member Functions
	atom_modifier (cvm::atom_group *ag)
	Construct from `cvm::atom_group`. More...

	~atom_modifier ()
	Destructor. More...

int	remove_atom (atom_iter ai)
	Remove an atom object from this group.

STL-style iterators and accessors
simple_atom &	operator[] (size_t const i)

simple_atom const &	operator[] (size_t const i) const

atom_iter	begin ()

const_atom_iter	begin () const

atom_iter	end ()

const_atom_iter	end () const

size_t	size () const

Add atom(s) to the atom group
int	add_atom (simple_atom const &a)

int	add_atom_numbers (std::string const &numbers_conf)

int	add_atoms_of_group (const atom_group *ag)

int	add_index_group (std::string const &index_group_name, bool silent=false)

int	add_atom_numbers_range (std::string const &range_conf)

int	add_atom_name_residue_range (std::string const &psf_segid, std::string const &range_conf)

int	add_atom_id (int aid)

Private Member Functions
void	update_from_soa ()
	Populate this temporary AoS object with the atoms from `m_ag`.

void	sync_to_soa () const
	Synchronize the atoms from this temporary AoS object to `m_ag`.

Private Attributes
cvm::atom_group *	m_ag
	Pointer to the SoA atom group to be modified.

std::vector< int >	m_atoms_ids
	Internal atom IDs (populated during initialization)

std::vector< simple_atom >	m_atoms
	AoS layout of the atoms.

std::unordered_map< int, int >	m_atoms_ids_count
	A map to avoid doubly counting atoms.

cvm::real	m_total_mass
	Total mass of the atom group.

cvm::real	m_total_charge
	Total charge of the atom group.

Detailed Description

The temporary AoS interface to modify cvm::atom_group.

Constructor & Destructor Documentation

cvm::atom_group::atom_modifier::atom_modifier ( cvm::atom_group * ag )

Construct from cvm::atom_group.

cvm::atom_group::atom_modifier::~atom_modifier ( )

Destructor.

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