A class to mutate a molecule. More...

#include <nuri/core/molecule.h>

Public Member Functions
	MoleculeMutator (Molecule &mol)
	Construct a new MoleculeMutator object.
	MoleculeMutator ()=delete
	MoleculeMutator (const MoleculeMutator &)=delete
MoleculeMutator &	operator= (const MoleculeMutator &)=delete
	MoleculeMutator (MoleculeMutator &&) noexcept=default
MoleculeMutator &	operator= (MoleculeMutator &&) noexcept=default
	~MoleculeMutator () noexcept
int	add_atom (const AtomData &atom)
	Add an atom to the molecule.
int	add_atom (AtomData &&atom) noexcept
	Add an atom to the molecule.
int	add_atom (const Molecule::Atom &atom)
	Add an atom to the molecule.
void	mark_atom_erase (int atom_idx)
	Mark an atom to be erased.
void	mark_atom_erase (Molecule::Atom atom)
	Mark an atom to be erased.
void	clear_atoms () noexcept
	Clear all atoms and bonds of the molecule.
std::pair< int, bool >	register_bond (int src, int dst, const BondData &bond)
	Register a bond to be added to the molecule.
std::pair< int, bool >	register_bond (int src, int dst, BondData &&bond) noexcept
	Register a bond to be added to the molecule.
std::pair< int, bool >	register_bond (int src, int dst, Molecule::Bond bond)
	Register a bond to be added to the molecule.
void	mark_bond_erase (int bid)
	Mark a bond to be erased.
void	mark_bond_erase (int src, int dst)
	Mark a bond to be erased.
void	mark_bond_erase (Molecule::Atom src, Molecule::Atom dst)
	Mark a bond to be erased.
void	clear_bonds () noexcept
	Clear all bonds of the molecule.
void	clear () noexcept
	Clear the molecule.
void	finalize () noexcept
	Finalize the mutation.
Molecule &	mol () noexcept
const Molecule &	mol () const noexcept

Detailed Description

A class to mutate a molecule.

Atom addition is directly applied to the molecule, but bond addition and atom/bond erasure are delayed until the finalize() method is called. This is because bulk bond addition is more efficient than individual bond addition, and atom erasure might change the atom indices of the remaining atoms, resulting in unexpected behavior if the mutation is not applied in the correct order. The finalize() method applies the mutations in the following order:

Add registered bonds.
Erase marked bonds.
Erase marked atoms.

If finalize() method is not explicitly called, the destructor will automatically call it.

Conformers of molecules will resize to the new number of atoms also at the finalize() call. Currently, there is no way to specify the new positions of the added atoms. Assign the new positions manually after the mutation if necessary.

Note: Having multiple instances of this class for the same molecule might result in an inconsistent state.

Constructor & Destructor Documentation

◆ MoleculeMutator() [1/4]

nuri::MoleculeMutator::MoleculeMutator ( Molecule & mol )

inline

Construct a new MoleculeMutator object.

Parameters

mol	The molecule to mutate.

◆ MoleculeMutator() [2/4]

nuri::MoleculeMutator::MoleculeMutator ( )

delete

◆ MoleculeMutator() [3/4]

nuri::MoleculeMutator::MoleculeMutator ( const MoleculeMutator & )

delete

◆ MoleculeMutator() [4/4]

nuri::MoleculeMutator::MoleculeMutator ( MoleculeMutator && )

defaultnoexcept

◆ ~MoleculeMutator()

nuri::MoleculeMutator::~MoleculeMutator ( )

inlinenoexcept

Member Function Documentation

◆ add_atom() [1/3]

int nuri::MoleculeMutator::add_atom ( AtomData && atom )

inlinenoexcept

Add an atom to the molecule.

Parameters

atom	The data of the atom to add.

Returns: The index of the added atom.

◆ add_atom() [2/3]

int nuri::MoleculeMutator::add_atom ( const AtomData & atom )

inline

Add an atom to the molecule.

Parameters

atom	The data of the atom to add.

Returns: The index of the added atom.

◆ add_atom() [3/3]

int nuri::MoleculeMutator::add_atom ( const Molecule::Atom & atom )

inline

Add an atom to the molecule.

Parameters

atom	An atom to add.

Returns: The index of the added atom.

◆ clear()

void nuri::MoleculeMutator::clear ( )

noexcept

Clear the molecule.

◆ clear_atoms()

void nuri::MoleculeMutator::clear_atoms ( )

noexcept

Clear all atoms and bonds of the molecule.

◆ clear_bonds()

void nuri::MoleculeMutator::clear_bonds ( )

noexcept

Clear all bonds of the molecule.

◆ finalize()

void nuri::MoleculeMutator::finalize ( )

noexcept

Finalize the mutation.

Note: The mutator internally calls discard() after applying changes. Thus, successive calls to finalize() have no effect.

See also: Molecule::sanitize()

This will effectively call Molecule::update_topology(), if any atoms or bonds are added or removed.

◆ mark_atom_erase() [1/2]

void nuri::MoleculeMutator::mark_atom_erase ( int atom_idx )

inline

Mark an atom to be erased.

Parameters

atom_idx Index of the atom to erase, after all additions.

Note: The behavior is undefined if the atom index is out of range at the moment of calling finalize().

◆ mark_atom_erase() [2/2]

void nuri::MoleculeMutator::mark_atom_erase ( Molecule::Atom atom )

inline

Mark an atom to be erased.

Parameters

atom	An atom to erase.

Note: The behavior is undefined if the atom does not belong to the molecule.

◆ mark_bond_erase() [1/3]

void nuri::MoleculeMutator::mark_bond_erase ( int bid )

inline

Mark a bond to be erased.

Parameters

bid	The index of the bond to erase.

Note: The behavior is undefined if the index is out of range.

◆ mark_bond_erase() [2/3]

void nuri::MoleculeMutator::mark_bond_erase	(	int	src,
		int	dst )

Mark a bond to be erased.

Parameters

src	Index of the source atom of the bond.
dst	Index of the destination atom of the bond.

Note: The behavior is undefined if any of the atom indices is out of range. This is a no-op if the bond does not exist.

◆ mark_bond_erase() [3/3]

void nuri::MoleculeMutator::mark_bond_erase	(	Molecule::Atom	src,
		Molecule::Atom	dst )

inline

Mark a bond to be erased.

Parameters

src	The source atom of the bond.
dst	The destination atom of the bond.

Note: The behavior is undefined if any of the atom does not belong to the molecule. This is a no-op if the bond does not exist.

◆ mol() [1/2]

const Molecule & nuri::MoleculeMutator::mol ( ) const

inlinenoexcept

◆ mol() [2/2]

Molecule & nuri::MoleculeMutator::mol ( )

inlinenoexcept

◆ operator=() [1/2]

MoleculeMutator & nuri::MoleculeMutator::operator= ( const MoleculeMutator & )

delete

◆ operator=() [2/2]

MoleculeMutator & nuri::MoleculeMutator::operator= ( MoleculeMutator && )

defaultnoexcept

◆ register_bond() [1/3]

std::pair< int, bool > nuri::MoleculeMutator::register_bond	(	int	src,
		int	dst,
		BondData &&	bond )

noexcept

Register a bond to be added to the molecule.

Parameters

src	Index of the source atom of the bond.
dst	Index of the destination atom of the bond.
bond	The data of the bond to add.

Returns: A pair of (tentative bond index, will be added). The tentative bond index is the index of the bond if it is added (before any erasure is applied), or the index of the existing bond if it is not added. The data of the existing bond is not modified.

Note: The behavior is undefined if any of the atom indices is out of range, or if src == dst.

◆ register_bond() [2/3]

std::pair< int, bool > nuri::MoleculeMutator::register_bond	(	int	src,
		int	dst,
		const BondData &	bond )

Register a bond to be added to the molecule.

Parameters

src	Index of the source atom of the bond.
dst	Index of the destination atom of the bond.
bond	The data of the bond to add.

Returns: A pair of (tentative bond index, will be added). The tentative bond index is the index of the bond if it is added (before any erasure is applied), or the index of the existing bond if it is not added. The data of the existing bond is not modified.

Note: The behavior is undefined if any of the atom indices is out of range, or if src == dst.

◆ register_bond() [3/3]

std::pair< int, bool > nuri::MoleculeMutator::register_bond	(	int	src,
		int	dst,
		Molecule::Bond	bond )

inline

Register a bond to be added to the molecule.

Parameters

src	Index of the source atom of the bond.
dst	Index of the destination atom of the bond.
bond	The bond to copy the data from.

Returns: A pair of (tentative bond index, will be added). The tentative bond index is the index of the bond if it is added (before any erasure is applied), or the index of the existing bond if it is not added. The data of the existing bond is not modified.

Note: The behavior is undefined if any of the atom indices is out of range, or if src == dst.

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

include/nuri/core/molecule.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MoleculeMutator() [1/4]

◆ MoleculeMutator() [2/4]

◆ MoleculeMutator() [3/4]

◆ MoleculeMutator() [4/4]

◆ ~MoleculeMutator()

Member Function Documentation

◆ add_atom() [1/3]

◆ add_atom() [2/3]

◆ add_atom() [3/3]

◆ clear()

◆ clear_atoms()

◆ clear_bonds()

◆ finalize()

◆ mark_atom_erase() [1/2]

◆ mark_atom_erase() [2/2]

◆ mark_bond_erase() [1/3]

◆ mark_bond_erase() [2/3]

◆ mark_bond_erase() [3/3]

◆ mol() [1/2]

◆ mol() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ register_bond() [1/3]

◆ register_bond() [2/3]

◆ register_bond() [3/3]