Read-only molecule class. More...

#include <nuri/core/molecule.h>

Public Types
using	GraphType = Graph<AtomData, BondData>
using	MutableAtom = GraphType::NodeRef
using	Atom = GraphType::ConstNodeRef
using	iterator = GraphType::iterator
using	const_iterator = GraphType::const_iterator
using	atom_iterator = iterator
using	const_atom_iterator = const_iterator
using	MutableBond = GraphType::EdgeRef
using	Bond = GraphType::ConstEdgeRef
using	bond_iterator = GraphType::edge_iterator
using	const_bond_iterator = GraphType::const_edge_iterator
using	MutableNeighbor = GraphType::AdjRef
using	Neighbor = GraphType::ConstAdjRef
using	neighbor_iterator = GraphType::adjacency_iterator
using	const_neighbor_iterator = GraphType::const_adjacency_iterator

Public Member Functions
	Molecule () noexcept=default
	Construct an empty Molecule object.
	~Molecule () noexcept=default
	Molecule (const Molecule &other) noexcept
	Molecule (Molecule &&other) noexcept
Molecule &	operator= (const Molecule &other) noexcept
Molecule &	operator= (Molecule &&other) noexcept
template<class Iterator, class = internal::enable_if_compatible_iter_t<Iterator, AtomData>>
	Molecule (Iterator begin, Iterator end)
	Construct a Molecule object from a range of atom data.
std::string &	name ()
const std::string &	name () const
void	reserve (int num_atoms)
void	reserve_bonds (int num_bonds)
bool	empty () const
	Check if the molecule has any atoms.
int	size () const
	Get the number of atoms in the molecule.
int	num_atoms () const
	Get the number of atoms in the molecule.
int	count_heavy_atoms () const
	Get the number of heavy atoms in the molecule (i.e., non-hydrogen atoms).
MutableAtom	atom (int atom_idx)
	Get a mutable atom of the molecule.
Atom	atom (int atom_idx) const
	Get an atom of the molecule.
MutableAtom	operator[] (int atom_idx)
	Get a mutable atom of the molecule.
Atom	operator[] (int atom_idx) const
	Get an atom of the molecule.
iterator	begin ()
	The begin iterator of the molecule over atoms.
const_iterator	begin () const
	The begin iterator of the molecule over atoms.
iterator	atom_begin ()
	The begin iterator of the molecule over atoms.
const_iterator	atom_begin () const
	The begin iterator of the molecule over atoms.
iterator	end ()
	The past-the-end iterator of the molecule over atoms.
const_iterator	end () const
	The past-the-end iterator of the molecule over atoms.
iterator	atom_end ()
	The past-the-end iterator of the molecule over atoms.
const_iterator	atom_end () const
	The past-the-end iterator of the molecule over atoms.
bool	bond_empty () const
	Check if the molecule has any bonds.
int	num_bonds () const
	Get the number of bonds in the molecule.
MutableBond	bond (int bond_idx)
	Get a mutable bond of the molecule.
Bond	bond (int bond_idx) const
	Get a bond of the molecule.
bond_iterator	find_bond (int src, int dst)
	Get a bond of the molecule.
const_bond_iterator	find_bond (int src, int dst) const
	Get a bond of the molecule.
bond_iterator	find_bond (Atom src, Atom dst)
	Get a bond of the molecule.
const_bond_iterator	find_bond (Atom src, Atom dst) const
	Get a bond of the molecule.
auto	bonds ()
	Get an iterable, modifiable view over bonds of the molecule.
auto	bonds () const
	Get an iterable, non-modifiable view over bonds of the molecule.
auto	cbonds () const
	Get an iterable, non-modifiable view over bonds of the molecule.
bond_iterator	bond_begin ()
	The begin iterator of the molecule over bonds.
const_bond_iterator	bond_begin () const
	The begin iterator of the molecule over bonds.
bond_iterator	bond_end ()
	The past-the-end iterator of the molecule over bonds.
const_bond_iterator	bond_end () const
	The past-the-end iterator of the molecule over bonds.
int	count_heavy_bonds () const
	Get the number of bonds between heavy atoms in the molecule.
int	num_neighbors (int atom) const
	Get the explicitly connected neighbor atoms of the atom.
neighbor_iterator	find_neighbor (int src, int dst)
	Find a neighbor of the atom.
const_neighbor_iterator	find_neighbor (int src, int dst) const
	Find a neighbor of the atom.
neighbor_iterator	find_neighbor (Atom src, Atom dst)
	Find a neighbor of the atom.
const_neighbor_iterator	find_neighbor (Atom src, Atom dst) const
	Find a neighbor of the atom.
neighbor_iterator	neighbor_begin (int atom_idx)
	The begin iterator of an atom over its neighbors.
const_neighbor_iterator	neighbor_begin (int atom_idx) const
	The begin iterator of an atom over its neighbors.
neighbor_iterator	neighbor_end (int atom_idx)
	The past-the-end iterator of an atom over its neighbors.
const_neighbor_iterator	neighbor_end (int atom_idx) const
	The past-the-end iterator of an atom over its neighbors.
MoleculeMutator	mutator ()
	Get a MoleculeMutator object associated with the molecule.
void	clear () noexcept
	Reset the molecule to an empty state.
void	clear_atoms () noexcept
	Clear all atoms and bonds of the molecule.
void	clear_bonds () noexcept
	Clear all bonds of the molecule.
const GraphType &	raw_graph () const
	Get the underlying graph of the molecule.
ABSL_MUST_USE_RESULT bool	add_hydrogens (bool update_confs=true, bool optimize=true)
	Make all implicit hydrogens explicit.
void	erase_hydrogens ()
	Erase all trivial hydrogens from the molecule.
bool	is_3d () const
	Check if the molecule has any 3D conformations.
std::vector< Matrix3Xd > &	confs ()
	Get all atomic coordinates of the conformers.
const std::vector< Matrix3Xd > &	confs () const
	Get all atomic coordinates of the conformers.
void	transform (const Eigen::Isometry3d &trans)
	Transform the molecule with the given affine transformation.
void	transform (int i, const Eigen::Isometry3d &trans)
	Transform a conformer of the molecule with the given affine transformation.
double	distsq (int src, int dst, int conf=0) const
	Calculate the squared distance between two atoms.
double	distsq (Bond bond, int conf=0) const
	Calculate the squared distance between two bonded atoms.
double	distance (int src, int dst, int conf=0) const
	Calculate the distance between two atoms.
double	distance (Bond bond, int conf=0) const
	Calculate the distance between two bonded atoms.
ArrayXd	bond_lengths (int conf=0) const
	Calculate the bond lengths of the molecule.
bool	rotate_bond (int ref_atom, int pivot_atom, double angle)
	Rotate a bond.
bool	rotate_bond (int bid, double angle)
	Rotate a bond.
bool	rotate_bond_conf (int i, int ref_atom, int pivot_atom, double angle)
	Rotate a bond of a conformer.
bool	rotate_bond_conf (int i, int bid, double angle)
	Rotate a bond of a conformer.
Substructure	substructure (SubstructCategory cat=SubstructCategory::kUnknown)
	Create and return a substurcture of the molecule.
Substructure	substructure (internal::IndexSet &&atoms, internal::IndexSet &&bonds, SubstructCategory cat=SubstructCategory::kUnknown)
	Create and return a substurcture of the molecule.
Substructure	atom_substructure (internal::IndexSet &&atoms, SubstructCategory cat=SubstructCategory::kUnknown)
	Create and return a substurcture of the molecule.
Substructure	bond_substructure (internal::IndexSet &&bonds, SubstructCategory cat=SubstructCategory::kUnknown) noexcept
	Create and return a substurcture of the molecule.
ConstSubstructure	substructure (SubstructCategory cat=SubstructCategory::kUnknown) const
	Create and return a substurcture of the molecule.
ConstSubstructure	substructure (internal::IndexSet &&atoms, internal::IndexSet &&bonds, SubstructCategory cat=SubstructCategory::kUnknown) const
	Create and return a substurcture of the molecule.
ConstSubstructure	atom_substructure (internal::IndexSet &&atoms, SubstructCategory cat=SubstructCategory::kUnknown) const
	Create and return a substurcture of the molecule.
ConstSubstructure	bond_substructure (internal::IndexSet &&bonds, SubstructCategory cat=SubstructCategory::kUnknown) const
	Create and return a substurcture of the molecule.
std::vector< Substructure > &	substructures ()
	Get the substructures.
const std::vector< Substructure > &	substructures () const
	Get the substructures.
void	update_topology ()
	Update topology of the molecule.
int	num_sssr () const
	Get size of SSSR.
const std::vector< std::vector< int > > &	ring_groups () const
	Get the ring groups of the molecule, i.e. all rings of a molecule, merged into groups of rings that share at least one atom.
int	num_fragments () const
	Get number of fragments (aka connected components).
template<class MoleculeLike>
void	merge (const MoleculeLike &other)
	Merge other molecule-like object into this molecule.
template<class KT, class VT>
void	add_prop (KT &&key, VT &&val)
internal::PropertyMap &	props ()
const internal::PropertyMap &	props () const

Public Attributes
friend	MoleculeMutator

Detailed Description

Read-only molecule class.

The few allowed mutable operations on the molecule are:

updating atom/bond properties,
modifing conformers, and
adding/removing hydrogens.

Note that it is the responsibility of the user to ensure the molecule is in a chemically valid state after property modification. For sanitization, use the MoleculeSanitizer class.

Member Typedef Documentation

◆ Atom

using nuri::Molecule::Atom = GraphType::ConstNodeRef

◆ atom_iterator

using nuri::Molecule::atom_iterator = iterator

◆ Bond

using nuri::Molecule::Bond = GraphType::ConstEdgeRef

◆ bond_iterator

using nuri::Molecule::bond_iterator = GraphType::edge_iterator

◆ const_atom_iterator

using nuri::Molecule::const_atom_iterator = const_iterator

◆ const_bond_iterator

using nuri::Molecule::const_bond_iterator = GraphType::const_edge_iterator

◆ const_iterator

using nuri::Molecule::const_iterator = GraphType::const_iterator

◆ const_neighbor_iterator

using nuri::Molecule::const_neighbor_iterator = GraphType::const_adjacency_iterator

◆ GraphType

using nuri::Molecule::GraphType = Graph<AtomData, BondData>

◆ iterator

using nuri::Molecule::iterator = GraphType::iterator

◆ MutableAtom

using nuri::Molecule::MutableAtom = GraphType::NodeRef

◆ MutableBond

using nuri::Molecule::MutableBond = GraphType::EdgeRef

◆ MutableNeighbor

using nuri::Molecule::MutableNeighbor = GraphType::AdjRef

◆ Neighbor

using nuri::Molecule::Neighbor = GraphType::ConstAdjRef

◆ neighbor_iterator

using nuri::Molecule::neighbor_iterator = GraphType::adjacency_iterator

Constructor & Destructor Documentation

◆ Molecule() [1/4]

nuri::Molecule::Molecule ( )

defaultnoexcept

Construct an empty Molecule object.

◆ ~Molecule()

nuri::Molecule::~Molecule ( )

defaultnoexcept

◆ Molecule() [2/4]

nuri::Molecule::Molecule ( const Molecule & other )

noexcept

◆ Molecule() [3/4]

nuri::Molecule::Molecule ( Molecule && other )

noexcept

◆ Molecule() [4/4]

template<class Iterator, class>

nuri::Molecule::Molecule	(	Iterator	begin,
		Iterator	end )

Construct a Molecule object from a range of atom data.

Template Parameters

Iterator The type of the iterator.

Parameters

begin	The begin iterator of the range, where AtomData must be constructible from value type of `begin`.
end	The past-the-end iterator of the range.

Member Function Documentation

◆ add_hydrogens()

ABSL_MUST_USE_RESULT bool nuri::Molecule::add_hydrogens	(	bool	update_confs = true,
		bool	optimize = true )

Make all implicit hydrogens explicit.

Parameters

update_confs	Whether to update the conformers after adding hydrogens. Default is true.
optimize	Whether to optimize the geometry of the molecule after initial hydrogen placement. Default is true. When this is false, the resulting molecule may have clashes between atoms.

Returns: Whether the operation was successful. Fails only if the molecule has more than one conformers and the geometry optimization fails. When this function returns false, the coordinates of the newly added hydrogens are not guaranteed to be chemically valid.

◆ add_prop()

template<class KT, class VT>

void nuri::Molecule::add_prop	(	KT &&	key,
		VT &&	val )

inline

◆ atom() [1/2]

MutableAtom nuri::Molecule::atom ( int atom_idx )

inline

Get a mutable atom of the molecule.

Parameters

atom_idx Index of the atom to get.

Returns: A mutable view over atom_idx -th atom of the molecule.

Note: If the atom index is out of range, the behavior is undefined. The returned reference is invalidated when the molecule is modified.

◆ atom() [2/2]

Atom nuri::Molecule::atom ( int atom_idx ) const

inline

Get an atom of the molecule.

Parameters

atom_idx Index of the atom to get.

Returns: A read-only view over atom_idx -th atom of the molecule.

Note: If the atom index is out of range, the behavior is undefined. The returned reference is invalidated when the molecule is modified.

◆ atom_begin() [1/2]

iterator nuri::Molecule::atom_begin ( )

inline

The begin iterator of the molecule over atoms.

See also: begin()

◆ atom_begin() [2/2]

const_iterator nuri::Molecule::atom_begin ( ) const

inline

The begin iterator of the molecule over atoms.

See also: begin()

◆ atom_end() [1/2]

iterator nuri::Molecule::atom_end ( )

inline

The past-the-end iterator of the molecule over atoms.

◆ atom_end() [2/2]

const_iterator nuri::Molecule::atom_end ( ) const

inline

The past-the-end iterator of the molecule over atoms.

◆ atom_substructure() [1/2]

Substructure nuri::Molecule::atom_substructure	(	internal::IndexSet &&	atoms,
		SubstructCategory	cat = SubstructCategory::kUnknown )

inline

Create and return a substurcture of the molecule.

Parameters

atoms	Indices of atoms in the substructure. All bonds between the atoms will also be included in the substructure.
cat	The category of the substructure.

◆ atom_substructure() [2/2]

ConstSubstructure nuri::Molecule::atom_substructure	(	internal::IndexSet &&	atoms,
		SubstructCategory	cat = SubstructCategory::kUnknown ) const

inline

Create and return a substurcture of the molecule.

Parameters

atoms	Indices of atoms in the substructure. All bonds between the atoms will also be included in the substructure.
cat	The category of the substructure.

◆ begin() [1/2]

iterator nuri::Molecule::begin ( )

inline

The begin iterator of the molecule over atoms.

See also: atom_begin()

◆ begin() [2/2]

const_iterator nuri::Molecule::begin ( ) const

inline

The begin iterator of the molecule over atoms.

See also: atom_begin()

◆ bond() [1/2]

MutableBond nuri::Molecule::bond ( int bond_idx )

inline

Get a mutable bond of the molecule.

Parameters

bond_idx Index of the bond to get.

Returns: A mutable view over bond bond_idx of the molecule.

Note: If the atom index is out of range, the behavior is undefined. The returned reference is invalidated when the molecule is modified.

◆ bond() [2/2]

Bond nuri::Molecule::bond ( int bond_idx ) const

inline

Get a bond of the molecule.

Parameters

bond_idx Index of the bond to get.

Returns: A read-only view over bond bond_idx of the molecule.

Note: If the atom index is out of range, the behavior is undefined. The returned reference is invalidated when the molecule is modified.

◆ bond_begin() [1/2]

bond_iterator nuri::Molecule::bond_begin ( )

inline

The begin iterator of the molecule over bonds.

◆ bond_begin() [2/2]

const_bond_iterator nuri::Molecule::bond_begin ( ) const

inline

The begin iterator of the molecule over bonds.

◆ bond_empty()

bool nuri::Molecule::bond_empty ( ) const

inline

Check if the molecule has any bonds.

◆ bond_end() [1/2]

bond_iterator nuri::Molecule::bond_end ( )

inline

The past-the-end iterator of the molecule over bonds.

◆ bond_end() [2/2]

const_bond_iterator nuri::Molecule::bond_end ( ) const

inline

The past-the-end iterator of the molecule over bonds.

◆ bond_lengths()

ArrayXd nuri::Molecule::bond_lengths ( int conf = 0 ) const

Calculate the bond lengths of the molecule.

Parameters

conf	Index of the conformer to use for the calculation.

Returns: An array of bond lengths. The order of the bond lengths is the same as the order of the bonds returned by bonds().

Note: The behavior is undefined if conf is out of range.

◆ bond_substructure() [1/2]

ConstSubstructure nuri::Molecule::bond_substructure	(	internal::IndexSet &&	bonds,
		SubstructCategory	cat = SubstructCategory::kUnknown ) const

inline

Create and return a substurcture of the molecule.

Parameters

bonds	Indices of bonds in the substructure. All atoms connected by the bonds will also be included in the substructure.
cat	The category of the substructure.

◆ bond_substructure() [2/2]

Substructure nuri::Molecule::bond_substructure	(	internal::IndexSet &&	bonds,
		SubstructCategory	cat = SubstructCategory::kUnknown )

inlinenoexcept

Create and return a substurcture of the molecule.

Parameters

bonds	Indices of bonds in the substructure. All atoms connected by the bonds will also be included in the substructure.
cat	The category of the substructure.

◆ bonds() [1/2]

auto nuri::Molecule::bonds ( )

inline

Get an iterable, modifiable view over bonds of the molecule.

◆ bonds() [2/2]

auto nuri::Molecule::bonds ( ) const

inline

Get an iterable, non-modifiable view over bonds of the molecule.

◆ cbonds()

auto nuri::Molecule::cbonds ( ) const

inline

Get an iterable, non-modifiable view over bonds of the molecule.

◆ clear()

void nuri::Molecule::clear ( )

noexcept

Reset the molecule to an empty state.

Note: Don't call this method if you have an active MoleculeMutator object. Call MoleculeMutator::clear() instead.

This method effectively resets the molecule to the state of a default constructed molecule. Unlike clear_atoms(), this will also clear name, conformers, substructures, and properties.

◆ clear_atoms()

void nuri::Molecule::clear_atoms ( )

noexcept

Clear all atoms and bonds of the molecule.

Note: Don't call this method if you have an active MoleculeMutator object. Call MoleculeMutator::clear_atoms() instead.

All conformers will be resized to 0. All substructures will contain no atoms.

◆ clear_bonds()

void nuri::Molecule::clear_bonds ( )

noexcept

Clear all bonds of the molecule.

Note: Don't call this method if you have an active MoleculeMutator object. Call MoleculeMutator::clear_bonds() instead.

Conformers and substructures are not affected.

◆ confs() [1/2]

std::vector< Matrix3Xd > & nuri::Molecule::confs ( )

inline

Get all atomic coordinates of the conformers.

Returns: Atomic coordinates of the conformers of the molecule.

Note: If any conformer's column size is not equal to the number of atoms, the behavior is undefined.

◆ confs() [2/2]

const std::vector< Matrix3Xd > & nuri::Molecule::confs ( ) const

inline

Get all atomic coordinates of the conformers.

Returns: Atomic coordinates of the conformers of the molecule.

◆ count_heavy_atoms()

int nuri::Molecule::count_heavy_atoms ( ) const

inline

Get the number of heavy atoms in the molecule (i.e., non-hydrogen atoms).

See also: size(), num_atoms()

Note: Time complexity is O(V).

◆ count_heavy_bonds()

int nuri::Molecule::count_heavy_bonds ( ) const

inline

Get the number of bonds between heavy atoms in the molecule.

See also: num_bonds()

Note: Time complexity is O(E).

◆ distance() [1/2]

double nuri::Molecule::distance	(	Bond	bond,
		int	conf = 0 ) const

inline

Calculate the distance between two bonded atoms.

Parameters

bond	The bond between the two atoms.
conf	Index of the conformer to use for the calculation.

Returns: The distance between the two atoms.

Note: The behavior is undefined the bond is not in the molecule, or if the conformer index is out of range.

◆ distance() [2/2]

double nuri::Molecule::distance	(	int	src,
		int	dst,
		int	conf = 0 ) const

inline

Calculate the distance between two atoms.

Parameters

src	Index of the source atom.
dst	Index of the destination atom.
conf	Index of the conformer to use for the calculation.

Returns: The distance between the two atoms.

Note: The behavior is undefined if any of the indices are out of range.

◆ distsq() [1/2]

double nuri::Molecule::distsq	(	Bond	bond,
		int	conf = 0 ) const

inline

Calculate the squared distance between two bonded atoms.

Parameters

bond	The bond between the two atoms.
conf	Index of the conformer to use for the calculation.

Returns: The squared distance between the two atoms.

Note: The behavior is undefined the bond is not in the molecule, or if the conformer index is out of range.

◆ distsq() [2/2]

double nuri::Molecule::distsq	(	int	src,
		int	dst,
		int	conf = 0 ) const

Calculate the squared distance between two atoms.

Parameters

src	Index of the source atom.
dst	Index of the destination atom.
conf	Index of the conformer to use for the calculation.

Returns: The squared distance between the two atoms.

Note: The behavior is undefined if any of the indices are out of range.

◆ empty()

bool nuri::Molecule::empty ( ) const

inline

Check if the molecule has any atoms.

◆ end() [1/2]

iterator nuri::Molecule::end ( )

inline

The past-the-end iterator of the molecule over atoms.

◆ end() [2/2]

const_iterator nuri::Molecule::end ( ) const

inline

The past-the-end iterator of the molecule over atoms.

◆ erase_hydrogens()

void nuri::Molecule::erase_hydrogens ( )

Erase all trivial hydrogens from the molecule.

Trivial hydrogens must satisfy the following conditions:

The hydrogen atom has single neighbor,
The neighbor is a heavy atom,
The two atoms are connected by a single bond, and
The hydrogen atom has no implicit hydrogens.

◆ find_bond() [1/4]

bond_iterator nuri::Molecule::find_bond	(	Atom	src,
		Atom	dst )

inline

Get a bond of the molecule.

Parameters

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

Returns: An iterator to the bond between src and dst of the molecule. If no such bond exists, the returned iterator is equal to bond_end().

◆ find_bond() [2/4]

const_bond_iterator nuri::Molecule::find_bond	(	Atom	src,
		Atom	dst ) const

inline

Get a bond of the molecule.

Parameters

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

Returns: An iterator to the bond between src and dst of the molecule. If no such bond exists, the returned iterator is equal to bond_end().

◆ find_bond() [3/4]

bond_iterator nuri::Molecule::find_bond	(	int	src,
		int	dst )

inline

Get a bond of the molecule.

Parameters

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

Returns: An iterator to the bond between src and dst of the molecule. If no such bond exists, the returned iterator is equal to bond_end().

◆ find_bond() [4/4]

const_bond_iterator nuri::Molecule::find_bond	(	int	src,
		int	dst ) const

inline

Get a bond of the molecule.

Parameters

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

Returns: An iterator to the bond between src and dst of the molecule. If no such bond exists, the returned iterator is equal to bond_end().

◆ find_neighbor() [1/4]

neighbor_iterator nuri::Molecule::find_neighbor	(	Atom	src,
		Atom	dst )

inline

Find a neighbor of the atom.

Parameters

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

Returns: An iterator to the neighbor wrapper between src and dst of the molecule. If no such bond exists, the returned iterator is equal to neighbor_end(src)

◆ find_neighbor() [2/4]

const_neighbor_iterator nuri::Molecule::find_neighbor	(	Atom	src,
		Atom	dst ) const

inline

Find a neighbor of the atom.

Parameters

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

Returns: An iterator to the neighbor wrapper between src and dst of the molecule. If no such bond exists, the returned iterator is equal to neighbor_end(src)

◆ find_neighbor() [3/4]

neighbor_iterator nuri::Molecule::find_neighbor	(	int	src,
		int	dst )

inline

Find a neighbor of the atom.

Parameters

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

Returns: An iterator to the neighbor wrapper between src and dst of the molecule. If no such bond exists, the returned iterator is equal to neighbor_end(src)

◆ find_neighbor() [4/4]

const_neighbor_iterator nuri::Molecule::find_neighbor	(	int	src,
		int	dst ) const

inline

Find a neighbor of the atom.

Parameters

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

Returns: An iterator to the neighbor wrapper between src and dst of the molecule. If no such bond exists, the returned iterator is equal to neighbor_end(src)

◆ is_3d()

bool nuri::Molecule::is_3d ( ) const

inline

Check if the molecule has any 3D conformations.

Returns: true if the molecule has any 3D conformations, false otherwise.

◆ merge()

template<class MoleculeLike>

void nuri::Molecule::merge ( const MoleculeLike & other )

inline

Merge other molecule-like object into this molecule.

Template Parameters

MoleculeLike Type of the other molecule-like object.

Parameters

other The other molecule-like object.

Warning: The resulting molecule might not be chemically valid. Use the MolculeSanitizer class to sanitize the molecule if necessary.

Note: Size of conformers will be updated, but the positions of the added atoms will not be set. It is the responsibility of the user to set the positions of the added atoms if necessary.; This method effectively calls update_topology().

◆ mutator()

MoleculeMutator nuri::Molecule::mutator ( )

inline

Get a MoleculeMutator object associated with the molecule.

Returns: The MoleculeMutator object to update this molecule.

See also: MoleculeMutator

◆ name() [1/2]

std::string & nuri::Molecule::name ( )

inline

◆ name() [2/2]

const std::string & nuri::Molecule::name ( ) const

inline

◆ neighbor_begin() [1/2]

neighbor_iterator nuri::Molecule::neighbor_begin ( int atom_idx )

inline

The begin iterator of an atom over its neighbors.

◆ neighbor_begin() [2/2]

const_neighbor_iterator nuri::Molecule::neighbor_begin ( int atom_idx ) const

inline

The begin iterator of an atom over its neighbors.

◆ neighbor_end() [1/2]

neighbor_iterator nuri::Molecule::neighbor_end ( int atom_idx )

inline

The past-the-end iterator of an atom over its neighbors.

◆ neighbor_end() [2/2]

const_neighbor_iterator nuri::Molecule::neighbor_end ( int atom_idx ) const

inline

The past-the-end iterator of an atom over its neighbors.

◆ num_atoms()

int nuri::Molecule::num_atoms ( ) const

inline

Get the number of atoms in the molecule.

See also: size()

◆ num_bonds()

int nuri::Molecule::num_bonds ( ) const

inline

Get the number of bonds in the molecule.

◆ num_fragments()

int nuri::Molecule::num_fragments ( ) const

inline

Get number of fragments (aka connected components).

Returns: The number of fragments.

◆ num_neighbors()

int nuri::Molecule::num_neighbors ( int atom ) const

inline

Get the explicitly connected neighbor atoms of the atom.

Parameters

atom	Index of the atom.

Returns: The number of bonds connected to the atom.

Note: If the atom index is out of range, the behavior is undefined.

See also: all_neighbors(), count_heavy(), count_hydrogens()

◆ num_sssr()

int nuri::Molecule::num_sssr ( ) const

inline

Get size of SSSR.

Returns: The number of rings in the smallest set of smallest rings.

◆ operator=() [1/2]

Molecule & nuri::Molecule::operator= ( const Molecule & other )

noexcept

◆ operator=() [2/2]

Molecule & nuri::Molecule::operator= ( Molecule && other )

noexcept

◆ operator[]() [1/2]

MutableAtom nuri::Molecule::operator[] ( int atom_idx )

inline

Get a mutable atom of the molecule.

Parameters

atom_idx Index of the atom to get.

Returns: A mutable view over atom_idx -th atom of the molecule.

Note: If the atom index is out of range, the behavior is undefined. The returned reference is invalidated when the molecule is modified.

◆ operator[]() [2/2]

Atom nuri::Molecule::operator[] ( int atom_idx ) const

inline

Get an atom of the molecule.

Parameters

atom_idx Index of the atom to get.

Returns: A read-only view over atom_idx -th atom of the molecule.

Note: If the atom index is out of range, the behavior is undefined. The returned reference is invalidated when the molecule is modified.

◆ props() [1/2]

internal::PropertyMap & nuri::Molecule::props ( )

inline

◆ props() [2/2]

const internal::PropertyMap & nuri::Molecule::props ( ) const

inline

◆ raw_graph()

const GraphType & nuri::Molecule::raw_graph ( ) const

inline

Get the underlying graph of the molecule.

Note: This is a low-level API and mostly used for internal purposes. Use the higher-level APIs provided by the Molecule class instead.

◆ reserve()

void nuri::Molecule::reserve ( int num_atoms )

inline

◆ reserve_bonds()

void nuri::Molecule::reserve_bonds ( int num_bonds )

inline

◆ ring_groups()

const std::vector< std::vector< int > > & nuri::Molecule::ring_groups ( ) const

inline

Get the ring groups of the molecule, i.e. all rings of a molecule, merged into groups of rings that share at least one atom.

Returns: List of the ring groups. If a ring group consists of single ring, the atom indices form a ring in the order of the returned vector.

◆ rotate_bond() [1/2]

bool nuri::Molecule::rotate_bond	(	int	bid,
		double	angle )

Rotate a bond.

Parameters

bid	The index of bond to rotate.
angle	Angle to rotate (in degrees).

Returns: true if the rotation was applied, false if the rotation was not applied.

Note: Rotatability only considers ring membership. The user is responsible to check bond order or other constraints.

The rotation is applied to all conformers of the molecule.

The source atom of the bond is fixed, and the destination atom will be rotated about the source atom -> destination atom axis. Positive angle means counter-clockwise rotation (as in the right-hand rule).

The behavior is undefined if any of the indices are out of range.

◆ rotate_bond() [2/2]

bool nuri::Molecule::rotate_bond	(	int	ref_atom,
		int	pivot_atom,
		double	angle )

Rotate a bond.

Parameters

ref_atom	Index of the reference atom.
pivot_atom	Index of the pivot atom.
angle	Angle to rotate (in degrees).

Returns: true if the rotation was applied, false if the rotation was not applied.

Note: Rotatability only considers ring membership. The user is responsible to check bond order or other constraints.

The rotation is applied to all conformers of the molecule.

The part of the reference atom is fixed, and the part of the pivot atom will be rotated about the reference atom -> pivot atom axis. Positive angle means counter-clockwise rotation (as in the right-hand rule).

The behavior is undefined if any of the indices are out of range, or if the atoms are not connected by a bond.

◆ rotate_bond_conf() [1/2]

bool nuri::Molecule::rotate_bond_conf	(	int	i,
		int	bid,
		double	angle )

Rotate a bond of a conformer.

Parameters

i	The index of the conformer to transform.
bid	The index of bond to rotate.
angle	Angle to rotate (in degrees).

Returns: true if the rotation was applied, false if the rotation was not applied (e.g. the bond is not rotatable, etc.).

Note: Rotatability only considers ring membership. The user is responsible to check bond order or other constraints.

The source atom of the bond is fixed, and the destination atom will be rotated about the source atom -> destination atom axis. Positive angle means counter-clockwise rotation (as in the right-hand rule).

The behavior is undefined if any of the indices are out of range.

◆ rotate_bond_conf() [2/2]

bool nuri::Molecule::rotate_bond_conf	(	int	i,
		int	ref_atom,
		int	pivot_atom,
		double	angle )

Rotate a bond of a conformer.

Parameters

i	The index of the conformer to transform.
ref_atom	Index of the pivot atom.
pivot_atom	Index of the pivot atom.
angle	Angle to rotate (in degrees).

Returns: true if the rotation was applied, false if the rotation was not applied.

Note: Rotatability only considers ring membership. The user is responsible to check bond order or other constraints.

The part of the pivot atom is fixed, and the part of the pivot atom will be rotated about the pivot atom -> pivot atom axis. Positive angle means counter-clockwise rotation (as in the right-hand rule).

The behavior is undefined if any of the indices are out of range, or if the atoms are not connected by a bond.

◆ size()

int nuri::Molecule::size ( ) const

inline

Get the number of atoms in the molecule.

See also: num_atoms()

◆ substructure() [1/4]

Substructure nuri::Molecule::substructure	(	internal::IndexSet &&	atoms,
		internal::IndexSet &&	bonds,
		SubstructCategory	cat = SubstructCategory::kUnknown )

inline

Create and return a substurcture of the molecule.

Parameters

atoms	Indices of atoms in the substructure.
bonds	Indices of bonds in the substructure.
cat	The category of the substructure.

Returns: The new substructure.

◆ substructure() [2/4]

ConstSubstructure nuri::Molecule::substructure	(	internal::IndexSet &&	atoms,
		internal::IndexSet &&	bonds,
		SubstructCategory	cat = SubstructCategory::kUnknown ) const

inline

Create and return a substurcture of the molecule.

Parameters

atoms	Indices of atoms in the substructure.
bonds	Indices of bonds in the substructure.
cat	The category of the substructure.

Returns: The new substructure.

◆ substructure() [3/4]

Substructure nuri::Molecule::substructure ( SubstructCategory cat = SubstructCategory::kUnknown )

inline

Create and return a substurcture of the molecule.

Parameters

cat	The category of the substructure.

Returns: The new substructure.

◆ substructure() [4/4]

ConstSubstructure nuri::Molecule::substructure ( SubstructCategory cat = SubstructCategory::kUnknown ) const

inline

Create and return a substurcture of the molecule.

Parameters

cat	The category of the substructure.

Returns: The new substructure.

◆ substructures() [1/2]

std::vector< Substructure > & nuri::Molecule::substructures ( )

inline

Get the substructures.

Returns: A reference to all substructures.

◆ substructures() [2/2]

const std::vector< Substructure > & nuri::Molecule::substructures ( ) const

inline

Get the substructures.

Returns: A const reference to all substructures.

◆ transform() [1/2]

void nuri::Molecule::transform ( const Eigen::Isometry3d & trans )

inline

Transform the molecule with the given affine transformation.

Parameters

trans The affine transformation to apply.

◆ transform() [2/2]

void nuri::Molecule::transform	(	int	i,
		const Eigen::Isometry3d &	trans )

inline

Transform a conformer of the molecule with the given affine transformation.

Parameters

i	The index of the conformer to transform.
trans	The affine transformation to apply.

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

◆ update_topology()

void nuri::Molecule::update_topology ( )

Update topology of the molecule.

This method is safe to call multiple times, but will be automatically called from the MoleculeMutator class anyway. Thus, user code normally don't need to call this method.

Note: This only changes ring atom/bond flags. If the molecule is modified in a way that changes aromaticity, the aromaticity flags should be updated manually or by using the MoleculeSanitizer class.

Warning: All molecule-related methods/functions assume that the molecule has valid topology data.

Member Data Documentation

◆ MoleculeMutator

friend nuri::Molecule::MoleculeMutator

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

include/nuri/core/molecule.h

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Typedef Documentation

◆ Atom

◆ atom_iterator

◆ Bond

◆ bond_iterator

◆ const_atom_iterator

◆ const_bond_iterator

◆ const_iterator

◆ const_neighbor_iterator

◆ GraphType

◆ iterator

◆ MutableAtom

◆ MutableBond

◆ MutableNeighbor

◆ Neighbor

◆ neighbor_iterator

Constructor & Destructor Documentation

◆ Molecule() [1/4]

◆ ~Molecule()

◆ Molecule() [2/4]

◆ Molecule() [3/4]

◆ Molecule() [4/4]

Member Function Documentation

◆ add_hydrogens()

◆ add_prop()

◆ atom() [1/2]

◆ atom() [2/2]

◆ atom_begin() [1/2]

◆ atom_begin() [2/2]

◆ atom_end() [1/2]

◆ atom_end() [2/2]

◆ atom_substructure() [1/2]

◆ atom_substructure() [2/2]

◆ begin() [1/2]

◆ begin() [2/2]

◆ bond() [1/2]

◆ bond() [2/2]

◆ bond_begin() [1/2]

◆ bond_begin() [2/2]

◆ bond_empty()

◆ bond_end() [1/2]

◆ bond_end() [2/2]

◆ bond_lengths()

◆ bond_substructure() [1/2]

◆ bond_substructure() [2/2]

◆ bonds() [1/2]

◆ bonds() [2/2]

◆ cbonds()

◆ clear()

◆ clear_atoms()

◆ clear_bonds()

◆ confs() [1/2]

◆ confs() [2/2]

◆ count_heavy_atoms()

◆ count_heavy_bonds()

◆ distance() [1/2]

◆ distance() [2/2]

◆ distsq() [1/2]

◆ distsq() [2/2]

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ erase_hydrogens()

◆ find_bond() [1/4]

◆ find_bond() [2/4]

◆ find_bond() [3/4]

◆ find_bond() [4/4]

◆ find_neighbor() [1/4]

◆ find_neighbor() [2/4]

◆ find_neighbor() [3/4]

◆ find_neighbor() [4/4]

◆ is_3d()

◆ merge()

◆ mutator()

◆ name() [1/2]

◆ name() [2/2]