Public Member Functions
boost::optional < AtomStereopermutator >	makePermutator (AtomIndex candidateIndex, const StereopermutatorList &stereopermutators, const boost::optional< AngstromPositions > &maybePositions=boost::none, const boost::optional< SubstitutionsGenerator::SubstitutionMap > &maybeSubstitutions=boost::none) const

boost::optional < BondStereopermutator >	makePermutator (const BondIndex &bond, const StereopermutatorList &stereopermutators, const boost::optional< AngstromPositions > &maybePositions=boost::none, const boost::optional< SubstitutionsGenerator::SubstitutionMap > &maybeSubstitutions=boost::none, BondStereopermutator::Alignment alignment=BondStereopermutator::Alignment::Eclipsed) const

StereopermutatorList	detectStereopermutators_ () const
	Generates a list of stereopermutators based on graph properties alone.

void	ensureModelInvariants_ () const
	Ensures basic expectations about what constitutes a Molecule are met.

bool	isValidIndex_ (AtomIndex index) const
	Returns whether the specified index is valid or not.

void	propagateGraphChange_ ()
	Updates the molecule's StereopermutatorList after a graph modification.

Constructors
	Impl () noexcept
	Default constructor.

	Impl (Utils::ElementType element) noexcept
	Mono-atomic constructor.

	Impl (Utils::ElementType a, Utils::ElementType b, BondType bondType) noexcept
	Diatomic constructor.

	Impl (Graph graph)
	Graph-only constructor.

	Impl (Graph graph, const AngstromPositions &positions, const boost::optional< std::vector< BondIndex > > &bondStereopermutatorCandidatesOptional=boost::none, const boost::optional< PeriodicBoundaryDuplicates > &periodics=boost::none)
	Graph and positions constructor.

	Impl (Graph graph, StereopermutatorList stereopermutators, boost::optional< AtomEnvironmentComponents > canonicalComponentsOption)
	Graph and stereopermutators constructor.

Modifiers
AtomIndex	addAtom (Utils::ElementType elementType, AtomIndex adjacentTo, BondType bondType)
	Adds an atom by attaching it to an existing atom.

BondIndex	addBond (AtomIndex a, AtomIndex b, BondType bondType)
	Adds a bond between existing atoms.

const BondStereopermutator &	addPermutator (const BondIndex &bond, BondStereopermutator::Alignment alignment)
	Add a new BondStereopermutator to the molecule.

void	applyPermutation (const std::vector< AtomIndex > &permutation)
	Applies an index permutation to all member state.

void	assignStereopermutator (AtomIndex a, const boost::optional< unsigned > &assignment)

void	assignStereopermutator (const BondIndex &edge, const boost::optional< unsigned > &assignment)

void	assignStereopermutatorRandomly (AtomIndex a, Random::Engine &engine)

void	assignStereopermutatorRandomly (const BondIndex &e, Random::Engine &engine)

std::vector< AtomIndex >	canonicalize (AtomEnvironmentComponents componentBitmask)
	Canonicalizes the graph, invalidating all atom and bond indices. More...

void	removeAtom (AtomIndex a)

void	removeBond (AtomIndex a, AtomIndex b)

bool	removePermutator (const BondIndex &bond)
	Removes the BondStereopermutator on a specified edge, if present. More...

bool	setBondType (AtomIndex a, AtomIndex b, BondType bondType)
	Changes an existing bond's type.

void	setElementType (AtomIndex a, Utils::ElementType elementType)
	Changes an existing atom's element type.

void	setShapeAtAtom (AtomIndex a, Shapes::Shape shape)

void	thermalizeStereopermutator (AtomIndex a, bool thermalization)
	Alters thermalization state of an atom stereopermutator.

Information
boost::optional < AtomEnvironmentComponents >	canonicalComponents () const
	Yield which components were used in canonicalization.

boost::optional< Shapes::Shape >	inferShape (AtomIndex index, const RankingInformation &ranking) const

std::string	dumpGraphviz () const
	Returns a graphivz string representation of the molecule.

const Graph &	graph () const
	Provides read-only access to the graph member.

std::size_t	hash () const
	Convolutional hash.

const StereopermutatorList &	stereopermutators () const
	Provides read-only access to the list of stereopermutators.

StereopermutatorList	inferStereopermutatorsFromPositions (const AngstromPositions &angstromWrapper, const boost::optional< std::vector< BondIndex > > &explicitBondStereopermutatorCandidatesOption=boost::none, boost::optional< const std::unordered_set< AtomIndex > & > uninteresting=boost::none, const boost::optional< SubstitutionsGenerator::SubstitutionMap > &substitutions=boost::none) const
	Yield which components were used in canonicalization.

bool	canonicalCompare (const Impl &other, AtomEnvironmentComponents componentBitmask) const
	Compares two canonical instances with one another.

boost::optional< std::vector < AtomIndex > >	modularIsomorphism (const Impl &other, AtomEnvironmentComponents componentBitmask) const
	Modular comparison of this Impl with another.

std::string	str () const
	Returns a command-line interface information string.

RankingInformation	rankPriority (AtomIndex a, const std::vector< AtomIndex > &excludeAdjacent={}, const boost::optional< AngstromPositions > &positionsOption=boost::none) const
	Yield which components were used in canonicalization.

Operators
bool	operator== (const Impl &other) const
	Equality operator, performs most strict equality comparison.

bool	operator!= (const Impl &other) const
	Negates. More...

Static Public Member Functions
static Utils::AtomCollection	applyCanonicalizationMap (const std::vector< AtomIndex > &canonicalizationIndexMap, const Utils::AtomCollection &atomCollection)

static bool	isGraphBasedBondStereopermutatorCandidate_ (BondType bondType)
	Returns whether an edge is double, triple or higher bond order.

Data Fields
Data
Graph	adjacencies_

StereopermutatorList	stereopermutators_

boost::optional < AtomEnvironmentComponents >	canonicalComponentsOption_

Member Function Documentation

void Scine::Molassembler::Molecule::Impl::assignStereopermutator	(	AtomIndex	a,
		const boost::optional< unsigned > &	assignment
	)

Sets the stereopermutator assignment at a particular atom

This sets the stereopermutator assignment at a specific atom index. For this, a stereopermutator must be instantiated and contained in the StereopermutatorList returned by stereopermutators(). The supplied assignment must be either boost::none or smaller than stereopermutatorPtr->numAssignments().

Note: Although molecules in which this occurs are infrequent, consider the StereopermutatorList you have accessed prior to calling this function and particularly any iterators thereto invalidated. This is because an assignment change can trigger a ranking change, which can in turn lead to the introduction of new stereopermutators or the removal of old ones.

void Scine::Molassembler::Molecule::Impl::assignStereopermutator	(	const BondIndex &	edge,
		const boost::optional< unsigned > &	assignment
	)

Sets the stereopermutator assignment on a bond

This sets the stereopermutator assignment at a specific bond index. For this, a stereopermutator must be instantiated and contained in the StereopermutatorList returned by stereopermutators(). The supplied assignment must be either boost::none or smaller than stereopermutatorPtr->numAssignments().

Note: Although molecules in which this occurs are infrequent, consider the StereopermutatorList you have accessed prior to calling this function and particularly any iterators thereto invalidated. This is because an assignment change can trigger a ranking change, which can in turn lead to the introduction of new stereopermutators or the removal of old ones.

void Scine::Molassembler::Molecule::Impl::assignStereopermutatorRandomly	(	AtomIndex	a,
		Random::Engine &	engine
	)

Assigns a stereopermutator stereopermutation at random

This sets the stereocetner assignment at a specific index, taking relative statistical occurence weights of each stereopermutation into account.

Precondition: There must be an AtomStereopermutator at the passed index

Exceptions

If	no AtomStereopermutator exists at the passed index

Note: Although molecules in which this occurs are infrequent, consider the StereopermutatorList you have accessed prior to calling this function and particularly any iterators to its members invalidated. This is because an assignment change can trigger a ranking change, which can in turn lead to the introduction of new stereopermutators or the removal of old ones.

void Scine::Molassembler::Molecule::Impl::assignStereopermutatorRandomly	(	const BondIndex &	e,
		Random::Engine &	engine
	)

Assigns a bond stereopermutator to a random assignment

Precondition: There must be a BondStereopermutator at the passed edge

Exceptions

If	no BondStereopermutator exists at the passed edge

Note: Although molecules in which this occurs are infrequent, consider the StereopermutatorList you have accessed prior to calling this function and particularly any iterators to its members invalidated. This is because an assignment change can trigger a ranking change, which can in turn lead to the introduction of new stereopermutators or the removal of old ones.

std::vector<AtomIndex> Scine::Molassembler::Molecule::Impl::canonicalize ( AtomEnvironmentComponents componentBitmask )

Canonicalizes the graph, invalidating all atom and bond indices.

Parameters

componentBitmask The components of the molecular graph to include in the canonicalization procedure.

Warning: Any comparisons made on canonical graphs must be made with a less or equally strict components bitmask. If you choose a stricter bitmask than you have used in the canonicalization procedure, you risk false positives and false negatives.; This invalidates all atom indices and bond indices and any references to constituting members of the molecule.

Note: Use

See Also: canonicalCompare to compare instances of canonicalized molecules.

Returns: Permutation mapping from old indices to new:
auto indexMapping = mol.canonicalize();

AtomIndex newIndex = indexMapping.at(oldIndex);

You can use this to update invalidated indices.

boost::optional<Shapes::Shape> Scine::Molassembler::Molecule::Impl::inferShape	(	AtomIndex	index,
		const RankingInformation &	ranking
	)		const

Determines what the local geometry at a non-terminal atom ought to be

Returns the expected shape name at a non-terminal atom.

Exceptions

if	the supplied atomic index is invalid

bool Scine::Molassembler::Molecule::Impl::operator!= ( const Impl & other ) const

Negates.

See Also: operator ==

void Scine::Molassembler::Molecule::Impl::removeAtom ( AtomIndex a )

Removes an atom from the graph, including bonds to it.

Removes an atom from the molecular graph, including bonds to the atom, after checking that removing it is safe, i.e. the removal does not disconnect the graph.

Exceptions

if	the supplied index is invalid or isSafeToRemoveAtom returns false.

void Scine::Molassembler::Molecule::Impl::removeBond	(	AtomIndex	a,
		AtomIndex	b
	)

Removes an atom after checking if removing that bond is safe, i.e. does not disconnect the graph. An example of bonds that can always be removed are ring-closing bonds, since they never disconnect the molecular graph.

Exceptions

if	isSafeToRemoveBond returns false.

Note: It is not safe to remove a bond just because one of the involved atoms is terminal, since that atom would then be disconnected from the rest of the molecule. This function merely removes a bond from the graph. It is, however, considered safe to remove the terminal vertex, which involves removing the bond to it.

bool Scine::Molassembler::Molecule::Impl::removePermutator ( const BondIndex & bond )

Removes the BondStereopermutator on a specified edge, if present.

Returns: Whether a permutator was deleted

void Scine::Molassembler::Molecule::Impl::setShapeAtAtom	(	AtomIndex	a,
		Shapes::Shape	shape
	)

Sets the local geometry at an atom index

This sets the local geometry at a specific atom index. There are a number of cases that this function treats differently, besides faulty arguments: If there is already a AtomStereopermutator instantiated at this atom index, its underlying shape is altered. If there is no AtomStereopermutator at this index, one is instantiated. In all cases, new or modified stereopermutators are default-assigned if there is only one possible assignment.

Exceptions

if	the supplied atomic index is invalid there is an BondStereopermutator at that index or the provided shape is a different size than that of an existing AtomStereopermutator or the expected shape

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

Molassembler/Molecule/MoleculeImpl.h

Public Member Functions

Static Public Member Functions

Data Fields

Member Function Documentation