Given Cartesian coordinates, construct graphs or molecules. More...

Data Structures
struct	ComponentMap
	Type used to represent a map from an atom collection index to an interpreted object. More...

struct	MoleculesResult
	Result type of an interpret call. More...

struct	GraphsResult
	Result type of a graph interpret call. More...

struct	FalsePositive
	Fn result datatype. More...

Enumerations
enum	BondDiscretizationOption { BondDiscretizationOption::Binary, BondDiscretizationOption::RoundToNearest }
	How floating-point bond orders are discretized into bond types. More...

Functions
MoleculesResult	molecules (const Utils::ElementTypeCollection &elements, const AngstromPositions &angstromWrapper, const Utils::BondOrderCollection &bondOrders, BondDiscretizationOption discretization=BondDiscretizationOption::Binary, const boost::optional< double > &stereopermutatorThreshold=1.4)
	The function that actually does all the work with the library-internal wrapper. More...

MoleculesResult	molecules (const Utils::ElementTypeCollection &elements, const AngstromPositions &angstromWrapper, BondDiscretizationOption discretization=BondDiscretizationOption::Binary, const boost::optional< double > &stereopermutatorThreshold=1.4)
	Interpret a molecule from positional information only. Calculates bond orders using Utils' BondDetector class. More...

MoleculesResult	molecules (const Utils::AtomCollection &atomCollection, const Utils::BondOrderCollection &bondOrders, BondDiscretizationOption discretization=BondDiscretizationOption::Binary, const boost::optional< double > &stereopermutatorThreshold=1.4)
	Interpret molecules from element types, positional information and a bond order collection. More...

MoleculesResult	molecules (const Utils::AtomCollection &atoms, const Utils::BondOrderCollection &periodicBonds, const std::unordered_set< unsigned > &uninterestingAtoms, const std::unordered_map< unsigned, unsigned > &ghostAtomMap, BondDiscretizationOption discretization=BondDiscretizationOption::Binary, const boost::optional< double > &stereopermutatorThreshold=1.4)
	Interpret molecules of a periodic system. More...

MoleculesResult	molecules (const Utils::AtomCollection &atomCollection, BondDiscretizationOption discretization=BondDiscretizationOption::Binary, const boost::optional< double > &stereopermutatorThreshold=1.4)
	Interpret molecules from Cartesian coordinates. More...

GraphsResult	graphs (const Utils::ElementTypeCollection &elements, const AngstromPositions &angstromWrapper, const Utils::BondOrderCollection &bondOrders, BondDiscretizationOption discretization=BondDiscretizationOption::Binary)
	The function that actually does all the work with the library-internal wrapper. More...

GraphsResult	graphs (const Utils::AtomCollection &atomCollection, const Utils::BondOrderCollection &bondOrders, BondDiscretizationOption discretization=BondDiscretizationOption::Binary)
	Interpret graphs from element types, positional information and a bond order collection. More...

std::vector< FalsePositive >	uncertainBonds (const Utils::AtomCollection &atomCollection, const Utils::BondOrderCollection &bondOrders)
	Suggests false positives from a binary interpretation of bond orders. More...

std::vector< FalsePositive >	badHapticLigandBonds (const Utils::AtomCollection &atomCollection, const Utils::BondOrderCollection &bondOrders)
	Suggests false positive haptic ligand bonds from a binary interpretation of bond orders. More...

Utils::BondOrderCollection	removeFalsePositives (const Utils::AtomCollection &atoms, Utils::BondOrderCollection bonds)
	Iteratively applies false positive detection schemes. More...

Detailed Description

Given Cartesian coordinates, construct graphs or molecules.

Enumeration Type Documentation

enum Scine::Molassembler::Interpret::BondDiscretizationOption

strong

How floating-point bond orders are discretized into bond types.

Enumerator
Binary	All bond orders >= 0.5 are considered single bonds.
RoundToNearest	Bond orders are rounded to the nearest integer.

Function Documentation

std::vector<FalsePositive> Scine::Molassembler::Interpret::badHapticLigandBonds	(	const Utils::AtomCollection &	atomCollection,
		const Utils::BondOrderCollection &	bondOrders
	)

Suggests false positive haptic ligand bonds from a binary interpretation of bond orders.

Generates a plane of best fit for each haptic ligand in the interpreted graphs. If the angle of the normal of this plane to the axis defined by the central atom and the site centroid is more than 30 degrees, tries to name a single bond whose removal improves the interpretation.

Note: Suggested bonds can disconnect haptic sites. When making changes to a bond order matrix based on suggestions from this function, apply them one at a time based on the highest probability received. Additionally, if multiple bonds must be removed to make a haptic ligand geometrically reasonable, you will need to iteratively call this function and alter suggested bond orders.

GraphsResult Scine::Molassembler::Interpret::graphs	(	const Utils::ElementTypeCollection &	elements,
		const AngstromPositions &	angstromWrapper,
		const Utils::BondOrderCollection &	bondOrders,
		BondDiscretizationOption	discretization = `BondDiscretizationOption::Binary`
	)

The function that actually does all the work with the library-internal wrapper.

Complexity \(\Theta(M)\) graph instantiations for each connected component found of at least linear complexity each

Parameters

elements	Element type collection
angstromWrapper	Positional information in Angstrom units
bondOrders	Bond orders
discretization	How to discretize fractional bond orders

Exceptions

invalid_argument If the number of particles in the element collection, angstrom wrapper or bond order collection do not match.

Returns: A list of found graphs and an index mapping to each graph

GraphsResult Scine::Molassembler::Interpret::graphs	(	const Utils::AtomCollection &	atomCollection,
		const Utils::BondOrderCollection &	bondOrders,
		BondDiscretizationOption	discretization = `BondDiscretizationOption::Binary`
	)

Interpret graphs from element types, positional information and a bond order collection.

Attempts to interpret (possibly multiple) graphs from element types, positional information and a bond order collection. Bond orders are discretized into bond types. Connected components within the space are identified and individually instantiated into Molecules.

Parameters

atomCollection	Element types and positional information in Bohr units.
bondOrders	Fractional bond orders
discretization	Decide how bond orders are discretized into bond types

Exceptions

invalid_argument If the number of particles in the atom collection and bond order collection do not match.

Note: Assumes that the provided atom collection's positions are in Bohr units.

MoleculesResult Scine::Molassembler::Interpret::molecules	(	const Utils::ElementTypeCollection &	elements,
		const AngstromPositions &	angstromWrapper,
		const Utils::BondOrderCollection &	bondOrders,
		BondDiscretizationOption	discretization = `BondDiscretizationOption::Binary`,
		const boost::optional< double > &	stereopermutatorThreshold = `1.4`
	)

The function that actually does all the work with the library-internal wrapper.

Complexity \(\Theta(M)\) molecule instantiations for each connected component found of at least linear complexity each

Parameters

elements	Element type collection
angstromWrapper	Positional information in Angstrom units
bondOrders	Bond orders
discretization	How to discretize fractional bond orders
stereopermutatorThreshold	From which fractional bond order on to try the interpretation of bond stereopermutator. If set as `boost::none`, no bond stereopermutators are interpreted.

Exceptions

invalid_argument If the number of particles in the element collection, angstrom wrapper or bond order collection do not match.

Returns: A list of found molecules and an index mapping to each molecule

MoleculesResult Scine::Molassembler::Interpret::molecules	(	const Utils::ElementTypeCollection &	elements,
		const AngstromPositions &	angstromWrapper,
		BondDiscretizationOption	discretization = `BondDiscretizationOption::Binary`,
		const boost::optional< double > &	stereopermutatorThreshold = `1.4`
	)

Interpret a molecule from positional information only. Calculates bond orders using Utils' BondDetector class.

Parameters

elements	Element type collection
angstromWrapper	Positional information in Angstrom units
discretization	How to discretize fractional bond orders
stereopermutatorThreshold	From which fractional bond order on to try the interpretation of bond stereopermutator. If set as `boost::none`, no bond stereopermutators are interpreted.

Exceptions

invalid_argument If the number of particles in the element collection and angstrom wrapper do not match.

Returns: A list of found molecules and an index mapping to each molecule

MoleculesResult Scine::Molassembler::Interpret::molecules	(	const Utils::AtomCollection &	atomCollection,
		const Utils::BondOrderCollection &	bondOrders,
		BondDiscretizationOption	discretization = `BondDiscretizationOption::Binary`,
		const boost::optional< double > &	stereopermutatorThreshold = `1.4`
	)

Interpret molecules from element types, positional information and a bond order collection.

Attempts to interpret (possibly multiple) Molecules from element types, positional information and a bond order collection. Bond orders are discretized into bond types. Connected components within the space are identified and individually instantiated into Molecules. The instantiation behavior of BondStereopermutators in the Molecules can be limited to edges whose bond order exceeds a particular value.

Parameters

atomCollection	Element types and positional information in Bohr units.
bondOrders	Fractional bond orders
discretization	Decide how bond orders are discretized into bond types
stereopermutatorThreshold	If specified, limits the instantiation of BondStereopermutators onto edges whose fractional bond orders exceed the provided threshold. If this is not desired, specify boost::none.

Exceptions

invalid_argument If the number of particles in the atom collection and bond order collection do not match.

Note: Assumes that the provided atom collection's positions are in Bohr units.

MoleculesResult Scine::Molassembler::Interpret::molecules	(	const Utils::AtomCollection &	atoms,
		const Utils::BondOrderCollection &	periodicBonds,
		const std::unordered_set< unsigned > &	uninterestingAtoms,
		const std::unordered_map< unsigned, unsigned > &	ghostAtomMap,
		BondDiscretizationOption	discretization = `BondDiscretizationOption::Binary`,
		const boost::optional< double > &	stereopermutatorThreshold = `1.4`
	)

Interpret molecules of a periodic system.

Interpret molecules into a simplified representation of structures with periodic boundary conditions.

Parameters

atoms	Atom collection with ghost atoms
periodicBonds	Bond orders including extra bonds to ghost atoms
uninterestingAtoms	List of atoms for which to skip shape classification and stereopermutator instantiation.
ghostAtomMap	Map from ghost atom indices to their base atom
discretization	Decide how bond orders are discretized into bond types
stereopermutatorThreshold	If specified, limits the instantiation of BondStereopermutators onto edges whose fractional bond orders exceed the provided threshold. If this is not desired, specify boost::none.

Precondition: Ghost atom indices must be a separate group of higher indices than both interesting and uninteresting atoms.

Exceptions

std::invalid_argument If the number of particles in the atom collection and bond order collection do not match.

Note: Assumes that the provided atom collection's positions are in Bohr units; Any molecules interpreted with uninteresting atoms cannot be passed to conformer generation routines.

Warning: Ranking across periodic boundaries is incorrect.

MoleculesResult Scine::Molassembler::Interpret::molecules	(	const Utils::AtomCollection &	atomCollection,
		BondDiscretizationOption	discretization = `BondDiscretizationOption::Binary`,
		const boost::optional< double > &	stereopermutatorThreshold = `1.4`
	)

Interpret molecules from Cartesian coordinates.

Attempts to interpret (possibly multiple) Molecules from element types and positional information. Bond orders are calculated from atom-pairwise spatial distances by van-der-Waals radii. The bond orders are then discretized into bond types. Connected components within the space are identified and individually instantiated into Molecules. The instantiation behavior of BondStereopermutators in the Molecules can be limited to edges whose bond order exceeds a particular value.

Parameters

atomCollection	Element types and positional information in Bohr units.
discretization	Decide how bond orders are discretized into bond types
stereopermutatorThreshold	If specified, limits the instantiation of BondStereopermutators onto edges whose fractional bond orders exceed the provided threshold

Note: Assumes that the provided atom collection's positions are in Bohr units.

Utils::BondOrderCollection Scine::Molassembler::Interpret::removeFalsePositives	(	const Utils::AtomCollection &	atoms,
		Utils::BondOrderCollection	bonds
	)

Iteratively applies false positive detection schemes.

Warning: Pretty darn conservative implementation, removes only a single bond from each false positive detection function call each iteration.

std::vector<FalsePositive> Scine::Molassembler::Interpret::uncertainBonds	(	const Utils::AtomCollection &	atomCollection,
		const Utils::BondOrderCollection &	bondOrders
	)

Suggests false positives from a binary interpretation of bond orders.

Collects instances where shape classification is uncertain. If two connected atoms are both uncertain (>= 50% probability that the point cloud could be part of a random sample), lists the bond as a possible false postive.

Warning: Do not alter both bonds if there is a bond pair that have overlapping indices. If suggested bonds overlap, remove only that bond with the higher probabiltiy.

Data Structures

Enumerations

Functions

Detailed Description

Enumeration Type Documentation

Function Documentation