Interpret.h File Reference

Interpret multiple molecules in positional information. More...

#include "Molassembler/Export.h"
#include "Molassembler/PeriodicBoundaries.h"
#include "boost/optional.hpp"

Include dependency graph for Interpret.h:

Go to the source code of this file.

Data Structures
struct	Scine::Molassembler::Interpret::ComponentMap
	Type used to represent a map from an atom collection index to an interpreted object. More...
struct	Scine::Molassembler::Interpret::ComponentMap::ComponentIndexPair
struct	Scine::Molassembler::Interpret::MoleculesResult
	Result type of an interpret call. More...
struct	Scine::Molassembler::Interpret::GraphsResult
	Result type of a graph interpret call. More...
struct	Scine::Molassembler::Interpret::FalsePositive
	Fn result datatype. More...

Namespaces
	Scine::Molassembler
	Central library namespace.
	Scine::Molassembler::Interpret
	Given Cartesian coordinates, construct graphs or molecules.

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

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

Detailed Description

Interpret multiple molecules in positional information.

Copyright

This code is licensed under the 3-clause BSD license. Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group. See LICENSE.txt for details. Contains functionality permitting the interpretation of several Molecules from three-dimensional structures with or without accompanying bond orders.