3.2.2. Config.hpp

This file defines configuration options for the library. Many of the options control verbosity of algorithms or which data to output when printing figures.

enum struct LabelType

Selector for which type of label to use in algorithms.

enumerator String

Vertices and edges are considered to be labelled with character strings. If only first-order terms are present, then strings are generated as a serialisation of the term.

enumerator Term

Vertices and edges are considered to be labelled with first-order terms. If only strings are present, then first-order terms are generated by parsing the strings. This may result in an TermParsingError if a string can not be parsed.

enum struct LabelRelation

Selector for which type of labelled morphism to use in an algorithm.

enumerator Isomorphism

Strings are considered isomorphic when they are equal. Terms are considered isomorphic when their most general unifier is a renaming.

enumerator Specialisation

A term \(t_2\) is more special than, or isomorphic to, a term \(t_1\) if there is a substitution which can be applied to \(t_1\) to make the terms equal. This relation means that the right-hand side of a comparison is the more specialised term.

enumerator Unification

Strings unify if they are equal, i.e., the same as with Isomorphism. Terms unify if a most general unifier (MGU) exists. The found MGU is used for substitution in some algorithms.

class LabelSettings

A class simply for grouping label settings.

LabelSettings(LabelType type, LabelRelation relation)

Construct label settings that only uses the vertex and edge labels.

LabelSettings(LabelType type, LabelRelation relation, LabelRelation stereoRelation)

Construct label settings that include both vertex and edge labels, and stereo information.

LabelSettings(LabelType type, LabelRelation relation, bool withStereo, LabelRelation stereoRelation)

friend bool operator==(LabelSettings a, LabelSettings b)

friend bool operator!=(LabelSettings a, LabelSettings b)

friend std::ostream &operator<<(std::ostream &s, const LabelSettings &ls)

LabelType type

LabelRelation relation

bool withStereo

LabelRelation stereoRelation

enum struct IsomorphismPolicy

For some functions there is a choice of how to handle given arguments where two different objects may be isomorphic. Most notably the case is with graphs (graph::Graph).

enumerator Check

Objects are checked for isomorphism as needed and exceptions are thrown when different objects are isomorphic. If in doubt, use this.

enumerator TrustMe

No checks are performed and the function trusts the caller to have performed the equivalent isomorphism checks. Only use this when you are completely sure that no exceptions would have been thrown if using Check.

Warning

Generally the library has undefined behaviour if you use this option but an exception would have been thrown with Check.

enum struct SmilesClassPolicy

When loading SMILES strings, the class labels can be recorded and mapped into the corresponding vertices of the loaded graph. This policy dictates what should happen when the same class label is written on multiple atoms.

enumerator NoneOnDuplicate

If a class label is duplicated, then no labels are mapped to vertices.

enumerator ThrowOnDuplicate

If a class label is duplicated, throw a InputError.

enumerator MapUnique

Map all class labels that are unique to vertices.

enum struct Action

Utility enum for deciding what to do in certain cases.

enumerator Error

Abort the function and produce an error message, e.g., through and exception.

enumerator Warn

Write a warning, but otherwise do as if it was Ignore.

enumerator Ignore

Ignore the case. The function taking the action as argument should describe what this means.

class MDLOptions

An aggregation of options for the various loading functions for MDL formats. Generally each option is defaulted to follow the specification of the formats, unless it is harmless to deviate (e.g., relaxed white-space parsing).

bool addHydrogens = true

Use the MDL valence model to add hydrogens to atoms with default valence, or disable all hydrogen addition.

bool allowAbstract = false

Allow non-standard atom symbols. The standard symbols are the element symbols and those specifying wildcard atoms.

bool applyV2000AtomAliases = true

In MOL V2000 CTAB blocks, replace atom labels by their aliases. After application, the atom is considered abstract without errors, and hydrogen addition is suppressed.

Action onPatternIsotope = Action::Error

Action onPatternCharge = Action::Error;

Action onPatternRadical = Action::Error;

What to do when an atom with symbol * has an isotope, charge, or radical. Action::Ignore means assuming the isotope, charge, or radical was not there.

Action onImplicitValenceOnAbstract = Action::Error

What to do when addHydrogens && allowAbstract and an abstract atom is encountered with implicit valence. Action::Ignore means adding no hydrogens.

Action onV2000UnhandledProperty = Action::Warn

What to do when a property line in a V2000 MOL file is not recognized. Action::Ignore means simply ignoring that particular line.

bool fullyIgnoreV2000UnhandledKnownProperty = false

Warnings are usually stored as “loading warnings”, even when they are ignored during parsing. Setting this to true will act as if onV2000UnhandledProperty = Action::Ignore and skip the storage, but only for a pre-defined known subset of properties.

Action onV3000UnhandledAtomProperty = Action::Warn

What to do when a property in atom line in a V3000 MOL file is not recognized. Action::Ignore means simply ignoring that particular property.

Action onV2000Charge4 = Action::Error

What to do when an atom in a V2000 MOL file has the charge 4 (doublet radical). Action::Ignore means assuming it was charge 0.

Action onV2000AbstractISO = Action::Error

What to do when an abstract atom in a V2000 MOL file has a non-default ISO or mass difference value.

Action onRAD1 = Action::Error

Action onRAD3 = Action::Error

Action onRAD4 = Action::Error

Action onRAD5 = Action::Error

Action onRAD6 = Action::Error

What to do when an atom has assigned the indicated radical state. Action::Ignore means pretending the atom has no radical state assigned.

Action onUnsupportedQueryBondType = Action::Error

What to do when a bond type 5, 6, or 7 are encountered (constrained query bond types). Action::Ignore means assigning a term variable, as if the type was 8.

Config &getConfig()

Returns:

the singleton Config instance used by the library.

3.2.2.1. Class Config

class Config

Holds all configuration settings.