3.1.11.2. graph/Graph

3.1.11.2.1. Class Graph

class mod.Graph

This class models an undirected graph with labels on vertices and edges, without loops and without parallel edges. Certain labels are regarded as models of chemical atoms and bonds. See Molecule Encoding for more information on this.

id

(Read-only) A unique instance id among Graph objects.

Type

int

numVertices

(Read-only) The number of vertices in the graph.

Type

int

vertices

(Read-only) An iterable of all vertices in the graph.

Type

GraphVertexRange

numEdges

(Read-only) The number of edges in the graph.

Type

int

edges

(Read-only) An iterable of all edges in the graph.

Type

GraphEdgeRange

aut(labelSettings=LabelSettings(LabelType.String, LabelRelation.Isomorphism))
Parameters

labelSettings (LabelSettings) – the label settings to use.

Returns

an object representing the automorphism group of the graph, with the given label settings.

Return type

GraphAutGroup

print()
print(first, second=None)

Print the graph, using either the default options or the options in first and second. If first and second are the same, only one depiction will be made.

Parameters

  • first (GraphPrinter) – the printing options used for the first depiction.

  • second (GraphPrinter) – the printing options used for the second depiction. If it is None then it is set to first.

Returns

the names for the PDF-files that will be compiled in post-processing. If first and second are the same, the two file prefixes are equal.

Return type

tuple[str, str]

printTermState()

Print the term state for the graph.

getGMLString(withCoords=False)
Returns

the GML representation of the graph, optionally with generated 2D coordinates.

Return type

str

Raises

LogicError when coordinates are requested, but none can be generated.

printGML(withCoords=False)

Print the GML representation of the graph, optionally with generated 2D coordinates.

Returns

the filename of the printed GML file.

Return type

str

Raises

LogicError when coordinates are requested, but none can be generated.

name

The name of the graph. The default name includes the unique instance id.

Type

str

smiles

(Read-only) If the graph models a molecule, this is the canonical SMILES string for it.

Type

str

Raises

LogicError if the graph is not a molecule.

smilesWithIds

(Read-only) If the graph models a molecule, this is the canonical SMILES string for it, that includes the internal vertex id as a class label on each atom.

Type

str

Raises

LogicError if the graph is not a molecule.

graphDFS

(Read-only) This is a GraphDFS of the graph.

Type

str

graphDFSWithIds

(Read-only) This is a GraphDFS of the graph, where each vertices have an explicit id, corresponding to its internal vertex id.

Type

str

linearEncoding

(Read-only) If the graph models a molecule this is the SMILES string string, otherwise it is the GraphDFS string.

Type

str

isMolecule

(Read-only) Whether or not the graph models a molecule. See Molecule Encoding.

Type

bool

energy

(Read-only) If the graph models a molecule, this is some energy value. The energy is calculated using Open Babel, unless already calculated or cached by Graph.cacheEnergy().

Type

float

cacheEnergy(e)

If the graph models a molecule, sets the energy to a given value.

Parameters

e (float) – the value for the energy to be set.

exactMass

(Read-only) The exact mass of the graph, if it is a molecule. It is the sum of the exact mass of each atom, with the mass of electrons subtracted corresponding to the integer charge. That is, the mass is \(\sum_a (mass(a) - mass(e)\cdot charge(a))\). If an atom has no specified isotope, then the most abundant is used.

Type

float

Raises

LogicError if it is not a molecule, including if some isotope has not been tabulated.

vLabelCount(label)
Parameters

label (str) – some label for querying.

Returns

the number of vertices in the graph with the given label.

Return type

int

eLabelCount(label)
Parameters

label (str) – some label for querying.

Returns

the number of edges in the graph with the given label.

Return type

int

isomorphism(other, maxNumMatches=1, labelSettings=LabelSettings(LabelType.String, LabelRelation.Isomorphism))
Parameters

  • other (Graph) – the codomain Graph for finding morphisms.

  • maxNumMatches (int) – the maximum number of isomorphisms to search for.

  • labelSettings (LabelSettings) – the label settings to use during the search.

Returns

the number of isomorphisms from this graph to other, but at most maxNumMatches.

Return type

int

monomorphism(other, maxNumMatches=1, labelSettings=LabelSettings(LabelType.String, LabelRelation.Isomorphism))
Parameters

  • other (Graph) – the codomain Graph for finding morphisms.

  • maxNumMatches (int) – the maximum number of monomorphisms to search for.

  • labelSettings (LabelSettings) – the label settings to use during the search.

Returns

the number of monomorphisms from this graph to other, though at most maxNumMatches.

Return type

int

makePermutation()
Returns

a graph isomorphic to this, but with the vertex indices randomly permuted.

Return type

Graph

image

(Write-only) A custom depiction for the graph. The depiction file used will be the string returned by the given function, with .pdf appended. The function will only be called once.

Type

Callable[[], str]

imageCommad

A command to be run in post-processing if a custom depiction is set. The command is only run once.

Type

str

getVertexFromExternalId(id)

If the graph was not loaded from an external data format, then this function always return a null descriptor. If the graph was loaded from a SMILES string, but any class label was not unique, then the function always return a null descriptor.

Note

In general there is no correlation between external and internal ids.

Parameters

id (int) – the external id to find the vertex descriptor for.

Returns

the vertex descriptor for the given external id. The descriptor is null if the external id was not used.

Return type

GraphVertex

minExternalId
maxExternalId

If the graph was not loaded from an external data format, then these attributes are always return 0. Otherwise, they are the minimum/maximum external id from which non-null vertices can be obtained from getVertexFromExternalId(). If no such minimum and maximum exists, then they are 0.

Type

int

instantiateStereo()

Make sure that stereo data is instantiated.

Raises

StereoDeductionError if the data was not instantiated and deduction failed.

mod.inputGraphs

A list of graphs to which explicitly loaded graphs as default are appended.

Type

list[Graph]

mod.graphGMLString(s, name=None, add=True)

Load a graph in GML format from a given string.

Parameters

  • s (str) – the string with the GML data to load from.

  • name (str) – the name of the graph. If none is given the default name is used.

  • add (bool) – whether to append the graph to inputGraphs or not.

Returns

the loaded graph.

Return type

Graph

Raises

InputError on bad input.

mod.graphGML(f, name=None, add=True)

Load a graph in GML format from a given file.

Parameters

  • f (str) – name of the GML file to be loaded.

  • name (str) – the name of the graph. If none is given the default name is used.

  • add (bool) – whether to append the graph to inputGraphs or not.

Returns

the loaded graph.

Return type

Graph

Raises

InputError on bad input.

mod.graphDFS(s, name=None, add=True)

Load a graph from a GraphDFS string.

Parameters

  • s (str) – the GraphDFS string to parse.

  • name (str) – the name of the graph. If none is given the default name is used.

  • add (bool) – whether to append the graph to inputGraphs or not.

Returns

the loaded graph.

Return type

Graph

Raises

InputError on bad input.

mod.smiles(s, name=None, add=True, allowAbstract=False, classPolicy=SmilesClassPolicy.NoneOnDuplicate)

Load a molecule from a SMILES string.

Parameters

  • s (str) – the SMILES string to parse.

  • name (str) – the name of the graph. If none is given the default name is used.

  • add (bool) – whether to append the graph to inputGraphs or not.

  • allowAbstract (bool) – whether to allow abstract vertex labels in bracketed atoms.

Returns

the loaded molecule.

Return type

Graph

Raises

InputError on bad input.