2.2.12.3. graph/Graph.hpp¶

2.2.12.3.1. Class `graph::Graph`¶

class graph::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. See also graph/GraphInterface.hpp for the documentation for the graph interface for this class.

2.2.12.3.1.1. Synopsis¶

struct MOD_DECL Graph {
    class Vertex;
    class Edge;
    class VertexIterator;
    class VertexRange;
    class EdgeIterator;
    class EdgeRange;
    class IncidentEdgeIterator;
    class IncidentEdgeRange;
public:
    struct Aut;
    struct AutGroup;
    std::string printStereo() const;
    std::string printStereo(const Printer &p) const;
private: // The actual class interface
    Graph(std::unique_ptr<lib::Graph::Single> g);
    Graph(const Graph&) = delete;
    Graph &operator=(const Graph&) = delete;
public:
    ~Graph();
    std::size_t getId() const;
    MOD_DECL friend std::ostream &operator<<(std::ostream &s, const Graph &g);
    lib::Graph::Single &getGraph() const;
public: // graph interface
    std::size_t numVertices() const;
    VertexRange vertices() const;
    std::size_t numEdges() const;
    EdgeRange edges() const;
public:
    AutGroup aut(LabelSettings labelSettings) const;
public:
    std::pair<std::string, std::string> print() const;
    std::pair<std::string, std::string> print(const Printer &first, const Printer &second) const;
    void printTermState() const;
    std::string getGMLString(bool withCoords = false) const;
    std::string printGML(bool withCoords = false) const;
    const std::string &getName() const;
    void setName(std::string name) const;
    const std::string &getSmiles() const;
    const std::string &getSmilesWithIds() const;
    const std::string &getGraphDFS() const;
    const std::string &getGraphDFSWithIds() const;
    const std::string &getLinearEncoding() const;
    bool getIsMolecule() const;
    double getEnergy() const;
    void cacheEnergy(double value) const;
    double getExactMass() const;
    unsigned int vLabelCount(const std::string &label) const;
    unsigned int eLabelCount(const std::string &label) const;
    std::size_t isomorphism(std::shared_ptr<Graph> g, std::size_t maxNumMatches, LabelSettings labelSettings) const;
    std::size_t monomorphism(std::shared_ptr<Graph> g, std::size_t maxNumMatches, LabelSettings labelSettings) const;
    std::shared_ptr<Graph> makePermutation() const;
    void setImage(std::shared_ptr<Function<std::string()> > image);
    std::shared_ptr<Function<std::string()> > getImage() const;
    void setImageCommand(std::string cmd);
    std::string getImageCommand() const;
    Vertex getVertexFromExternalId(int id) const;
    int getMinExternalId() const;
    int getMaxExternalId() const;
    void instantiateStereo() const;
private:
    struct Pimpl;
    std::unique_ptr<Pimpl> p;
public:
    static std::shared_ptr<Graph> graphGMLString(const std::string &data);
    static std::shared_ptr<Graph> graphGML(const std::string &file);
    static std::shared_ptr<Graph> graphDFS(const std::string &graphDFS);
    static std::shared_ptr<Graph> smiles(const std::string &smiles);
    static std::shared_ptr<Graph> smiles(const std::string &smiles, bool allowAbstract, SmilesClassPolicy classPolicy);
    static std::shared_ptr<Graph> makeGraph(std::unique_ptr<lib::Graph::Single> g);
    static std::shared_ptr<Graph> makeGraph(std::unique_ptr<lib::Graph::Single> g, std::map<int, std::size_t> externalToInternalIds);
};

2.2.12.3.1.2. Details¶

std::string printStereo() const¶

std::string printStereo(const Printer &p) const¶

Print the stereo configuration for the vertex.

Returns: the name of the PDF-file that will be compiled in post-processing.

std::size_t getId() const¶

Returns: the unique instance id among Graph objects.

std::size_t numVertices() const¶

Returns: the number of vertices in the graph.

VertexRange vertices() const¶

Returns: a range of all vertices in the graph.

std::size_t numEdges() const¶

Returns: the number of edges in the graph.

EdgeRange edges() const¶

Returns: a range of all edges in the graph.

AutGroup aut(LabelSettings labelSettings) const¶

Returns: an object representing the automorphism group of the graph.

std::pair<std::string, std::string> print() const¶

std::pair<std::string, std::string> print(const Printer &first, const Printer &second) const¶

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.

Returns: a pair of 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.

void printTermState() const¶: Print the term state for the graph.

std::string getGMLString(bool withCoords = false) const¶

Returns: the GML representation of the graph, optionally with generated 2D coordinates.
Throws: LogicError when coordinates are requested, but none can be generated.

std::string printGML(bool withCoords = false) const¶

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

Returns: the filename of the printed GML file.
Throws: LogicError when coordinates are requested, but none can be generated.

const std::string &getName() const¶
void setName(std::string name) const¶: Access the name of the graph.

const std::string &getSmiles() const¶

Returns: the canonical SMILES string of the graph, if it’s a molecule.
Throws: LogicError if the graph is not a molecule.

const std::string &getSmilesWithIds() const¶

Returns: the canonical SMILES string of the graph, that includes the internal vertex id as a class label on each atom, if it’s a molecule.
Throws: LogicError if the graph is not a molecule.

const std::string &getGraphDFS() const¶

Returns: a GraphDFS string of the graph.

const std::string &getGraphDFSWithIds() const¶

Returns: a GraphDFS string of the graph, where each vertices have an explicit id, corresponding to its internal vertex id.

const std::string &getLinearEncoding() const¶

Returns: the SMILES string if the graph is a molecule, otherwise the GraphDFS string.

bool getIsMolecule() const¶

Returns: whether or not the graph models a molecule. See Molecule Encoding.

double getEnergy() const¶

Returns: some energy value if the graph is a molecule. The energy is calculated using Open Babel, unless already calculated or cached by Graph::cacheEnergy().

void cacheEnergy(double value) const¶

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

Throws: LogicError if the graph is not a molecule.

double getExactMass() const¶

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

unsigned int vLabelCount(const std::string &label) const¶

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

unsigned int eLabelCount(const std::string &label) const¶

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

std::size_t isomorphism(std::shared_ptr<Graph> g, std::size_t maxNumMatches, LabelSettings labelSettings) const¶

Returns: the number of isomorphisms found from this graph to g, but at most maxNumMatches.

std::size_t monomorphism(std::shared_ptr<Graph> g, std::size_t maxNumMatches, LabelSettings labelSettings) const¶

Returns: the number of monomorphisms from this graph to g, though at most maxNumMatches.

std::shared_ptr<Graph> makePermutation() const¶

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

void setImage(std::shared_ptr<Function<std::string()>> image)¶: Set 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. Give nullptr to use auto-generated depiction.

std::shared_ptr<Function<std::string()>> getImage() const¶

Returns: the current custom depiction file function.

void setImageCommand(std::string cmd)¶: Set a command to be run in post-processing if a custom depiction is set. The command is only run once.

std::string getImageCommand() const¶

Returns: the current post-processing command.

Vertex getVertexFromExternalId(int id) const¶

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.

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

int getMinExternalId() const¶
int getMaxExternalId() const¶: If the graph was not loaded from an external data format, then these functions always return 0. Otherwise, return the minimum/maximum external id from which non-null vertices can be obtained from getVertexFromExternalId(). If no such minimum and maximum exists, then 0 will be returned.

void instantiateStereo() const¶

Make sure that stereo data is instantiated.

Throws: StereoDeductionError if the data was not instantiated and deduction failed.

static std::shared_ptr<Graph> graphGMLString(const std::string &data)¶

Returns: a graph created from the given GML data.
Throws: InputError on bad input.

static std::shared_ptr<Graph> graphGML(const std::string &file)¶

Returns: a graph loaded from the given GML file.
Throws: InputError on bad input.

static std::shared_ptr<Graph> graphDFS(const std::string &graphDFS)¶

Returns: a graph loaded from the given GraphDFS string.
Throws: InputError on bad input.

static std::shared_ptr<Graph> smiles(const std::string &smiles)¶

static std::shared_ptr<Graph> smiles(const std::string &smiles, bool allowAbstract, SmilesClassPolicy classPolicy)¶

Returns: a graph representing a molecule, loaded from the given SMILES string. The allowAbstract argument defaults to false and classPolicy defaults to SmilesClassPolicy::NoneOnDuplicate.
Throws: InputError on bad input.
Throws: InputError if classPolicy == SmilesClassPolicy::NoneOnDuplicate and a class label is duplicated.

static std::shared_ptr<Graph> makeGraph(std::unique_ptr<lib::Graph::Single> g)¶

static std::shared_ptr<Graph> makeGraph(std::unique_ptr<lib::Graph::Single> g, std::map<int, std::size_t> externalToInternalIds)¶

Returns: a graph wrapping the given internal graph object. If an id mapping is given, it will be used for the getVertexFromExternalId() function.

2.2.12.3. graph/Graph.hpp¶

2.2.12.3.1. Class graph::Graph¶

2.2.12.3.1.1. Synopsis¶

2.2.12.3.1.2. Details¶

2.2.12.3.1. Class `graph::Graph`¶