ggl::chem::MoleculeComponent_GML_grammar Class Reference

MoleculeComponent parser. More...

#include <MoleculeComponent_GML_grammar.hh>

Inheritance diagram for ggl::chem::MoleculeComponent_GML_grammar:

Data Structures
struct	definition
	The definition of the GML grammar. More...

Public Member Functions
	MoleculeComponent_GML_grammar (MoleculeComponent &toFill)

Static Public Member Functions
static std::pair < MoleculeComponent, int >	parseGML (const std::string &GML_string) throw (std::invalid_argument)

Protected Types
typedef std::map< int, size_t >	MapIntSizeT
	type for mapping integers to size_t More...

Protected Attributes
MoleculeComponent &	toFill

Detailed Description

  Parses a GML string representation of a
  ggl::MoleculeDecomposition::MoleculeComponent object. This includes its
  properties as well as the additional constraints needed for matching.

  Example :

      ======= GRAPH IN GML =========================

      molcomp [
        description " '-Cl' (attached to a primary carbon with no other clorine atoms attached)"
        priority 4
        energy  -11.7
        node [ id 0 label "C" ]
        node [ id 1 label "Cl" ]
        edge [ source 0 target 1 label "-" ]
        constrainAdj [
        id 0
        op =
        count 1
        nodeLabels [ label "Cl" ]
        ]
        constrainAdj [
           id 0
           op =
           count 2
           nodeLabels [ label "H" ]
        ]
      ]

      ==============================================

Author

Martin Mann (c) 2010 http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 94 of file MoleculeComponent_GML_grammar.hh.

Member Typedef Documentation

typedef std::map<int, size_t> ggl::chem::MoleculeComponent_GML_grammar::MapIntSizeT

protected

Definition at line 109 of file MoleculeComponent_GML_grammar.hh.

Constructor & Destructor Documentation

ggl::chem::MoleculeComponent_GML_grammar::MoleculeComponent_GML_grammar ( MoleculeComponent &  toFill )

explicit

Constructs the definitions of a GML graph grammar to parse a GML graph string representation and to fill the encoded graph into a given boost graph object.

Parameters

toFill

the object to add nodes and edges to

Member Function Documentation

static std::pair< MoleculeComponent, int > ggl::chem::MoleculeComponent_GML_grammar::parseGML ( const std::string &  GML_string ) throw (std::invalid_argument)

static

Parses a GML string and generates a MoleculeComponent::PatternGraph object

Parameters

GML_string

the string to parse

Returns

pair.first = the graph encoding of the molecule pair.second = -1 if parsing was successfull, in error case it returns the string position that caused the parsing error

Exceptions

std::invalid_argument

in case a check fails

Field Documentation

MoleculeComponent& ggl::chem::MoleculeComponent_GML_grammar::toFill

protected

The boost core graph object that is filled to represent the next parsed Rule.

Definition at line 116 of file MoleculeComponent_GML_grammar.hh.

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The documentation for this class was generated from the following file:

• src/ggl/chem/MoleculeComponent_GML_grammar.hh