Class: Chem::MDL::MdlMolecule

Inherits:
Object
  • Object
show all
Includes:
MdlMolParser, Chem::Molecule, Enumerable
Defined in:
lib/chem/db/mdl.rb,
lib/chem/db/sdf.rb

Constant Summary

Constants included from Chem::Molecule

Chem::Molecule::DESCRIPTORNAME, Chem::Molecule::ELEMNUM, Chem::Molecule::EpsHeader, Chem::Molecule::MDLCountLineFormat, Chem::Molecule::MDLHeaderLine2Format

Instance Attribute Summary collapse

Attributes included from MdlMolParser

#filename, #mol_name

Attributes included from Chem::Molecule

#cdk2atom, #cdk_mol, #name, #ob_mol, #source

Attributes included from Graph

#adjacencies

Class Method Summary collapse

Instance Method Summary collapse

Methods included from MdlMolParser

#date_time, #dimensional_codes, #entry, #open, #parse, #program_name

Methods included from Chem::Molecule

#-, #adjacent_index, #assign_2d_geometry, #bit_mat, #box_size, #breadth_first_search, #canonical_ring, #cdk_BCUT, #cdk_CPSA, #cdk_RotatableBondsCount, #cdk_calc_descriptor, #cdk_calc_descriptors, #cdk_find_all_rings, #cdk_fingerprint, #cdk_gasteiger_marsili_partial_charges, #cdk_generate_2D, #cdk_generate_randomly, #cdk_generate_vicinity, #cdk_hose_code, #cdk_hueckel, #cdk_mcs, #cdk_properties, #cdk_rule_of_file, #cdk_save_as, #cdk_setup, #cdk_sssr, #cdk_wiener_numbers, #cdk_xlogp, #composition, #connected?, #deep_dup, #delete, #delete_bond, #depth_first_search, #divide, #f_dfs, #find_smallest_ring, #find_sssr, #fingerprint, #generate_pubchem_subskey, #hilight, #induced_sub, #match, #match_by_ullmann, #method_missing, #molecular_weight, #n_hydrogen, #ob_export_as, #ob_save_as, #oxidation_number, #pubchem_subskeys, #remove_hydrogens!, #save, #save_as_mdl, #save_as_pdf, #subset_in_composition?, #to_cansmi, #to_eps, #to_inchi, #to_sybyl, #typ_str, #use_open_babel

Methods included from Graph

#adjacent_to, #clustering_coefficient, #each, #morgan, #terminal_nodes

Constructor Details

#initialize ⇒ MdlMolecule

Returns a new instance of MdlMolecule.



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# File 'lib/chem/db/mdl.rb', line 254

def initialize
  @nodes = []
  @edges = []
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Chem::Molecule

Instance Attribute Details

#edges ⇒ Object (readonly)

Returns the value of attribute edges.



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# File 'lib/chem/db/mdl.rb', line 252

def edges
  @edges
end

#nodes ⇒ Object (readonly)

Returns the value of attribute nodes.



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# File 'lib/chem/db/mdl.rb', line 252

def nodes
  @nodes
end

#sdf_data ⇒ Object

Returns the value of attribute sdf_data.



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# File 'lib/chem/db/sdf.rb', line 8

def sdf_data
  @sdf_data
end

Class Method Details

.parse(file) ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 264

def self.parse(file)
  mol = MdlMolecule.new
  input = open(file)
  mol.parse input
end

.parse_io(input) ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 259

def self.parse_io(input)
  mol = MdlMolecule.new
  mol.parse input
end