Class: Rubabel::MoleculeData

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/rubabel/molecule_data.rb

Overview

A hash-like interface for dealing with tag data in molecules inspired by the MoleculeData implementation in pybel. This does not actually hash the data, it just reads it from the OBMol object each time and acts like a hash.

Constant Summary collapse

OB_PAIR_DATA_TYPE = 
OpenBabel::OBPairData.new.get_data_type
OB_COMMENT_DATA_TYPE = 
OpenBabel::OBCommentData.new.get_data_type
DATA_TYPES = 
[OB_PAIR_DATA_TYPE, OB_COMMENT_DATA_TYPE]

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Enumerable

#index_by, #uniq_by

Constructor Details

#initialize(obmol) ⇒ MoleculeData

Returns a new instance of MoleculeData.



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# File 'lib/rubabel/molecule_data.rb', line 18

def initialize(obmol)
  @obmol = obmol
end

Instance Attribute Details

#obmol ⇒ Object

Returns the value of attribute obmol.



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# File 'lib/rubabel/molecule_data.rb', line 16

def obmol
  @obmol
end

Instance Method Details

#[](key) ⇒ Object 



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# File 'lib/rubabel/molecule_data.rb', line 48

def [](key)
  pair_data.find {|pd| pd.get_attribute == key }.get_value
end

#[]=(key, val) ⇒ Object

returns the val



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# File 'lib/rubabel/molecule_data.rb', line 53

def []=(key,val)
  if key?(key)
    OpenBabel.to_pair_data(@obmol.get_data(key)).set_value(val)
    val
  else
    pd = OpenBabel::OBPairData.new
    pd.set_attribute(key)
    pd.set_value(val)
    @obmol.clone_data(pd)
    val
  end
end

#delete(key, &block) ⇒ Object 



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# File 'lib/rubabel/molecule_data.rb', line 78

def delete(key, &block)
  if key?(key)
    val = self[key]
    @obmol.delete_data( @obmol.get_data(key) )
    val
  else
    block ? block.call : nil
  end
end

#each(&block) ⇒ Object 



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# File 'lib/rubabel/molecule_data.rb', line 32

def each(&block)
  block or return enum_for(__method__)
  pair_data.each do |pd|
    block.call [pd.get_attribute, pd.get_value]
  end
end

#key?(key) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rubabel/molecule_data.rb', line 66

def key?(key)
  pair_data.any? {|pd| pd.get_attribute == key }
end

#keys ⇒ Object 



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# File 'lib/rubabel/molecule_data.rb', line 70

def keys
  pair_data.map(&:get_attribute)
end

#pair_data(&block) ⇒ Object 



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# File 'lib/rubabel/molecule_data.rb', line 22

def pair_data(&block)
  block or return enum_for(__method__)
  # TODO: should do this with an ob iterator
  @obmol.get_data.each do |ob_gd|
    if DATA_TYPES.include?( ob_gd.get_data_type )
      block.call( OpenBabel.to_pair_data( ob_gd ) )
    end
  end
end

#size ⇒ Object Also known as: length 



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# File 'lib/rubabel/molecule_data.rb', line 43

def size
  pair_data.to_a.size
end

#to_a ⇒ Object 



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# File 'lib/rubabel/molecule_data.rb', line 39

def to_a
  each.to_a
end

#values ⇒ Object 



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# File 'lib/rubabel/molecule_data.rb', line 74

def values
  pair_data.map(&:get_value)
end