Module: Chem::Bond

Included in:
CDK::CDKBond, CMLBond, GSpanBond, MDL::MDLBond, MDL::RxnBond, PDB::PDBBond, SmilesBond, Sybyl::SybylBond, TINKER::TinkerBond
Defined in:
lib/chem/model.rb,
lib/chem/db/mdl.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#color ⇒ Object

set [r, g, b] for visualization



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# File 'lib/chem/model.rb', line 90

def color
  @color
end

#v ⇒ Object

Returns valency of bond use bond_type



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# File 'lib/chem/model.rb', line 60

def v
  @v
end

Instance Method Details

#bond_type ⇒ Object

Returns Bond Type this method may be overridden by concrete class :single:: Single bond :double:: Double bond :triple:: Triple bond :aromatic:: Aromatic Bond :single_or_double:: Single or Double bond :single_or_aromatic:: Single or Aromatic bond :double_or_aromatic:: Double or Aromatic bond :any:: Any bond



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# File 'lib/chem/model.rb', line 81

def bond_type ; :any ; end

#stereo ⇒ Object

Returns Bond Stereo this method may be overridden by concrete class :not_stereo:: Not Stereo :up:: Up :down:: Down :cis_trans:: Cis or Trans :either:: Either



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# File 'lib/chem/model.rb', line 69

def stereo ; :either ; end

#to_mdl(from, to) ⇒ Object 



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# File 'lib/chem/db/mdl.rb', line 56

def to_mdl(from, to)
  "%3d%3d%3d%3d      " % [from, to, v, 0]
end

#topology ⇒ Object

Returns Topology of bond this method may be overridden by concrete class :either:: Either :ring:: Ring :chain:: Chain



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# File 'lib/chem/model.rb', line 88

def topology ; :either ; end