chemruby 0.9.3
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- data/README +120 -0
- data/Rakefile +195 -0
- data/ext/extconf.rb +4 -0
- data/ext/subcomp.c +416 -0
- data/lib/chem.rb +130 -0
- data/lib/chem/appl.rb +1 -0
- data/lib/chem/appl/chem3dole.rb +36 -0
- data/lib/chem/appl/tinker/nucleic.rb +40 -0
- data/lib/chem/appl/tinker/tinker_reader.rb +43 -0
- data/lib/chem/data.rb +4 -0
- data/lib/chem/data/atomic_weight.rb +124 -0
- data/lib/chem/data/character.rb +2 -0
- data/lib/chem/data/electronegativity.rb +14 -0
- data/lib/chem/data/periodic_table.rb +6 -0
- data/lib/chem/data/prime_numbers.rb +1 -0
- data/lib/chem/data/vdw_radii.rb +1 -0
- data/lib/chem/db.rb +64 -0
- data/lib/chem/db/cansmi.rb +234 -0
- data/lib/chem/db/cdx.rb +1525 -0
- data/lib/chem/db/eps.rb +164 -0
- data/lib/chem/db/g98.rb +909 -0
- data/lib/chem/db/gspan.rb +130 -0
- data/lib/chem/db/iupac.rb +5 -0
- data/lib/chem/db/iupac/a_1.rb +46 -0
- data/lib/chem/db/iupac/iuparser.rb +226 -0
- data/lib/chem/db/iupac/iuparser.ry +97 -0
- data/lib/chem/db/iupac/postfix.rb +2 -0
- data/lib/chem/db/kcf.rb +390 -0
- data/lib/chem/db/kcf_glycan.rb +19 -0
- data/lib/chem/db/kegg.rb +516 -0
- data/lib/chem/db/linucs/linparser.rb +144 -0
- data/lib/chem/db/linucs/linucs.ry +53 -0
- data/lib/chem/db/mdl.rb +379 -0
- data/lib/chem/db/molconnz.rb +12 -0
- data/lib/chem/db/mopac.rb +88 -0
- data/lib/chem/db/msi.rb +107 -0
- data/lib/chem/db/pdb_dic.rb +115 -0
- data/lib/chem/db/pdf.rb +131 -0
- data/lib/chem/db/pubchem.rb +113 -0
- data/lib/chem/db/rmagick.rb +70 -0
- data/lib/chem/db/sdf.rb +37 -0
- data/lib/chem/db/smbl.rb +88 -0
- data/lib/chem/db/smiles.rb +2 -0
- data/lib/chem/db/smiles/smiles.ry +203 -0
- data/lib/chem/db/smiles/smiparser.rb +375 -0
- data/lib/chem/db/swf.rb +74 -0
- data/lib/chem/db/sybyl.rb +150 -0
- data/lib/chem/db/tinker.rb +77 -0
- data/lib/chem/db/types/type_cansmi.rb +9 -0
- data/lib/chem/db/types/type_cdx.rb +24 -0
- data/lib/chem/db/types/type_gspan.rb +31 -0
- data/lib/chem/db/types/type_kcf.rb +28 -0
- data/lib/chem/db/types/type_kcf_glycan.rb +26 -0
- data/lib/chem/db/types/type_kegg.rb +92 -0
- data/lib/chem/db/types/type_mdl.rb +31 -0
- data/lib/chem/db/types/type_pdf.rb +33 -0
- data/lib/chem/db/types/type_png.rb +31 -0
- data/lib/chem/db/types/type_rxn.rb +25 -0
- data/lib/chem/db/types/type_sdf.rb +25 -0
- data/lib/chem/db/types/type_sybyl.rb +30 -0
- data/lib/chem/db/types/type_xyz.rb +26 -0
- data/lib/chem/db/vector.rb +128 -0
- data/lib/chem/db/xyz.rb +39 -0
- data/lib/chem/model.rb +119 -0
- data/lib/chem/model/skeleton.rb +37 -0
- data/lib/chem/utils.rb +11 -0
- data/lib/chem/utils/geometry.rb +27 -0
- data/lib/chem/utils/graph_db.rb +146 -0
- data/lib/chem/utils/math.rb +17 -0
- data/lib/chem/utils/prop.rb +123 -0
- data/lib/chem/utils/sssr.rb +101 -0
- data/lib/chem/utils/sub.rb +78 -0
- data/lib/chem/utils/transform.rb +110 -0
- data/lib/chem/utils/traverse.rb +37 -0
- data/lib/chem/utils/ullmann.rb +134 -0
- data/lib/graph.rb +41 -0
- data/lib/graph/cluster.rb +20 -0
- data/lib/graph/morgan.rb +38 -0
- data/sample/frequent_subgraph.rb +46 -0
- data/sample/images/ex1.rb +11 -0
- data/sample/images/ex2.rb +4 -0
- data/sample/images/ex3.rb +5 -0
- data/sample/images/ex4.rb +17 -0
- data/sample/images/ex5.rb +10 -0
- data/sample/images/mol/adenine.mol +26 -0
- data/sample/images/mol/atp.mol +69 -0
- data/sample/images/temp/ex5.mol +344 -0
- data/sample/kegg_db.rb +116 -0
- data/setup.rb +1551 -0
- data/test/all.rb +6 -0
- data/test/coord_test.rb +17 -0
- data/test/ctab_test.rb +31 -0
- data/test/data/A_21.tar.gz +0 -0
- data/test/data/A_21/aceanthrylene.cdx +0 -0
- data/test/data/A_21/aceanthrylene.mol +40 -0
- data/test/data/A_21/acenaphthylene.cdx +0 -0
- data/test/data/A_21/acenaphthylene.mol +31 -0
- data/test/data/A_21/acephenanthrylene.cdx +0 -0
- data/test/data/A_21/acephenanthrylene.mol +40 -0
- data/test/data/A_21/anthracene.cdx +0 -0
- data/test/data/A_21/anthracene.mol +35 -0
- data/test/data/A_21/as-indacene.cdx +0 -0
- data/test/data/A_21/as-indacene.mol +31 -0
- data/test/data/A_21/azulene.cdx +0 -0
- data/test/data/A_21/azulene.mol +26 -0
- data/test/data/A_21/biphenylene.cdx +0 -0
- data/test/data/A_21/biphenylene.mol +31 -0
- data/test/data/A_21/chrysene.cdx +0 -0
- data/test/data/A_21/chrysene.mol +44 -0
- data/test/data/A_21/coronen.cdx +0 -0
- data/test/data/A_21/coronen.mol +59 -0
- data/test/data/A_21/fluoranthene.cdx +0 -0
- data/test/data/A_21/fluoranthene.mol +40 -0
- data/test/data/A_21/fluorene.cdx +0 -0
- data/test/data/A_21/fluorene.mol +33 -0
- data/test/data/A_21/heptacene.cdx +0 -0
- data/test/data/A_21/heptacene.mol +71 -0
- data/test/data/A_21/heptalene.cdx +0 -0
- data/test/data/A_21/heptalene.mol +30 -0
- data/test/data/A_21/heptaphene.cdx +0 -0
- data/test/data/A_21/heptaphene.mol +71 -0
- data/test/data/A_21/hexacene.cdx +0 -0
- data/test/data/A_21/hexacene.mol +62 -0
- data/test/data/A_21/hexaphene.cdx +0 -0
- data/test/data/A_21/hexaphene.mol +62 -0
- data/test/data/A_21/indene.cdx +0 -0
- data/test/data/A_21/indene.mol +24 -0
- data/test/data/A_21/iupac.txt +41 -0
- data/test/data/A_21/naphthacene.cdx +0 -0
- data/test/data/A_21/naphthacene.mol +44 -0
- data/test/data/A_21/naphthalene.cdx +0 -0
- data/test/data/A_21/naphthalene.mol +26 -0
- data/test/data/A_21/ovalene.cdx +0 -0
- data/test/data/A_21/ovalene.mol +78 -0
- data/test/data/A_21/pentacene.cdx +0 -0
- data/test/data/A_21/pentacene.mol +53 -0
- data/test/data/A_21/pentalene.cdx +0 -0
- data/test/data/A_21/pentalene.mol +22 -0
- data/test/data/A_21/pentaphene.cdx +0 -0
- data/test/data/A_21/pentaphene.mol +53 -0
- data/test/data/A_21/perylene.cdx +0 -0
- data/test/data/A_21/perylene.mol +49 -0
- data/test/data/A_21/phenalene.cdx +0 -0
- data/test/data/A_21/phenalene.mol +33 -0
- data/test/data/A_21/phenanthrene.cdx +0 -0
- data/test/data/A_21/phenanthrene.mol +35 -0
- data/test/data/A_21/picene.cdx +0 -0
- data/test/data/A_21/picene.mol +53 -0
- data/test/data/A_21/pleiadene.cdx +0 -0
- data/test/data/A_21/pleiadene.mol +44 -0
- data/test/data/A_21/pyranthrene.cdx +0 -0
- data/test/data/A_21/pyranthrene.mol +72 -0
- data/test/data/A_21/pyrene.cdx +0 -0
- data/test/data/A_21/pyrene.mol +40 -0
- data/test/data/A_21/rubicene.cdx +0 -0
- data/test/data/A_21/rubicene.mol +63 -0
- data/test/data/A_21/s-indacene.cdx +0 -0
- data/test/data/A_21/s-indacene.mol +31 -0
- data/test/data/A_21/tetraphenylene.cdx +0 -0
- data/test/data/A_21/tetraphenylene.mol +57 -0
- data/test/data/A_21/trinaphthylene.cdx +0 -0
- data/test/data/A_21/trinaphthylene.mol +71 -0
- data/test/data/A_21/triphenylene.cdx +0 -0
- data/test/data/A_21/triphenylene.mol +44 -0
- data/test/data/C00147.kcf +25 -0
- data/test/data/G00147.kcf +13 -0
- data/test/data/atp.mol +69 -0
- data/test/data/cyclohexane.mol +17 -0
- data/test/data/cyclohexane.ps +485 -0
- data/test/data/fullerene.mol +155 -0
- data/test/data/glycan +33 -0
- data/test/data/hypericin.cdx +0 -0
- data/test/data/hypericin.cdxml +596 -0
- data/test/data/hypericin.chm +0 -0
- data/test/data/hypericin.ct +85 -0
- data/test/data/hypericin.f1d +0 -0
- data/test/data/hypericin.f1q +0 -0
- data/test/data/hypericin.gif +0 -0
- data/test/data/hypericin.mol +88 -0
- data/test/data/hypericin.mol2 +159 -0
- data/test/data/hypericin.msm +123 -0
- data/test/data/hypericin.pdf +359 -0
- data/test/data/hypericin.png +0 -0
- data/test/data/hypericin.ps +0 -0
- data/test/data/hypericin.skc +0 -0
- data/test/data/hypericin2.gif +0 -0
- data/test/data/hypericin2.ps +0 -0
- data/test/data/kegg/genomes/hsa/hsa_enzyme.list +4 -0
- data/test/data/kegg/genomes/hsa/hsa_pfam.list +4 -0
- data/test/data/kegg/ligand/mol/C00147.mol +26 -0
- data/test/data/kegg/ligand/reaction +14 -0
- data/test/data/kegg/ligand/reaction.lst +1 -0
- data/test/data/kegg/ligand/reaction_mapformula.lst +3 -0
- data/test/data/reaction +14 -0
- data/test/data/reaction.lst +1 -0
- data/test/data/reaction_mapformula.lst +3 -0
- data/test/data/rxn/C00001.mol +6 -0
- data/test/data/rxn/C00011.mol +10 -0
- data/test/data/rxn/C00014.mol +6 -0
- data/test/data/rxn/C01010.mol +18 -0
- data/test/data/rxn/sample.rxn +50 -0
- data/test/data/rxn/substitution.rxn +45 -0
- data/test/data/test.eps +0 -0
- data/test/data/test.mol +28 -0
- data/test/data/test.sdf +143 -0
- data/test/data/test.skc +0 -0
- data/test/data/test.xyz +4 -0
- data/test/data/test_lf.sdf +143 -0
- data/test/heavy_test_pubchem.rb +16 -0
- data/test/multiple_test.rb +22 -0
- data/test/test_adj.rb +54 -0
- data/test/test_canonical_smiles.rb +46 -0
- data/test/test_cdx.rb +32 -0
- data/test/test_chem.rb +18 -0
- data/test/test_cluster.rb +19 -0
- data/test/test_db.rb +11 -0
- data/test/test_eps.rb +24 -0
- data/test/test_geometry.rb +11 -0
- data/test/test_gspan.rb +28 -0
- data/test/test_iupac.rb +36 -0
- data/test/test_kcf.rb +24 -0
- data/test/test_kcf_glycan.rb +10 -0
- data/test/test_kegg.rb +118 -0
- data/test/test_linucs.rb +21 -0
- data/test/test_mdl.rb +45 -0
- data/test/test_mol2.rb +62 -0
- data/test/test_morgan.rb +21 -0
- data/test/test_pdf.rb +12 -0
- data/test/test_prop.rb +86 -0
- data/test/test_rmagick.rb +15 -0
- data/test/test_sbdb.rb +23 -0
- data/test/test_sdf.rb +30 -0
- data/test/test_smiles.rb +84 -0
- data/test/test_sssr.rb +18 -0
- data/test/test_sub.rb +47 -0
- data/test/test_subcomp.rb +37 -0
- data/test/test_traverse.rb +29 -0
- data/test/test_writer.rb +13 -0
- data/test/test_xyz.rb +15 -0
- data/test/type_test.rb +25 -0
- metadata +290 -0
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#
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# = gspan.rb - IO modules for gSpan format
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#
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# Copyright:: Copyright (C) 2005-2006
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# Tadashi Kadowaki <kadowaki@kuicr.kyoto-u.ac.jp>
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# Nobuya Tanaka <tanaka@kuicr.kyoto-u.ac.jp>
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$: << "/home/tanaka/proj/chemruby/lib/"
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$: << "/home/tanaka/proj/chemruby/ext/"
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require 'chem'
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module Chem
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class GSpan
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FIRST_NODE = /\((\d+)\)/
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REG_NODE = / (\d+) \((\d+)+.(\d+)\)/
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# Parse one-lined gSpan formatted string and return
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# molecule object.
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def self.parse str, name = ""
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mol = GSpanMolecule.new
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mol.name = name
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first_atom = GSpanAtom.new(FIRST_NODE.match(str)[1].to_i)
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mol.nodes.push(first_atom)
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str.scan(REG_NODE) do |s|
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bond = GSpanBond.new( s[0].to_i )
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if s[2] == 'f'
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from_atom = mol.nodes[ s[1].to_i ]
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to_atom = GSpanAtom.new( s[3].to_i )
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mol.nodes.push(to_atom)
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else # s[2] == 'b'
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from_atom = mol.nodes[ mol.nodes.size-1 ]
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to_atom = mol.nodes[ s[3].to_i ]
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end
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mol.edges.push([bond, from_atom, to_atom ])
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end
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mol
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end
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# Save molecule as gSpan formatted file.
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# Example :
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# Chem::GSpan.save(mols , "filename") # mols : an array of molecules
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def self.save mols, filename
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open(filename, "w") do |out|
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mols.each_with_index do |mol, mol_idx|
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out.puts "t # #{mol_idx} -1 #{mol.name}"
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mol.nodes.each_with_index do |node, idx|
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out.puts "v %d %d" % [idx, node.atomic_number]
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end
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mol.edges.each_with_index do |(bond, node1, node2), idx|
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out.puts "e %d %d %d" % [mol.nodes.index(node1), mol.nodes.index(node2), bond.v]
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end
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out.puts
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end
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end
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end
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end
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# Concrete class of gSpan molecule
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class GSpanMolecule
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include Molecule
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include Enumerable
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def initialize
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@nodes = []
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@edges = []
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end
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end
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class GSpanAtom
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include Atom
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def initialize element
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@element = Number2Element[element]
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end
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def self.parse_line line
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self.new(line.split[2].to_i)
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end
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end
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class GSpanBond
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include Bond
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def initialize v
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@v = v
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end
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end
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def self.parse_gspan file
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t = "t"[0]
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v = "v"[0]
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e = "e"[0]
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mols = []
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mol = GSpanMolecule.new
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open(file).each do |line|
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case line[0]
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when t
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mol = GSpanMolecule.new
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mols.push(mol)
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when v
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mol.nodes.push(GSpanAtom.parse_line(line))
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when e
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ary = line.split
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node1 = mol.nodes[ary[1].to_i]
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node2 = mol.nodes[ary[2].to_i]
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mol.edges.push([GSpanBond.new(ary[3].to_i), node1, node2])
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else
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end
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end
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mols
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end
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end
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a_1_1 = [1, "meth",
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2, "eth",
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3, "prop",
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4, "but",
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5, "pent",
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6, "hex",
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7, "hept",
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8, "oct",
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9, "non",
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10, "dec",
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11, "undec",
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12, "dodec",
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13, "tridec",
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14, "tetradec",
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15, "pentadec",
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16, "hexadec",
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17, "heptadec",
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18, "octadec",
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19, "nonadec",
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20, "icos",
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21, "henicos",
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23, "tricos",
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22, "docos",
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24, "tetracos",
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25, "pentacos",
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26, "hexacos",
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27, "heptacos",
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28, "octacos",
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29, "nonacos",
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30, "triacont",
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31, "hentriacont",
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32, "dotriacont",
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33, "tritriacont",
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40, "tetracont",
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50, "pentacont",
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60, "hexacont",
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70, "heptacont",
|
38
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80, "octacont",
|
39
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+
90, "nonacont",
|
40
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+
100, "hect",
|
41
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+
132, "dotriacontahect"]
|
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+
|
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a = Hash[*a_1_1]
|
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+
|
45
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+
$reg_a_1_1 = /undec|tritriacont|tridec|tricos|triacont|tetradec|tetracos|tetracont|prop|pentadec|pentacos|pentacont|pent|octadec|octacos|octacont|oct|nonadec|nonacos|nonacont|non|meth|icos|hexadec|hexacos|hexacont|hex|heptadec|heptacos|heptacont|hept|hentriacont|henicos|hect|eth|dotriacontahect|dotriacont|dodec|docos|dec|but/
|
46
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+
|
@@ -0,0 +1,226 @@
|
|
1
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+
#
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2
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+
# DO NOT MODIFY!!!!
|
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# This file is automatically generated by racc 1.4.4
|
4
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# from racc grammer file "iuparser.ry".
|
5
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#
|
6
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+
|
7
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require 'racc/parser'
|
8
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+
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9
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+
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10
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class IupacParser < Racc::Parser
|
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+
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12
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module_eval <<'..end iuparser.ry modeval..id57c30dc50e', 'iuparser.ry', 16
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+
|
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def next_token
|
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@q.shift
|
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end
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+
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def parse( line )
|
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line.downcase!
|
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@q = []
|
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+
|
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+
until line.empty? do
|
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case line
|
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when /\A(hex|prop|meth|non|but|dec)/
|
25
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+
@q.push([:SKELETON, $&])
|
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+
when /\A(ane)/
|
27
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@q.push([:POSTFIX, $&])
|
28
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when /\Ayl/
|
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+
@q.push([:YL, 'yl'])
|
30
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+
when /\A(di|tri)/
|
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+
@q.push([:GREEK_NUM, $&])
|
32
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+
when /\A\d+/
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+
@q.push([:NUMBER, $&.to_i])
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+
when /\A-/
|
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@q.push([:HYPHEN, '-'])
|
36
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+
when /\A,/
|
37
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+
@q.push([:COMMA, ','])
|
38
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+
when /\A[()]/
|
39
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+
@q.push([:ROUND_B, $&])
|
40
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+
end
|
41
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+
line = $'
|
42
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+
end
|
43
|
+
@q.push([:EOL, nil])
|
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+
do_parse
|
45
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+
end
|
46
|
+
|
47
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+
# class IupacParser
|
48
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+
# rule
|
49
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+
# iupac : name EOF
|
50
|
+
# {
|
51
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+
# puts 'The END'
|
52
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+
# }
|
53
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# name : SKELETON POSTFIX
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# {
|
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# p val
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# result = val
|
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# }
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# end
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+
|
60
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# ---- inner
|
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# def next_token
|
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# @q.shift
|
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+
# end
|
65
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+
|
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# def parse( line )
|
67
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+
# @q = []
|
68
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+
|
69
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+
# # line.strip
|
70
|
+
# until line.empty? do
|
71
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+
# case line
|
72
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+
# when /hex/# $reg_a_1_1
|
73
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+
# @q.push [:SKELETON, $&]
|
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+
# when /ane/# $reg_postfix
|
75
|
+
# @q.push [:POSTFIX, $&]
|
76
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+
# when /\A\d+/
|
77
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+
# @q.push [:NUMBER, $&.to_i ]
|
78
|
+
# when /\A./
|
79
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+
# @q.push [$&, $&]
|
80
|
+
# else
|
81
|
+
# raise RuntimeError, 'must not happen'
|
82
|
+
# end
|
83
|
+
# line = $'
|
84
|
+
# end
|
85
|
+
# @q.push [ :EOL, nil ]
|
86
|
+
# p @q
|
87
|
+
# do_parse
|
88
|
+
# end
|
89
|
+
|
90
|
+
..end iuparser.ry modeval..id57c30dc50e
|
91
|
+
|
92
|
+
##### racc 1.4.4 generates ###
|
93
|
+
|
94
|
+
racc_reduce_table = [
|
95
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+
0, 0, :racc_error,
|
96
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+
4, 11, :_reduce_none,
|
97
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+
0, 12, :_reduce_none,
|
98
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+
3, 12, :_reduce_none,
|
99
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+
2, 12, :_reduce_none,
|
100
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+
3, 13, :_reduce_none,
|
101
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+
1, 13, :_reduce_none,
|
102
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+
2, 15, :_reduce_none,
|
103
|
+
3, 15, :_reduce_none,
|
104
|
+
1, 14, :_reduce_none,
|
105
|
+
3, 14, :_reduce_none ]
|
106
|
+
|
107
|
+
racc_reduce_n = 11
|
108
|
+
|
109
|
+
racc_shift_n = 23
|
110
|
+
|
111
|
+
racc_action_table = [
|
112
|
+
5, 18, 16, 8, 16, 9, 10, 9, 10, 9,
|
113
|
+
14, 11, 12, 19, 15, 13, 3, 21, 13, 22 ]
|
114
|
+
|
115
|
+
racc_action_check = [
|
116
|
+
2, 9, 8, 2, 14, 2, 2, 8, 8, 14,
|
117
|
+
6, 3, 5, 12, 6, 5, 1, 15, 16, 18 ]
|
118
|
+
|
119
|
+
racc_action_pointer = [
|
120
|
+
nil, 16, -2, 11, nil, 9, 5, nil, 0, -1,
|
121
|
+
nil, nil, 9, nil, 2, 9, 12, nil, 13, nil,
|
122
|
+
nil, nil, nil ]
|
123
|
+
|
124
|
+
racc_action_default = [
|
125
|
+
-2, -11, -11, -11, -4, -11, -11, -6, -11, -11,
|
126
|
+
-9, 23, -11, -7, -11, -11, -11, -3, -11, -1,
|
127
|
+
-5, -10, -8 ]
|
128
|
+
|
129
|
+
racc_goto_table = [
|
130
|
+
4, 1, 2, 20, nil, nil, 17 ]
|
131
|
+
|
132
|
+
racc_goto_check = [
|
133
|
+
3, 1, 2, 5, nil, nil, 3 ]
|
134
|
+
|
135
|
+
racc_goto_pointer = [
|
136
|
+
nil, 1, 2, -2, nil, -11 ]
|
137
|
+
|
138
|
+
racc_goto_default = [
|
139
|
+
nil, nil, nil, nil, 6, 7 ]
|
140
|
+
|
141
|
+
racc_token_table = {
|
142
|
+
false => 0,
|
143
|
+
Object.new => 1,
|
144
|
+
:SKELETON => 2,
|
145
|
+
:POSTFIX => 3,
|
146
|
+
:EOL => 4,
|
147
|
+
:HYPHEN => 5,
|
148
|
+
:YL => 6,
|
149
|
+
:GREEK_NUM => 7,
|
150
|
+
:NUMBER => 8,
|
151
|
+
:COMMA => 9 }
|
152
|
+
|
153
|
+
racc_use_result_var = true
|
154
|
+
|
155
|
+
racc_nt_base = 10
|
156
|
+
|
157
|
+
Racc_arg = [
|
158
|
+
racc_action_table,
|
159
|
+
racc_action_check,
|
160
|
+
racc_action_default,
|
161
|
+
racc_action_pointer,
|
162
|
+
racc_goto_table,
|
163
|
+
racc_goto_check,
|
164
|
+
racc_goto_default,
|
165
|
+
racc_goto_pointer,
|
166
|
+
racc_nt_base,
|
167
|
+
racc_reduce_table,
|
168
|
+
racc_token_table,
|
169
|
+
racc_shift_n,
|
170
|
+
racc_reduce_n,
|
171
|
+
racc_use_result_var ]
|
172
|
+
|
173
|
+
Racc_token_to_s_table = [
|
174
|
+
'$end',
|
175
|
+
'error',
|
176
|
+
'SKELETON',
|
177
|
+
'POSTFIX',
|
178
|
+
'EOL',
|
179
|
+
'HYPHEN',
|
180
|
+
'YL',
|
181
|
+
'GREEK_NUM',
|
182
|
+
'NUMBER',
|
183
|
+
'COMMA',
|
184
|
+
'$start',
|
185
|
+
'name',
|
186
|
+
'prefix',
|
187
|
+
'num_subs',
|
188
|
+
'nums',
|
189
|
+
'substituent']
|
190
|
+
|
191
|
+
Racc_debug_parser = false
|
192
|
+
|
193
|
+
##### racc system variables end #####
|
194
|
+
|
195
|
+
# reduce 0 omitted
|
196
|
+
|
197
|
+
# reduce 1 omitted
|
198
|
+
|
199
|
+
# reduce 2 omitted
|
200
|
+
|
201
|
+
# reduce 3 omitted
|
202
|
+
|
203
|
+
# reduce 4 omitted
|
204
|
+
|
205
|
+
# reduce 5 omitted
|
206
|
+
|
207
|
+
# reduce 6 omitted
|
208
|
+
|
209
|
+
# reduce 7 omitted
|
210
|
+
|
211
|
+
# reduce 8 omitted
|
212
|
+
|
213
|
+
# reduce 9 omitted
|
214
|
+
|
215
|
+
# reduce 10 omitted
|
216
|
+
|
217
|
+
def _reduce_none( val, _values, result )
|
218
|
+
result
|
219
|
+
end
|
220
|
+
|
221
|
+
end # class IupacParser
|
222
|
+
|
223
|
+
|
224
|
+
# parser = IupacParser.new
|
225
|
+
|
226
|
+
# parser.parse("hexane")
|
@@ -0,0 +1,97 @@
|
|
1
|
+
class IupacParser
|
2
|
+
rule
|
3
|
+
name : prefix SKELETON POSTFIX EOL
|
4
|
+
prefix :
|
5
|
+
| prefix HYPHEN num_subs
|
6
|
+
| prefix num_subs
|
7
|
+
num_subs : nums HYPHEN substituent
|
8
|
+
| substituent
|
9
|
+
substituent : SKELETON YL
|
10
|
+
| GREEK_NUM SKELETON YL
|
11
|
+
nums : NUMBER
|
12
|
+
| nums COMMA NUMBER
|
13
|
+
end
|
14
|
+
|
15
|
+
---- inner
|
16
|
+
|
17
|
+
def next_token
|
18
|
+
@q.shift
|
19
|
+
end
|
20
|
+
|
21
|
+
def parse( line )
|
22
|
+
line.downcase!
|
23
|
+
@q = []
|
24
|
+
|
25
|
+
until line.empty? do
|
26
|
+
case line
|
27
|
+
when /\A(hex|prop|meth|non|but|dec)/
|
28
|
+
@q.push([:SKELETON, $&])
|
29
|
+
when /\A(ane)/
|
30
|
+
@q.push([:POSTFIX, $&])
|
31
|
+
when /\Ayl/
|
32
|
+
@q.push([:YL, 'yl'])
|
33
|
+
when /\A(di|tri)/
|
34
|
+
@q.push([:GREEK_NUM, $&])
|
35
|
+
when /\A\d+/
|
36
|
+
@q.push([:NUMBER, $&.to_i])
|
37
|
+
when /\A-/
|
38
|
+
@q.push([:HYPHEN, '-'])
|
39
|
+
when /\A,/
|
40
|
+
@q.push([:COMMA, ','])
|
41
|
+
when /\A[()]/
|
42
|
+
@q.push([:ROUND_B, $&])
|
43
|
+
end
|
44
|
+
line = $'
|
45
|
+
end
|
46
|
+
@q.push([:EOL, nil])
|
47
|
+
do_parse
|
48
|
+
end
|
49
|
+
|
50
|
+
# class IupacParser
|
51
|
+
# rule
|
52
|
+
# iupac : name EOF
|
53
|
+
# {
|
54
|
+
# puts 'The END'
|
55
|
+
# }
|
56
|
+
# name : SKELETON POSTFIX
|
57
|
+
# {
|
58
|
+
# p val
|
59
|
+
# result = val
|
60
|
+
# }
|
61
|
+
# end
|
62
|
+
|
63
|
+
# ---- inner
|
64
|
+
|
65
|
+
# def next_token
|
66
|
+
# @q.shift
|
67
|
+
# end
|
68
|
+
|
69
|
+
# def parse( line )
|
70
|
+
# @q = []
|
71
|
+
|
72
|
+
# # line.strip
|
73
|
+
# until line.empty? do
|
74
|
+
# case line
|
75
|
+
# when /hex/# $reg_a_1_1
|
76
|
+
# @q.push [:SKELETON, $&]
|
77
|
+
# when /ane/# $reg_postfix
|
78
|
+
# @q.push [:POSTFIX, $&]
|
79
|
+
# when /\A\d+/
|
80
|
+
# @q.push [:NUMBER, $&.to_i ]
|
81
|
+
# when /\A./
|
82
|
+
# @q.push [$&, $&]
|
83
|
+
# else
|
84
|
+
# raise RuntimeError, 'must not happen'
|
85
|
+
# end
|
86
|
+
# line = $'
|
87
|
+
# end
|
88
|
+
# @q.push [ :EOL, nil ]
|
89
|
+
# p @q
|
90
|
+
# do_parse
|
91
|
+
# end
|
92
|
+
|
93
|
+
---- footer
|
94
|
+
|
95
|
+
# parser = IupacParser.new
|
96
|
+
|
97
|
+
# parser.parse("hexane")
|