chemruby 0.9.3

data/lib/chem.rb

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+#
+# Chem module.  See documentation for the file chem.rb for an overview
+#
+# $Id: chem.rb 158 2006-02-09 07:16:48Z tanaka $
+#
+# == Introduction
+#
+# Chem module is a facade of ChemRuby. You will find all the input format
+# that ChemRuby support can be invoked via Chem module.
+#
+# == Examples
+#
+# === Example 1: Parse molecular file
+#
+#   require 'chem'
+#
+#   mol = Chem.open_mol("/usr/local/foo/mol/C00147.mol")
+#
+# === 
+
+
+require 'stringio'
+
+require 'chem/data'
+require 'chem/utils'
+require 'chem/model'
+require 'chem/appl'
+require 'chem/db'
+
+require 'tempfile'
+
+module Chem
+
+  autoload   :MDL,   'chem/db/mdl.rb'
+  autoload   :CDX,   'chem/db/cdx.rb'
+  autoload   :G98,   'chem/db/g98.rb'
+  autoload   :GSpan, 'chem/db/gspan.rb'
+
+  module_function
+
+  # returns first entry
+  def find_first str
+    p str
+  end
+
+  # format_class = Chem.autodetect("file.mol")
+  #
+  # Automatically detect file type and returns
+  # appropriate class to parse it 
+  def self.autodetect file
+    ChemTypeRegistry.find{|format| format.detect_file file}
+  end
+
+  # Makes possible to open chemical files.
+  # Guesses the file type based on the extension of the file name.
+  #
+  # Examples : So if the file name is "benzene.mol",
+  # 
+  # mol = Chem.open_mol("benzene.mol") # returns MDLMolecule object
+  #
+  def open_mol file, format_type = nil
+    format = nil
+    if format_type == nil
+      format = Chem.autodetect(file)
+    else
+      format = ChemTypeRegistry.find{|format| format.detect_type format_type}
+    end
+    raise NotImplementedError unless format
+    return format.parse(file) if format
+  end
+
+  alias :parse_file :open_mol
+  module_function :parse_file
+
+  # 
+  def self.save(array, filename)
+    format = autodetect filename
+    format.save(array, filename)
+  end
+
+  def parse_smiles smiles
+    require 'chem/db/smiles'
+    require 'chem/db/smiles/smiparser'
+    ::SmilesParser.parse_smiles(smiles)
+  end
+
+  def open_kegg dir
+    require 'chem/db/kegg'
+    Chem::KEGG::KeggDirectory.new(dir)
+  end
+
+  module Molecule
+
+    # Saves files for arbitrary format.
+    # file type is automatically detected by file extensions.
+    # 
+    # You can optionally pass parameters as second argument.
+    # = Options
+    # :type::     => :png # Explicit file type
+    #
+    def save(filename, params = {}, &block)
+
+      format_type = params[:type]
+      format = ChemTypeRegistry.find{|format| format.detect_type format_type}
+
+      unless format_type
+        format = ChemTypeRegistry.find{|format| format.detect_file filename}
+      else
+        format = ChemTypeRegistry.find{|format| format.detect_type format_type}
+      end
+
+      unless format
+        raise(NotImplementedError)
+      end
+      format.save(self, filename, params)
+    end
+
+  end
+
+end
+
+# Syntax sugar for Chem.parse_smiles("smiles_string")
+# Returns molecular object.
+# Example
+# SMILES("C1CCCC1")
+def SMILES smiles
+  Chem.parse_smiles(smiles)
+end
+
+  

data/lib/chem/appl.rb

@@ -0,0 +1 @@
+

data/lib/chem/appl/chem3dole.rb

@@ -0,0 +1,36 @@
+#!/usr/bin/ruby
+
+require 'win32ole'
+controle = WIN32OLE.new('Chem3D.Control')
+application = WIN32OLE.new('Chem3D.Application')
+documents = application.documents
+#cd = WIN32OLE.new('ChemDraw.Application')
+#bounds = WIN32OLE.new('Chem3D.Bounds')
+
+#documents.application.visible = true
+
+error = open("error.txt", "w")
+
+Dir.glob('/home/nobuya/src/mol/mol/C*.mol').each do |file|
+  /(C\d+).mol/ =~ file
+  input = 'c:\\cygwin\\home\\nobuya\\src\\mol\\mol\\' + $1 + '.mol'
+  output = 'c:\\cygwin\\home\\nobuya\\mop\\' + $1 + '.mop'
+
+  puts input
+  document = documents.open(input)
+  if document
+    document.saveAs(output)
+    document.close
+  else
+    error.puts(input)
+  end
+end
+
+__END__
+p document = documents.open('c:\cygwin\home\nobuya\src\mol\mol\C00001.mol')
+p documents.Item(0)
+p document.stericEnergy
+document.saveAs('c:\cygwin\home\nobuya\xyz\C00001.xyz')
+
+
+

data/lib/chem/appl/tinker/nucleic.rb

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+#
+# chem/appl/tinker/nucleic.rb - Tinker/nucleic wrapper
+# 
+#
+#  $Id: nucleic.rb 128 2006-02-03 02:53:22Z tanaka $
+#
+
+# = Chem::TINKER
+# Tinker protein wrapper.
+# Example : 
+#   #!/usr/bin/env ruby
+#   require 'chem'
+#
+# === SEE ALSO
+# * http://dasher.wustl.edu/tinker/
+
+
+module Chem
+
+  class TinkerNucleic
+
+    def initialize(cmd_line)
+      @cmd_line = cmd_line + ' -stdout'
+    end
+
+    def exec
+      begin
+	@io = IO.popen(@cmd_line, "w+")
+	@result = @io.read
+	return @result
+      ensure
+	@io.close
+      end
+    end
+    attr_reader :io, :result
+
+  end
+
+end
+

data/lib/chem/appl/tinker/tinker_reader.rb

@@ -0,0 +1,43 @@
+#!/usr/local/bin/ruby
+
+
+if __FILE__ == $0
+  def make_nucleic
+    nucleic = "gtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtaggcctgataagacgcggacagcgtcgcatcaggcatcttgtgcaaatgtcggatgcggcgtga"
+    require 'bio'
+    open("|nucleic", "w") do |out|
+      out.puts "nnn"
+      out.puts "Generated by Ruby"
+      out.puts "amber98.prm"
+      out.puts
+      nucleic.each_byte do |c|
+        out.puts c.chr
+      end
+      out.puts
+      sleep(1)
+      out.puts "Y"
+    end
+  end
+#  make_nucleic
+#  sleep(1)
+  mol = TinkerReader.new(open('nnn.xyz', 'r')).mol
+  require 'pov_writer'
+  pov = PovWriter.new
+  output = open("nucleic.pov", 'w')
+  output.puts pov.atom('O', 0.90, 0.00, 0.00)
+  output.puts pov.atom('H', 0.50, 0.50, 0.90)
+  output.puts pov.atom('N', 0.50, 0.00, 0.50)
+  output.puts pov.atom('C', 0.50, 0.50, 0.50)
+  output.puts pov.atom('S', 0.50, 0.50, 0.10)
+  output.puts pov.atom('P', 0.50, 0.50, 0.10)
+  mol.atoms.each do |index, atom|
+    output.puts "object {atom_#{atom.element} translate <#{atom.x}, #{atom.y}, #{atom.z}>}"
+  end
+  mol.bonds.each do |bond|
+    output.puts pov.bond(bond.b, bond.e)
+  end
+#  output.puts(pov.helix(mol))
+  output.puts pov.light
+  output.puts pov.camera(120, -50, -100, 120, 0, -100)
+  output.close
+end

data/lib/chem/data.rb

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+require 'chem/data/periodic_table'
+require 'chem/data/atomic_weight'
+require 'chem/data/electronegativity'
+require 'chem/data/character'

data/lib/chem/data/atomic_weight.rb

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+# Table of atomic weight
+# extracted from http://www.chem.qmul.ac.uk/iupac/AtWt/index.html
+
+module Chem
+  AtomicWeight = {
+    :H => 1.00794,
+    :He => 4.002602,
+    :Li => 6.941,
+    :Be => 9.012182,
+    :B  => 10.811,
+    :C  => 12.0107,
+    :N  => 14.0067,
+    :O  => 15.9994,
+    :F  => 18.9984032,
+    :Ne => 20.1797,
+    :Na => 22.989770,
+    :Mg => 24.3050,
+    :Al => 26.981538,
+    :Si => 28.0855,
+    :P  => 30.973761,
+    :S  => 32.065,
+    :Cl => 35.453,
+    :Ar => 39.948,
+    :K  => 39.0983,
+    :Ca => 40.078,
+    :Sc => 44.955910,
+    :Ti => 47.867,
+    :V  => 50.9415,
+    :Cr => 51.9961,
+    :Mn => 54.938049,
+    :Fe => 55.845,
+    :Co => 58.933200,
+    :Ni => 58.6934,
+    :Cu => 63.546,
+    :Zn => 65.409,
+    :Ga => 69.723,
+    :Ge => 72.64,
+    :As => 74.92160,
+    :Se => 78.96,
+    :Br => 79.904,
+    :Kr => 83.798,
+    :Rb => 85.4678,
+    :Sr => 87.62,
+    :Y  => 88.90585,
+    :Zr => 91.224,
+    :Nb => 92.90638,
+    :Mo => 95.94,
+    :Tc => 98,
+    :Ru => 101.07,
+    :Rh => 102.90550,
+    :Pd => 106.42,
+    :Ag => 107.8682,
+    :Cd => 112.411,
+    :In => 114.818,
+    :Sn => 118.710,
+    :Sb => 121.760,
+    :Te => 127.60,
+    :I  => 126.90447,
+    :Xe => 131.293,
+    :Cs => 132.90545,
+    :Ba => 137.327,
+    :La => 138.9055,
+    :Ce => 140.116,
+    :Pr => 140.90765,
+    :Nd => 144.24,
+    :Pm => 145,
+    :Sm => 150.36,
+    :Eu => 151.964,
+    :Gd => 157.25,
+    :Tb => 158.92534,
+    :Dy => 162.500,
+    :Ho => 164.93032,
+    :Er => 167.259,
+    :Tm => 168.93421,
+    :Yb => 173.04,
+    :Lu => 174.967,
+    :Hf => 178.49,
+    :Ta => 180.9479,
+    :W  => 183.84,
+    :Re => 186.207,
+    :Os => 190.23,
+    :Ir => 192.217,
+    :Pt => 195.078,
+    :Au => 196.96655,
+    :Hg => 200.59,
+    :Tl => 204.3833,
+    :Pb => 207.2,
+    :Bi => 208.98038,
+    :Po => 209,
+    :At => 210,
+    :Rn => 222,
+    :Fr => 223,
+    :Ra => 226,
+    :Ac => 227,
+    :Th => 232.0381,
+    :Pa => 231.03588,
+    :U  => 238.02891,
+    :Np => 237,
+    :Pu => 244,
+    :Am => 243,
+    :Cm => 247,
+    :Bk => 247,
+    :Cf => 251,
+    :Es => 252,
+    :Fm => 257,
+    :Md => 258,
+    :No => 259,
+    :Lr => 262,
+    :Rf => 261,
+    :Db => 262,
+    :Sg => 266,
+    :Bh => 264,
+    :Hs => 277,
+    :Mt => 268,
+    :Ds => 281,
+    :Rg => 272,
+    :Uub=> 285,
+    :Uut=> 284,
+    :Uuq=> 289,
+    :Uup=> 288,
+    #116   Uuh    Ununhexium                  see Note above 
+    #118   Uuo    Ununoctium                  see Note above 
+  }
+end

data/lib/chem/data/character.rb

@@ -0,0 +1,2 @@
+NaturalBondOrder = {:C => 4, :H => 1, :O => 2, :N => 3, :Mg => 2, :P => 5, :S => 2, :Cl => 1, :Fe => 0,
+  :R => 4, :* => 4}

data/lib/chem/data/electronegativity.rb

@@ -0,0 +1,14 @@
+# Table of Electro negativity
+ElectroNegativity = {:H => 2.20, :He => 0, :Li => 0.98, :Be => 1.57, :B => 2.04, :C => 2.55, :N => 3.04, :O => 3.44, :F => 3.98,
+  :Ne => 0, :Na => 0.93, :Mg => 1.31, :Al => 1.61, :Si => 1.90, :P => 2.19, :S => 2.58, :Cl => 3.16,
+  :Ar => 0, :K => 0.82, :Ca => 1.00, :Sc => 1.36, :Ti => 1.54, :V => 1.63, :Cr => 1.66, :Mn => 1.55,
+  :Fe => 1.83, :Co => 1.88, :Ni => 1.91, :Cu => 1.90, :Zn => 1.65, :Ga => 1.81, :Ge => 2.01, :As => 2.18,
+  :Se => 2.55, :Br => 2.96, :Kr => 3.00, :Rb => 0.82, :Sr => 0.95, :Y => 1.22, :Zr => 1.33, :Nb => 1.6,
+  :Mo => 2.16, :Tc => 1.9, :Ru => 2.2, :Rh => 2.28, :Pd => 2.20, :Ag => 1.93, :Cd => 1.69, :In => 1.78,
+  :Sn => 1.96, :Sb => 2.05, :Te => 2.1, :I => 2.66, :Xe => 2.6, :Cs => 0.79, :Ba => 0.89, :Lu => 1.27,
+  :Hf => 1.3, :Ta => 1.5, :W => 2.36, :Re => 1.9, :Os => 2.2, :Ir => 2.20, :Pt => 2.28, :Au => 2.54,
+  :Hg => 2.00, :Tl => 1.62, :Pb => 2.33, :Bi => 2.02, :Po => 2.0, :At => 2.2, :Rn => 0, :Fr => 0.7,
+  :Ra => 0.9, :Lr => 0, :Rf => 0, :Db => 0, :Sg => 0, :Bh => 0, :Hs => 0, :Mt => 0,
+  :Ds => 0, :Rg => 0, :Uub => 0, :Uut => 0, :Uuq => 0, :Uup => 0, :Uuh => 0, :Uus => 0,
+  :Uuo => 0,
+  :R => 2.55, :* => 2.55}# special atoms are tree as carbon

data/lib/chem/data/periodic_table.rb

@@ -0,0 +1,6 @@
+
+module Chem
+  Element2Number = {:Bk=>97, :Si=>14, :In=>49, :Fr=>87, :V=>23, :Na=>11, :Tb=>65, :Po=>84, :Pd=>46, :Al=>13, :Ho=>67, :Ba=>56, :As=>33, :Rn=>86, :Nb=>41, :Hg=>80, :P=>15, :Bi=>83, :Be=>4, :Ru=>44, :S=>16, :O=>8, :Ra=>88, :Es=>99, :Xe=>54, :He=>2, :N=>7, :Am=>95, :Pr=>59, :Er=>68, :Au=>79, :Rh=>45, :Ce=>58, :Tm=>69, :Gd=>64, :Ir=>77, :Sr=>38, :La=>57, :Cm=>96, :Ca=>20, :C=>6, :Sm=>62, :Hf=>72, :Ag=>47, :At=>85, :F=>9, :Tc=>43, :Zn=>30, :Lu=>71, :B=>5, :Np=>93, :Ga=>31, :XX=>101, :Sn=>50, :Os=>76, :Eu=>63, :Dy=>66, :Yb=>70, :K=>19, :Tl=>81, :I=>53, :Ar=>18, :Th=>90, :Zr=>40, :Pt=>78, :Fe=>26, :Ge=>32, :Cr=>24, :Cf=>98, :Kr=>36, :Rb=>37, :ZZ=>103, :Ta=>73, :W=>74, :Sc=>21, :Mn=>25, :Pu=>94, :Mg=>12, :Se=>34, :Ti=>22, :Cd=>48, :Sb=>51, :Fm=>100, :Cs=>55, :Nd=>60, :Co=>27, :Pb=>82, :Cl=>17, :Cu=>29, :Y=>39, :Re=>75, :U=>92, :Pa=>91, :Mo=>42, :H=>1, :D=>0, :Te=>52, :Li=>3, :Br=>35, :YY=>102, :Pm=>61, :Ac=>89, :Ni=>28, :Ne=>10}
+
+  Number2Element = [:D, :H, :He, :Li, :Be, :B, :C, :N, :O, :F, :Ne, :Na, :Mg, :Al, :Si, :P, :S, :Cl, :Ar, :K, :Ca, :Sc, :Ti, :V, :Cr, :Mn, :Fe, :Co, :Ni, :Cu, :Zn, :Ga, :Ge, :As, :Se, :Br, :Kr, :Rb, :Sr, :Y, :Zr, :Nb, :Mo, :Tc, :Ru, :Rh, :Pd, :Ag, :Cd, :In, :Sn, :Sb, :Te, :I, :Xe, :Cs, :Ba, :La, :Ce, :Pr, :Nd, :Pm, :Sm, :Eu, :Gd, :Tb, :Dy, :Ho, :Er, :Tm, :Yb, :Lu, :Hf, :Ta, :W, :Re, :Os, :Ir, :Pt, :Au, :Hg, :Tl, :Pb, :Bi, :Po, :At, :Rn, :Fr, :Ra, :Ac, :Th, :Pa, :U, :Np, :Pu, :Am, :Cm, :Bk, :Cf, :Es, :Fm, :XX, :YY, :ZZ]
+end

data/lib/chem/data/prime_numbers.rb

@@ -0,0 +1 @@
+PrimeNumber = [2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97, 101, 103, 107, 109, 113, 127, 131, 137, 139, 149, 151, 157, 163, 167, 173, 179, 181, 191, 193, 197, 199, 211, 223, 227, 229, 233, 239, 241, 251, 257, 263, 269, 271, 277, 281, 283, 293, 307, 311, 313, 317, 331, 337, 347, 349, 353, 359, 367, 373, 379, 383, 389, 397, 401, 409, 419, 421, 431, 433, 439, 443, 449, 457, 461, 463, 467, 479, 487, 491, 499, 503, 509, 521, 523, 541, 547, 557, 563, 569, 571, 577, 587, 593, 599, 601, 607, 613, 617, 619, 631, 641, 643, 647, 653, 659, 661, 673, 677, 683, 691, 701, 709, 719, 727, 733, 739, 743, 751, 757, 761, 769, 773, 787, 797, 809, 811, 821, 823, 827, 829, 839, 853, 857, 859, 863, 877, 881, 883, 887, 907, 911, 919, 929, 937, 941, 947, 953, 967, 971, 977, 983, 991, 997, 1009, 1013, 1019, 1021, 1031, 1033, 1039, 1049, 1051, 1061, 1063, 1069, 1087, 1091, 1093, 1097, 1103, 1109, 1117, 1123, 1129, 1151, 1153, 1163, 1171, 1181, 1187, 1193, 1201, 1213, 1217, 1223, 1229, 1231, 1237, 1249, 1259, 1277, 1279, 1283, 1289, 1291, 1297, 1301, 1303, 1307, 1319, 1321, 1327, 1361, 1367, 1373, 1381, 1399, 1409, 1423, 1427, 1429, 1433, 1439, 1447, 1451, 1453, 1459, 1471, 1481, 1483, 1487, 1489, 1493, 1499, 1511, 1523, 1531, 1543, 1549, 1553, 1559, 1567, 1571, 1579, 1583, 1597, 1601, 1607, 1609, 1613, 1619, 1621, 1627, 1637, 1657, 1663, 1667, 1669, 1693, 1697, 1699, 1709, 1721, 1723, 1733, 1741, 1747, 1753, 1759, 1777, 1783, 1787, 1789, 1801, 1811, 1823, 1831, 1847, 1861, 1867, 1871, 1873, 1877, 1879, 1889, 1901, 1907, 1913, 1931, 1933, 1949, 1951, 1973, 1979, 1987, 1993, 1997, 1999, 2003, 2011, 2017, 2027, 2029, 2039, 2053, 2063, 2069, 2081, 2083, 2087, 2089, 2099, 2111, 2113, 2129, 2131, 2137, 2141, 2143, 2153, 2161, 2179, 2203, 2207, 2213, 2221, 2237, 2239, 2243, 2251, 2267, 2269, 2273, 2281, 2287, 2293, 2297, 2309, 2311, 2333, 2339, 2341, 2347, 2351, 2357, 2371, 2377, 2381, 2383, 2389, 2393, 2399, 2411, 2417, 2423, 2437, 2441, 2447, 2459, 2467, 2473, 2477, 2503, 2521, 2531, 2539, 2543, 2549, 2551, 2557, 2579, 2591, 2593, 2609, 2617, 2621, 2633, 2647, 2657, 2659, 2663, 2671, 2677, 2683, 2687, 2689, 2693, 2699, 2707, 2711, 2713, 2719, 2729, 2731, 2741, 2749, 2753, 2767, 2777, 2789, 2791, 2797, 2801, 2803, 2819, 2833, 2837, 2843, 2851, 2857, 2861, 2879, 2887, 2897, 2903, 2909, 2917, 2927, 2939, 2953, 2957, 2963, 2969, 2971, 2999, 3001, 3011, 3019, 3023, 3037, 3041, 3049, 3061, 3067, 3079, 3083, 3089, 3109, 3119, 3121, 3137, 3163, 3167, 3169, 3181, 3187, 3191, 3203, 3209, 3217, 3221, 3229, 3251, 3253, 3257, 3259, 3271, 3299, 3301, 3307, 3313, 3319, 3323, 3329, 3331, 3343, 3347, 3359, 3361, 3371, 3373, 3389, 3391, 3407, 3413, 3433, 3449, 3457, 3461, 3463, 3467, 3469, 3491, 3499, 3511, 3517, 3527, 3529, 3533, 3539, 3541, 3547, 3557, 3559, 3571, 3581, 3583, 3593, 3607, 3613, 3617, 3623, 3631, 3637, 3643, 3659, 3671, 3673, 3677, 3691, 3697, 3701, 3709, 3719, 3727, 3733, 3739, 3761, 3767, 3769, 3779, 3793, 3797, 3803, 3821, 3823, 3833, 3847, 3851, 3853, 3863, 3877, 3881, 3889, 3907, 3911, 3917, 3919, 3923, 3929, 3931, 3943, 3947, 3967, 3989, 4001, 4003, 4007, 4013, 4019, 4021, 4027, 4049, 4051, 4057, 4073, 4079, 4091, 4093, 4099, 4111, 4127, 4129, 4133, 4139, 4153, 4157, 4159, 4177, 4201, 4211, 4217, 4219, 4229, 4231, 4241, 4243, 4253, 4259, 4261, 4271, 4273, 4283, 4289, 4297, 4327, 4337, 4339, 4349, 4357, 4363, 4373, 4391, 4397, 4409, 4421, 4423, 4441, 4447, 4451, 4457, 4463, 4481, 4483, 4493, 4507, 4513, 4517, 4519, 4523, 4547, 4549, 4561, 4567, 4583, 4591, 4597, 4603, 4621, 4637, 4639, 4643, 4649, 4651, 4657, 4663, 4673, 4679, 4691, 4703, 4721, 4723, 4729, 4733, 4751, 4759, 4783, 4787, 4789, 4793, 4799, 4801, 4813, 4817, 4831, 4861, 4871, 4877, 4889, 4903, 4909, 4919, 4931, 4933, 4937, 4943, 4951, 4957, 4967, 4969, 4973, 4987, 4993, 4999, 5003, 5009, 5011, 5021, 5023, 5039, 5051, 5059, 5077, 5081, 5087, 5099, 5101, 5107, 5113, 5119, 5147, 5153, 5167, 5171, 5179, 5189, 5197, 5209, 5227, 5231, 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data/lib/chem/data/vdw_radii.rb

@@ -0,0 +1 @@
+$vdw={"Ag"=>1.72, "Ar"=>1.88, "As"=>1.85, "Au"=>1.66, "Br"=>1.85, "C"=>1.70, "Cd"=>1.58, "Cl"=>1.75, "Cu"=>1.40, "F"=>1.47, "Ga"=>1.87, "H"=>1.20, "He"=>1.40, "Hg"=>1.55, "I"=>1.98, "In"=>1.93, "K"=>2.75, "Kr"=>2.02, "Li"=>1.82, "Mg"=>1.73, "N"=>1.55, "Na"=>2.27, "Ne"=>1.54, "Ni"=>1.63, "O"=>1.52, "P"=>1.80, "Pb"=>2.02, "Pd"=>1.63, "Pt"=>1.72, "S"=>1.80, "Se"=>1.90, "Si"=>2.10, "Sn"=>2.17, "Te"=>2.06, "Tl"=>1.96, "U"=>1.86, "Xe"=>2.16, "Zn"=>1.39}

data/lib/chem/db.rb

@@ -0,0 +1,64 @@
+
+#require 'chem/db/smiles'
+
+module Chem
+
+  ChemTypeRegistry = []
+
+  module Db
+    module_function
+
+
+    # Load type files
+    # User would not call this method
+    def load # :nodoc
+      $LOAD_PATH.each do |path|
+        dir = File.join(path, 'chem/db/types')
+        next unless File.directory?(dir)
+        Dir.entries(dir).each do |entry|
+          if File.extname(entry) == ".rb" and not /^_/.match(entry)
+            begin
+              require(File.join(dir, entry))
+            rescue LoadError => e
+            end
+          end
+        end
+      end
+    end
+
+  end
+
+end
+
+Chem::Db::load
+
+__END__
+# Following script is obsolete
+# auto.rb is maintained manually
+#
+# if $0 == __FILE__
+#   $: << ".."
+#   $: << "../../ext"
+#   require 'chem'
+#   require 'find'
+
+#   open("db/auto.rb", "w") do |out|
+
+#     out.puts "["
+#     puts "List all classes that require autoload"
+#     Find.find("db/") do |file|
+#       Find.prune if /\.svn/.match(file) or /~/.match(file) or /\.ry/.match(file)
+#       next if File.directory?(file)
+#       open(file) do |input|
+#         input.each do |line|
+#           if m = / class +([^ ]+)/.match(line)
+#             out.puts "  [:%-30s , 'chem/%s']," % [m[1].chop, file.strip]
+#           end
+#         end
+#       end
+#     end
+#     out.puts "].each do |mod, file|"
+#     out.puts "  Chem.autoload mod, file"
+#     out.puts "end"
+#   end
+# end