chemruby 0.9.3

data/lib/chem/db/smiles/smiparser.rb

@@ -0,0 +1,375 @@
+#
+# DO NOT MODIFY!!!!
+# This file is automatically generated by racc 1.4.4
+# from racc grammer file "smiles.ry".
+#
+
+require 'racc/parser'
+
+
+class SmilesParser < Racc::Parser
+
+module_eval <<'..end smiles.ry modeval..id6e4480ccfa', 'smiles.ry', 84
+
+def next_token
+  @q.shift
+end
+
+def construct mol, tree, prev = nil
+  tree.each do |node|
+    if node.instance_of?(Array)
+      construct(mol, node, prev)
+    else
+      mol.nodes.push(node)
+      mol.join(prev, node) if prev
+      #      if node.pos != nil
+      if node.smiles_pos
+        node.smiles_pos.each do |smiles_pos|
+          if @ring[smiles_pos]
+            mol.join(node, @ring[smiles_pos])
+            # re-use ring closure digits
+            # Higher-numbered ring closures are not supported yet.
+            @ring[smiles_pos] = nil
+          else
+            @ring[smiles_pos] = node
+          end
+        end
+      end
+      prev = node
+    end
+  end
+end
+
+def initialize
+  super
+  @ring = []
+end
+
+@@parser = SmilesParser.new
+
+def self.parse_smiles( smiles )
+  @@parser.parse( smiles )
+end
+
+ElementRegex = Regexp.new('\A(' + Chem::Number2Element.inject([]){|ret, el| ret.push(el.to_s)}.sort.reverse.join("|") + ')', Regexp::IGNORECASE)
+
+def parse( line )
+  @q = []
+  
+  line.strip!
+  until line.empty? do
+    case line
+    when /\A\[([^\]]+)\]/
+      # [nH] : aromatic N-H
+      @q.push [:ATOM_SYMBOL, $&] # [m[1], m[2], m[3], m[4], m[5], m[6]]]
+    when ElementRegex
+      prop = {}
+      prop[:is_aromatic] = (97 <= $&[0]) #and 122 < $&[0]
+      @q.push [:SYMBOL, [$&.capitalize.intern , prop]]
+    when /\A\d+/
+      @q.push [:NUMBER, $& ]
+    when /\\/
+      @q.push [:BSLASH, :BSLASH]
+    when /\A./
+      @q.push [$&, $&]
+    else
+      raise RuntimeError, 'must not happen'
+    end
+    line = $'
+  end
+  @q.push [ :EOL, nil ]
+#  p @q
+  mol = Chem::SmilesMol.new
+  construct(mol, do_parse)
+  mol
+end
+
+..end smiles.ry modeval..id6e4480ccfa
+
+##### racc 1.4.4 generates ###
+
+racc_reduce_table = [
+ 0, 0, :racc_error,
+ 0, 16, :_reduce_none,
+ 3, 16, :_reduce_2,
+ 1, 17, :_reduce_3,
+ 2, 17, :_reduce_4,
+ 1, 18, :_reduce_none,
+ 2, 18, :_reduce_6,
+ 1, 18, :_reduce_none,
+ 1, 22, :_reduce_8,
+ 1, 22, :_reduce_9,
+ 1, 19, :_reduce_none,
+ 2, 19, :_reduce_11,
+ 1, 20, :_reduce_none,
+ 1, 20, :_reduce_none,
+ 1, 20, :_reduce_none,
+ 1, 20, :_reduce_none,
+ 1, 20, :_reduce_none,
+ 1, 20, :_reduce_none,
+ 1, 20, :_reduce_none,
+ 3, 21, :_reduce_19 ]
+
+racc_reduce_n = 20
+
+racc_shift_n = 26
+
+racc_action_table = [
+     4,     7,     8,     7,     8,    19,     9,    11,    13,    15,
+    17,     2,     5,     6,    22,     7,     8,    20,     9,    11,
+    13,    15,    17,     2,     5,     6,     7,     8,   nil,     9,
+    11,    13,    15,    17,     2,     5,     6,    25,     7,     8,
+   nil,     9,    11,    13,    15,    17,     2,     5,     6 ]
+
+racc_action_check = [
+     1,    16,    16,     1,     1,     3,     1,     1,     1,     1,
+     1,     1,     1,     1,    10,    10,    10,     4,    10,    10,
+    10,    10,    10,    10,    10,    10,    21,    21,   nil,    21,
+    21,    21,    21,    21,    21,    21,    21,    21,     6,     6,
+   nil,     6,     6,     6,     6,     6,     6,     6,     6 ]
+
+racc_action_pointer = [
+   nil,     0,   nil,     0,    17,   nil,    35,   nil,   nil,   nil,
+    12,   nil,   nil,   nil,   nil,   nil,    -2,   nil,   nil,   nil,
+   nil,    23,   nil,   nil,   nil,   nil ]
+
+racc_action_default = [
+    -1,   -20,   -17,   -10,   -20,   -18,   -20,    -8,    -9,   -12,
+   -20,   -13,    -3,   -14,    -5,   -15,   -20,   -16,    -7,   -11,
+    26,   -20,    -2,    -4,    -6,   -19 ]
+
+racc_goto_table = [
+    23,    10,     1,    24,   nil,   nil,    21,   nil,   nil,   nil,
+   nil,    23 ]
+
+racc_goto_check = [
+     3,     2,     1,     4,   nil,   nil,     2,   nil,   nil,   nil,
+   nil,     3 ]
+
+racc_goto_pointer = [
+   nil,     2,     0,   -10,   -13,   nil,   nil,   nil ]
+
+racc_goto_default = [
+   nil,   nil,   nil,    12,    14,    16,    18,     3 ]
+
+racc_token_table = {
+ false => 0,
+ Object.new => 1,
+ :EOL => 2,
+ :SYMBOL => 3,
+ :ATOM_SYMBOL => 4,
+ :NUMBER => 5,
+ "-" => 6,
+ "=" => 7,
+ "#" => 8,
+ ":" => 9,
+ "/" => 10,
+ :BSLASH => 11,
+ "." => 12,
+ "(" => 13,
+ ")" => 14 }
+
+racc_use_result_var = true
+
+racc_nt_base = 15
+
+Racc_arg = [
+ racc_action_table,
+ racc_action_check,
+ racc_action_default,
+ racc_action_pointer,
+ racc_goto_table,
+ racc_goto_check,
+ racc_goto_default,
+ racc_goto_pointer,
+ racc_nt_base,
+ racc_reduce_table,
+ racc_token_table,
+ racc_shift_n,
+ racc_reduce_n,
+ racc_use_result_var ]
+
+Racc_token_to_s_table = [
+'$end',
+'error',
+'EOL',
+'SYMBOL',
+'ATOM_SYMBOL',
+'NUMBER',
+'"-"',
+'"="',
+'"#"',
+'":"',
+'"/"',
+'BSLASH',
+'"."',
+'"("',
+'")"',
+'$start',
+'smiles',
+'smile',
+'node',
+'atom_pos',
+'bond',
+'branch',
+'atom']
+
+Racc_debug_parser = false
+
+##### racc system variables end #####
+
+ # reduce 0 omitted
+
+ # reduce 1 omitted
+
+module_eval <<'.,.,', 'smiles.ry', 9
+  def _reduce_2( val, _values, result )
+                   return val[1]
+   result
+  end
+.,.,
+
+module_eval <<'.,.,', 'smiles.ry', 13
+  def _reduce_3( val, _values, result )
+                   result = val
+   result
+  end
+.,.,
+
+module_eval <<'.,.,', 'smiles.ry', 17
+  def _reduce_4( val, _values, result )
+                   result.push(val[1])
+   result
+  end
+.,.,
+
+ # reduce 5 omitted
+
+module_eval <<'.,.,', 'smiles.ry', 23
+  def _reduce_6( val, _values, result )
+                   val[1].bond = val[0]
+                   result = val[1]
+   result
+  end
+.,.,
+
+ # reduce 7 omitted
+
+module_eval <<'.,.,', 'smiles.ry', 31
+  def _reduce_8( val, _values, result )
+                   node = Chem::SmilesAtom.new
+                   node.element = val[0][0]
+                   node.is_aromatic = val[0][1][:is_aromatic]
+                   result = node
+   result
+  end
+.,.,
+
+module_eval <<'.,.,', 'smiles.ry', 54
+  def _reduce_9( val, _values, result )
+                   m = /(\d*)([A-Za-z][a-z]?)(@*)(H\d*)?(\d*[+-]+)?/.match(val[0])
+#                   m = /(\d*)([A-Za-z][a-z]?)(@*)(H?\d*)(-?\d*)?/.match(val[0])
+                   node = Chem::SmilesAtom.new
+                   node.mass           = m[1].to_i
+                   node.element        = m[2].capitalize.intern
+                   node.is_aromatic    = (97 <= m[2][0]) #and 122 < $&[0]
+                   node.chiral         = m[3]
+
+                   if m[4] and not m[4] == ""
+                     hydrogen = /H(\d)+/.match(m[4])
+                     node.hydrogen_count = hydrogen ? hydrogen[1].to_i : 1
+                   end
+                   if m[5]
+                     charge = /(\d*)([+-]+)/.match(m[5])
+                     sign   = (charge[2][0..0] == "+") ? 1 : -1
+                     n      = charge[1] == "" ? charge[2].length : charge[1].to_i
+                     node.charge = sign * n
+                   end
+
+                   result              = node
+   result
+  end
+.,.,
+
+ # reduce 10 omitted
+
+module_eval <<'.,.,', 'smiles.ry', 60
+  def _reduce_11( val, _values, result )
+                   val[0].smiles_pos = val[1].split("").collect{|c| c.to_i}
+                   result = val[0]
+   result
+  end
+.,.,
+
+ # reduce 12 omitted
+
+ # reduce 13 omitted
+
+ # reduce 14 omitted
+
+ # reduce 15 omitted
+
+ # reduce 16 omitted
+
+ # reduce 17 omitted
+
+ # reduce 18 omitted
+
+module_eval <<'.,.,', 'smiles.ry', 71
+  def _reduce_19( val, _values, result )
+                   result = val[1]
+   result
+  end
+.,.,
+
+ def _reduce_none( val, _values, result )
+  result
+ end
+
+end   # class SmilesParser
+
+
+module Chem
+  
+  class SmilesAtom
+    include Atom
+    attr_accessor :bond, :element, :element, :chiral, :hydrogen_count, :charge, :smiles_pos, :is_aromatic
+    def inspect
+      "{%s %s(%s)}" % [@bond, @element, smiles_pos ? smiles_pos.join : ""]
+    end
+  end
+  
+  class SmilesBond
+    include Bond
+  end
+
+  class SmilesMol
+    
+    include Molecule
+    include Enumerable
+
+    attr_reader :nodes, :edges
+
+    def initialize
+      @nodes = []
+      @edges = []
+    end
+    
+    def join from, to
+      return if to.bond == '.'
+      bond = SmilesBond.new
+
+      case to.bond
+      when '='
+        bond.v = 2
+      when '#'
+        bond.v = 3
+      else
+        bond.v = 1
+      end
+      @edges.push([bond, from, to])
+    end
+
+  end
+
+end

data/lib/chem/db/swf.rb

@@ -0,0 +1,74 @@
+#!/usr/local/bin/ruby
+
+require 'ming/ming'
+require 'molfile_reader'
+require 'transform'
+
+include Ming
+
+module Chem
+
+  # Flash SWF writer
+  # Obsolete
+  class SWFWriter
+
+    def initialize mol
+      @m = SWFMovie.new
+      @m.set_rate(5.0)
+      @m.set_dimension(1000, 1000)
+      @m.set_background(0xff, 0xff, 0xff)
+      #    @m.add(make_atom(mol))
+      0.upto(200) do |n|
+        rotate(Math::PI * 0.01 * n, mol)
+      end
+    end
+
+    def rotate n, mol
+      t = Transform.translate(500.0, 500.0, 0) * Transform.scale(100, 100, 10) *
+        Transform.rotate_z(n) * Transform.rotate_x(n)
+      mol.transform(t)
+      ib = @m.add(make_bond(mol))
+      #    ia = @m.add(make_atom(mol))
+      @m.next_frame
+      @m.remove(ib)
+      #    @m.remove(ia)
+    end
+
+    def make_atom mol
+      a = SWFText.new
+      f = SWFFont.new("EfontSerifB.fdb")
+      a.set_font(f)
+      a.set_color(0x00, 0x80, 0x40)
+      height = 28
+      a.set_height(height * 2)
+      mol.atoms.each do |atom|
+        a.move_to(atom.pos[0] - height, atom.pos[1] + height)
+        a.add_string(atom.element)
+      end
+      a
+    end
+
+    def make_bond mol
+      s = SWFShape.new
+      mol.bonds.each do |bond|
+
+        s.set_line(1, 0x0, 0, 0)
+        s.move_pen_to(bond.b.pos[0], bond.b.pos[1])
+        s.draw_line_to(bond.e.pos[0], bond.e.pos[1])
+      end
+      s
+    end
+
+    def save fn
+      @m.save(fn)
+    end
+
+  end
+
+end
+
+if __FILE__ == $0
+  s = SWFWriter.new(MolfileReader.new(open('mol1.mol', 'r')).parse_mol)
+  s.save('anim.swf')
+  puts 'Created!'
+end

data/lib/chem/db/sybyl.rb

@@ -0,0 +1,150 @@
+
+module Chem
+
+  module Molecule
+
+    # Return sybyl formatted molecule
+    def to_sybyl
+    end
+
+  end
+
+  module Atom
+
+    def to_sybyl
+      "      1 C1         -3.262565   -0.588014   -0.082185 C.3       1 <1>        -0.020001 "
+      "%7d" % [1]
+    end
+
+  end
+
+  module Sybyl
+    SybylAtomTypes = {
+      "LP" => "lone pair",
+      "Du" => "dummy atom",
+      "Du.C" => "dummy carbon",
+      "Hal" => "halogen",
+      "Het" => "heteroatom = N, O, S, P",
+      "Hev" => "heavy atom (non hydrogen)",
+
+      "H" => "hydrogen",
+      "H.spc" => "hydrogen in Single Point Charge (SPC) water model",
+      "H.t3p" => "hydrogen in Transferable intermolecular Potential (TIP3P) water model",
+
+      "C.2" => "carbon sp2",
+      "C.1" => "carbon sp",
+      "C.ar" => "carbon aromatic",
+      "C.cat" => "carbocation (C+) used only in a guadinium group",
+      "C.3" => "carbon sp3",
+
+      "N.3" => "nitrogen sp3",
+      "N.2" => "nitrogen sp2",
+      "Any" => "any atom",
+      "N.1" => "nitrogen sp",
+      "N.ar" => "nitrogen aromatic",
+      "N.am" => "nitrogen amide",
+      "N.pl3" => "nitrogen trigonal planar",
+      "N.4" => "nitrogen sp3 positively charged",
+      "Li" => "lithium",
+      "Na" => "sodium",
+
+      "O.3" => "oxygen sp3",
+      "O.2" => "oxygen sp2",
+      "O.co2" => "oxygen in carboxylate and phosphate groups",
+      "O.spc" => "oxygen in Single Point Charge (SPC) water model",
+      "O.t3p" => "oxygen in Transferable Intermolecular Potential (TIP3P) water model",
+
+      "Mg" => "magnesium",
+      "Al" => "aluminum",
+      "Si" => "silicon",
+      "K" => "potassium",
+      "Ca" => "calcium",
+
+      "S.3" => "sulfur sp3",
+      "S.2" => "sulfur sp2",
+      "S.O" => "sulfoxide sulfur",
+      "S.O2" => "sulfone sulfur",
+
+      "Cr.th" => "chromium (tetrahedral)",
+      "Cr.oh" => "chromium (octahedral)",
+
+      "Mn" => "manganese",
+      "Fe" => "iron",
+      "P.3" => "phosphorous sp3",
+      "Co.oh" => "cobalt (octahedral)",
+      "F" => "fluorine",
+      "Cu" => "copper",
+      "Cl" => "chlorine",
+      "Zn" => "zinc",
+      "Br" => "bromine",
+      "Se" => "selenium",
+      "I" => "iodine",
+      "Mo" => "molybdenum",
+      "Sn" => "tin",
+    }
+
+    class SybylAtom
+
+      include Atom
+
+      def element ; @element ||= @line[53..60].split(".")[0].strip.intern ; end
+      def x       ; @x       ||= @line[16..27].to_f                       ; end
+      def y       ; @y       ||= @line[28..39].to_f                       ; end
+      def z       ; @z       ||= @line[40..51].to_f                       ; end
+      def initialize line ;      @line = line                             ; end
+
+    end
+
+    class SybylBond
+
+      include Bond
+
+      attr_reader :b, :e
+      def initialize line
+        # @line = line
+        @b = line[6..10].to_i
+        @e = line[11..15].to_i
+        @v = line[16..17].to_i
+      end
+
+    end
+
+    class SybylMolecule
+
+      include Molecule
+      include Enumerable
+
+      def n_atoms ;  @n_atoms ||= @count_line[0..4].to_i ;                end
+      def n_bonds ;  @n_bonds ||= @count_line[5..10].to_i ;               end
+      #    def charge?
+      def initialize filename
+        @nodes = []
+        @edges = []
+        File.open(filename) do |input|
+          input.read.split("\n@").each do |line|
+            ary = line.split("\n")
+            case ary[0]
+            when /<TRIPOS>MOLECULE/
+              parse_mol ary
+            when /<TRIPOS>ATOM/
+              ary[1..-1].each{|line| @nodes.push(SybylAtom.new(line))}
+            when /<TRIPOS>BOND/
+              ary[1..-1].each do |line|
+                bond = SybylBond.new(line)
+                @edges.push([bond, @nodes[bond.e - 1], @nodes[bond.b - 1]])
+              end
+            end
+          end
+        end
+      end
+
+      private
+      def parse_mol ary
+        @count_line = ary[2]
+      end
+
+    end
+
+  end
+
+end