chemruby 0.9.3

data/lib/chem/db/linucs/linparser.rb

@@ -0,0 +1,144 @@
+#
+# DO NOT MODIFY!!!!
+# This file is automatically generated by racc 1.4.4
+# from racc grammer file "linucs.ry".
+#
+
+require 'racc/parser'
+
+
+class LinucsParser < Racc::Parser
+
+module_eval <<'..end linucs.ry modeval..idcf977ebdbe', 'linucs.ry', 11
+
+def next_token
+  @q.shift
+end
+
+def parse( line )
+  @q = []
+  
+  line.strip!
+  until line.empty? do
+    case line
+    when /\A\[/
+      @q.push [:Ll, :Ll]
+    when /A\]/
+      @q.push [:Lr, :Lr]
+    when /\A\[([^\]]+)\]/
+      @q.push [:ATOM_SYMBOL, $&] # [m[1], m[2], m[3], m[4], m[5], m[6]]]
+    when /\A(Cl|C|F|H|N|O|Au|U)/
+      @q.push [:SYMBOL, $&.intern ]
+    when /\A[a-zA-Z_]/
+      @q.push [:SYMBOL, $&.intern ]
+    when /\A\d+/
+      @q.push [:NUMBER, $&.to_i ]
+    when /\\/
+      @q.push [:BSLASH, :BSLASH]
+    when /\A./
+      @q.push [$&, $&]
+    else
+      raise RuntimeError, 'must not happen'
+    end
+    line = $'
+  end
+  @q.push [ :EOL, nil ]
+  mol = Chem::SmilesMol.new
+  construct(mol, do_parse)
+  mol
+end
+
+
+..end linucs.ry modeval..idcf977ebdbe
+
+##### racc 1.4.4 generates ###
+
+racc_reduce_table = [
+ 0, 0, :racc_error,
+ 0, 5, :_reduce_none,
+ 3, 5, :_reduce_none,
+ 1, 6, :_reduce_none,
+ 2, 6, :_reduce_none ]
+
+racc_reduce_n = 5
+
+racc_shift_n = 8
+
+racc_action_table = [
+     2,     6,     7,     3,     5 ]
+
+racc_action_check = [
+     1,     4,     4,     1,     2 ]
+
+racc_action_pointer = [
+   nil,     0,     4,   nil,    -1,   nil,   nil,   nil ]
+
+racc_action_default = [
+    -1,    -5,    -5,    -3,    -5,     8,    -2,    -4 ]
+
+racc_goto_table = [
+     1,     4 ]
+
+racc_goto_check = [
+     1,     2 ]
+
+racc_goto_pointer = [
+   nil,     0,     0 ]
+
+racc_goto_default = [
+   nil,   nil,   nil ]
+
+racc_token_table = {
+ false => 0,
+ Object.new => 1,
+ :EOL => 2,
+ :node => 3 }
+
+racc_use_result_var = true
+
+racc_nt_base = 4
+
+Racc_arg = [
+ racc_action_table,
+ racc_action_check,
+ racc_action_default,
+ racc_action_pointer,
+ racc_goto_table,
+ racc_goto_check,
+ racc_goto_default,
+ racc_goto_pointer,
+ racc_nt_base,
+ racc_reduce_table,
+ racc_token_table,
+ racc_shift_n,
+ racc_reduce_n,
+ racc_use_result_var ]
+
+Racc_token_to_s_table = [
+'$end',
+'error',
+'EOL',
+'node',
+'$start',
+'linucs',
+'linuc']
+
+Racc_debug_parser = false
+
+##### racc system variables end #####
+
+ # reduce 0 omitted
+
+ # reduce 1 omitted
+
+ # reduce 2 omitted
+
+ # reduce 3 omitted
+
+ # reduce 4 omitted
+
+ def _reduce_none( val, _values, result )
+  result
+ end
+
+end   # class LinucsParser

data/lib/chem/db/linucs/linucs.ry

@@ -0,0 +1,53 @@
+
+class LinucsParser
+rule
+      linucs :
+             | linucs linuc EOL
+       linuc : node
+             | linuc node
+end
+
+---- inner
+
+def next_token
+  @q.shift
+end
+
+def parse( line )
+  @q = []
+  
+  line.strip!
+  until line.empty? do
+    case line
+    when /\A\[/
+      @q.push [:Ll, :Ll]
+    when /A\]/
+      @q.push [:Lr, :Lr]
+    when /\A\[([^\]]+)\]/
+      @q.push [:ATOM_SYMBOL, $&] # [m[1], m[2], m[3], m[4], m[5], m[6]]]
+    when /\A(Cl|C|F|H|N|O|Au|U)/
+      @q.push [:SYMBOL, $&.intern ]
+    when /\A[a-zA-Z_]/
+      @q.push [:SYMBOL, $&.intern ]
+    when /\A\d+/
+      @q.push [:NUMBER, $&.to_i ]
+    when /\\/
+      @q.push [:BSLASH, :BSLASH]
+    when /\A./
+      @q.push [$&, $&]
+    else
+      raise RuntimeError, 'must not happen'
+    end
+    line = $'
+  end
+  @q.push [ :EOL, nil ]
+  mol = Chem::SmilesMol.new
+  construct(mol, do_parse)
+  mol
+end
+
+
+---- footer
+
+
+

data/lib/chem/db/mdl.rb

@@ -0,0 +1,379 @@
+#
+# chem/db/mdl.rb - MDL molfile format class
+#
+
+
+module Chem
+
+  module Molecule
+
+    MDLCountLineFormat = "%3d%3d%3d%3d%3d%3d%3d%3d%3d  0999 V2000"
+
+    def save_as_mdl filename
+      File.open(filename, "w") do |out|
+        out.puts filename
+        out.puts # ChemRuby
+        out.puts
+        out.puts MDLCountLineFormat % [nodes.length, edges.length, 0, 0, 0, 0, 0, 0, 0]
+        nodes.each do |node|
+          out.puts node.to_mdl
+        end
+        edges.each do |edge, atom1, atom2|
+          out.puts edge.to_mdl(nodes.index(atom1) + 1, nodes.index(atom2) + 1)
+        end
+      end
+    end
+
+  end
+
+  module Atom
+
+    MDLAtomLineFormat = "%10.4f%10.4f%10.4f %2s%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d"
+
+    def to_mdl mapping = 0
+      MDLAtomLineFormat % [x, y, z, element, 0, 0, 0, 0, 0, 0, 0, 0, 0, mapping, 0, 0]
+    end
+
+  end
+
+  module Bond
+
+    def to_mdl from, to
+      "%3d%3d%3d%3d      " % [from, to, v, 0]
+    end
+
+  end
+
+  module Reaction
+
+    def to_mdl_rxn
+      return # fix me
+#      out = STDOUT
+      out.puts "$RXN"
+      out.puts
+      out.puts "ISIS     112620051015"
+      out.puts
+      out.puts "%3d%3d" % [@reactants.length, @products.length]
+      @reactants.each{ |mol| output_mdl_mol(mol, out)}
+      @products.each{ |mol| output_mdl_mol(mol, out)}
+    end
+
+    private
+    def output_mdl_mol mol, out
+      out.puts "$MOL"
+      mol.nodes.each do |node|
+        out.puts node.to_mdl(10)
+      end
+      out.puts "M  END"
+    end
+
+  end
+
+  module MDL
+
+    class MDLAtom
+
+      require 'chem/utils/transform'
+      include Atom
+      include Chem::Transform::ThreeDimension
+
+      Stereo = {
+        0 => :not_stereo,
+        1 => :odd,
+        2 => :even,
+        3 => :either
+      }
+
+      attr_accessor :number
+
+      def initialize line  ; @line              = line                       ; end
+
+      # Returns atomic symbol
+      def element          ; @element         ||= @line[30..32].strip.intern ; end
+      def x                ; @x               ||= @line[0..9].to_f           ; end
+      def y                ; @y               ||= @line[10..19].to_f         ; end
+      # Coordinates for z-axis
+      def z                ; @z               ||= @line[20..29].to_f         ; end
+      # Difference from mass in periodic table.
+      def mass_difference  ; @mass_difference ||= @line[33..35]              ; end
+      def charge           ; @charge          ||= @line[36..38].to_i         ; end
+      def stereo_parity    ; @stereo_parity   ||= @line[39..41].to_i         ; end
+      def hydrogen_count   ; @hydrogen_count  ||= @line[42..44].to_i         ; end
+      def stereo_care_box  ; @stereo_care_box ||= @line[45..47].to_i         ; end
+
+      def valence          ; @valence         ||= @line[48..50].to_i         ; end
+      def h0_designator    ; @h0_designator   ||= @line[51..53].to_i         ; end
+      # 54..56 Not used
+      # 57..59 Not used
+      def mapping          ; @mapping         ||= @line[60..62].to_i         ; end
+      def inversion        ; @inversion       ||= @line[63..65].to_i         ; end
+      def exact_charge     ; @exact_charge    ||= @line[66..68].to_i         ; end
+
+    end
+
+    class MDLBond
+
+      include Bond
+
+      Stereo = {
+        0 => :not_stereo,
+        1 => :up,
+        3 => :cis_trans,
+        4 => :either,
+        6 => :down
+      }
+
+      BondType = {
+        1 => :single,
+        2 => :double,
+        3 => :triple,
+        4 => :aromatic,
+        5 => :single_or_double,
+        6 => :single_or_aromatic,
+        7 => :double_or_aromatic,
+        8 => :any
+      }
+
+      ReactingCenter = {
+        0  => :unmarked,
+        1  => :center,
+        -1 => :not,
+        2  => :no_change,
+        4  => :made_or_broken,
+        8  => :order_changes
+      }
+
+      Topology = {
+        0 => :either,
+        1 => :ring,
+        2 => :chain
+      }
+
+      def initialize line  ; @line              = line                                       ; end
+
+      def v                ; @v               ||= @line[6..8].to_i                           ; end
+
+      def topology         ; @topology        ||= Topology[@line[13..15].to_i]               ; end
+      def reacting_center  ; @reacting_center ||= ReactingCenter[@line[16..18].to_i]         ; end
+      def stereo           ; @stereo          ||= Stereo[@line[9..11].to_i]                  ; end
+      def bond_type        ; @v               ||= BondType[self.v]                           ; end
+
+    end
+
+    module MdlMolParser
+
+      attr_reader :filename
+      def open(filename)
+        @filename = filename
+        input = File.open(filename)
+        parse(input)
+      end
+
+      def entry
+        @title
+      end
+      alias name entry
+
+      def parse input
+        input.readline
+        @title = input.readline
+        raise MDLException if input.readline == nil
+        line = input.readline
+        n_atom = line[0..2].to_i
+        n_bond = line[3..5].to_i
+
+        if 0 > n_atom or 999 < n_atom or 0 > n_bond or 999 < n_bond
+          raise "counts line format error"
+        end
+
+        n_atom.times do |n|
+          mol = MDLAtom.new(input.readline)
+          mol.number = n + 1
+          @nodes.push(mol)
+        end
+
+        n_bond.times do |n|
+          line = input.readline
+          b = MDLBond.new line
+          b_n = line[0..2].to_i
+          e_n = line[3..5].to_i
+          if (b_n > n_atom || b_n < 1 || e_n > n_atom || e_n < 1)
+            p line
+            raise "MDL bond line format error"
+          end
+
+          @edges.push([b, @nodes[b_n - 1], @nodes[e_n - 1]])
+        end
+        input.each do |line|
+          break if /M  END/.match(line)
+        end
+        self
+      end
+    end
+
+    class MdlMolecule
+      
+      include Molecule
+      include Enumerable
+      include MdlMolParser
+
+      attr_reader :nodes, :edges
+
+      def initialize
+        @nodes = []
+        @edges = []
+      end
+
+      def self.parse_io input
+        mol = MdlMolecule.new
+        mol.parse input
+      end
+
+      def self.parse file
+        mol = MdlMolecule.new
+        input = open(file)
+        mol.parse input
+      end
+
+    end
+
+    class RxnAtom
+      include Atom
+      attr_accessor :reactant, :product
+
+      def reactant= rct
+        @reactant = @representative = rct
+      end
+
+      def method_missing name, *args
+        @representative.send(name, *args)
+      end
+      
+
+      def product= prd
+        @product = prd
+        @representative = prd unless @representative
+      end
+
+      def x       ; @representative.x       ; end
+      def y       ; @representative.y       ; end
+      def element ; @representative.element ; end
+
+    end
+
+    class RxnBond
+      include Bond
+      attr_accessor :reactant, :product
+      attr_reader   :v
+
+      def v
+        if @reactant and @product
+          return @product.v - @reactant.v
+        elsif @reactant
+          return - @reactant.v
+        else
+          return @product.v
+        end
+      end
+
+    end
+
+    class MdlReaction
+
+      include Molecule
+      include Reaction
+      include Enumerable
+
+      attr_reader :nodes, :edges
+
+      def initialize
+        @nodes = []
+        @edges = []
+        @reactants = []
+        @products  = []
+      end
+
+      attr_reader :filename
+      def open_rxn(filename)
+        @filename = filename
+        input = File.open(filename)
+        n_reactants, n_products = parse_header(input)
+        read_mol(input, n_reactants, @reactants, @r_atoms = {})
+        read_mol(input, n_products,  @products,  @p_atoms = {})
+        construct
+        self
+      end
+
+      private
+      def construct
+        @p2r = {}
+        @r2p = {}
+        (@r_atoms.keys + @p_atoms.keys).each do |k|
+          ratom = RxnAtom.new
+          ratom.reactant = @r_atoms[k]
+          ratom.product  = @p_atoms[k]
+          @p2r[@p_atoms[k]] = @r_atoms[k]
+          @r2p[@r_atoms[k]] = @p_atoms[k]
+          @nodes.push(ratom)
+        end
+        get_edge_hash(@reactants, r_edge_hash = {})
+        get_edge_hash(@products,  p_edge_hash = {})
+        already = []
+        @reactants.each do |mol|
+          mol.edges.each do |edge, atom1, atom2|
+            bond = RxnBond.new
+            bond.reactant = edge
+            if @r2p[atom1] and @r2p[atom2]
+              bond.product = p_edge_hash[[@r2p[atom1], @r2p[atom2]].sort_by{|a| a.number}]
+              already.push(bond.product)
+            end
+            @edges.push(bond)
+          end
+        end
+        @products.each do |mol|
+          mol.edges.each do |bond, atom1, atom2|
+            next if already.include?(bond)
+            r_bond = RxnBond.new
+            r_bond.product = bond
+            @edges.push([r_bond, atom1, atom2])
+          end
+        end
+      end
+
+      private
+      def get_edge_hash mols, hash
+        mols.each do |mol|
+          mol.edges.each do |edge, atom1, atom2|
+            hash[[atom1, atom2].sort_by{|a| a.number}] = edge
+          end
+        end
+      end
+
+      private 
+      def read_mol input, n, mols, atoms
+        n.times do
+          loop do
+            line = input.readline # $MOL
+            break if /\$MOL/.match(line)
+          end
+          mol = MdlMolecule.parse_io(input)
+          mol.nodes.each do |a|
+            next if a.mapping == 0
+            atoms[a.mapping] = a
+          end
+          mols.push mol
+        end
+      end
+
+      private
+      def parse_header input
+        4.times{|n| input.readline}
+        input.readline.split.collect{|n| n.to_i}
+      end
+
+    end
+
+  end
+
+end
+