chemruby 0.9.3 → 1.1.9

data/lib/chem/db/rmagick.rb

@@ -21,14 +21,16 @@ module Chem
     # Draws line
     # This method may be invoked from chem/db/vector.rb
     def line(from, to, color)
-      @canvas.stroke("rgb(%f, %f, %f)" % color)
+      @canvas.stroke("rgb(%f, %f, %f)" % to_256(color))
       @canvas.line(from[0], from[1], to[0], to[1])
     end
 
     def fill(nodes, color, params = {})
-      @canvas.fill("rgb(%f, %f, %f)" % params[:color]) if params[:color]
+      @canvas.stroke("rgb(%f, %f, %f)" % to_256(color))
+      @canvas.fill("rgb(%f, %f, %f)" % to_256(color)) if color
       path = nodes.inject([]){|ret, node| ret << node[0] ; ret << node[1]}
       @canvas.polygon(* path)
+      @canvas.fill("black")
     end
 
     def text(str, x, y, params = {})
@@ -36,7 +38,7 @@ module Chem
       metrics = @canvas.get_type_metrics(@img, str)
       @canvas.stroke('transparent')
       @canvas.pointsize(params[:pontsize])             if params[:pointsize]
-      @canvas.fill("rgb(%f, %f, %f)" % params[:color]) if params[:color]
+      @canvas.fill("rgb(%f, %f, %f)" % to_256(params[:color])) if params[:color]
 
       @canvas.text(x - metrics.width / 2.0,
                    y + metrics.height / 4.0,

data/lib/chem/db/sdf.rb

@@ -4,6 +4,10 @@ module Chem
 
   module MDL
 
+    class MdlMolecule
+      attr_accessor :sdf_data
+    end    
+
     class SdfParser
       include Enumerable
 
@@ -19,10 +23,32 @@ module Chem
         first_entry = true
         from = 0
         @input.each("$$$$") do |entry|
-          from = entry.index("\n") + 1unless first_entry
+          from = entry.index("\n") + 1 unless first_entry
           first_entry = false
           next if entry[from..-1].length < 3
-          yield MdlMolecule.parse_io(StringIO.new(entry[from..-1]))
+          molio = StringIO.new(entry[from..-1])
+          mol = MdlMolecule.parse_io(molio)
+          mol.sdf_data = {}
+          data_header = nil
+
+          molio.each do |line|
+            if line[0..0] == ">"
+              if /<([^>]+)>/.match(line)
+                data_header = $1
+              elsif /(DT\d+)/.match(line)
+                data_header = $1
+              end
+              mol.sdf_data[data_header] = []
+            elsif /^$/.match(line)
+              if mol.sdf_data[data_header].respond_to?(:join)
+                mol.sdf_data[data_header] = mol.sdf_data[data_header].join("\n")
+              end
+              # end of data
+            else
+              mol.sdf_data[data_header] << line.chop
+            end
+          end
+          yield mol
         end
 
       end

data/lib/chem/db/smiles/smiles.ry

@@ -93,16 +93,15 @@ def construct mol, tree, prev = nil
     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])
+        node.smiles_pos.each do |sp|
+          if @ring[sp]
+            mol.join(node, @ring[sp])
             # re-use ring closure digits
             # Higher-numbered ring closures are not supported yet.
-            @ring[smiles_pos] = nil
+            @ring[sp] = nil
           else
-            @ring[smiles_pos] = node
+            @ring[sp] = node
           end
         end
       end
@@ -116,13 +115,15 @@ def initialize
   @ring = []
 end
 
-@@parser = SmilesParser.new
-
 def self.parse_smiles( smiles )
-  @@parser.parse( smiles )
+  SmilesParser.new.parse( smiles)
 end
 
-ElementRegex = Regexp.new('\A(' + Chem::Number2Element.inject([]){|ret, el| ret.push(el.to_s)}.sort.reverse.join("|") + ')', Regexp::IGNORECASE)
+ElementRegex   = Regexp.new('\A(Cl|Br|B|C|N|O|P|S|F|I|H)', Regexp::IGNORECASE)
+InorganicRegex = /\A\[([^\]]+)\]/
+NumberRegex    = /\A\d+/
+BackSlashRegex = /\\/
+OtherRegex     = /\A./
 
 def parse( line )
   @q = []
@@ -130,18 +131,18 @@ def parse( line )
   line.strip!
   until line.empty? do
     case line
-    when /\A\[([^\]]+)\]/
+    when InorganicRegex
       # [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+/
+    when NumberRegex
       @q.push [:NUMBER, $& ]
-    when /\\/
+    when BackSlashRegex
       @q.push [:BSLASH, :BSLASH]
-    when /\A./
+    when OtherRegex
       @q.push [$&, $&]
     else
       raise RuntimeError, 'must not happen'
@@ -149,7 +150,6 @@ def parse( line )
     line = $'
   end
   @q.push [ :EOL, nil ]
-#  p @q
   mol = Chem::SmilesMol.new
   construct(mol, do_parse)
   mol
@@ -161,10 +161,12 @@ module Chem
   
   class SmilesAtom
     include Atom
-    attr_accessor :bond, :element, :element, :chiral, :hydrogen_count, :charge, :smiles_pos, :is_aromatic
+    attr_accessor :bond, :element, :element, :chiral, :hydrogen_count, :charge, :is_aromatic, :smiles_pos
+
     def inspect
-      "{%s %s(%s)}" % [@bond, @element, smiles_pos ? smiles_pos.join : ""]
+      "{%s %s(%s)}" % [@bond, @element, smiles_pos ? smiles_pos.join("-") : ""]
     end
+
   end
   
   class SmilesBond
@@ -187,14 +189,14 @@ module Chem
       return if to.bond == '.'
       bond = SmilesBond.new
 
-      case to.bond
-      when '='
-        bond.v = 2
-      when '#'
-        bond.v = 3
-      else
-        bond.v = 1
-      end
+      bond.v = case to.bond
+               when '='
+                 2
+               when '#'
+                 3
+               else
+                 1
+               end
       @edges.push([bond, from, to])
     end
 

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

@@ -9,7 +9,7 @@ require 'racc/parser'
 
 class SmilesParser < Racc::Parser
 
-module_eval <<'..end smiles.ry modeval..id6e4480ccfa', 'smiles.ry', 84
+module_eval <<'..end smiles.ry modeval..idae4de8f30f', 'smiles.ry', 84
 
 def next_token
   @q.shift
@@ -22,16 +22,15 @@ def construct mol, tree, prev = nil
     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])
+        node.smiles_pos.each do |sp|
+          if @ring[sp]
+            mol.join(node, @ring[sp])
             # re-use ring closure digits
             # Higher-numbered ring closures are not supported yet.
-            @ring[smiles_pos] = nil
+            @ring[sp] = nil
           else
-            @ring[smiles_pos] = node
+            @ring[sp] = node
           end
         end
       end
@@ -45,13 +44,15 @@ def initialize
   @ring = []
 end
 
-@@parser = SmilesParser.new
-
 def self.parse_smiles( smiles )
-  @@parser.parse( smiles )
+  SmilesParser.new.parse( smiles)
 end
 
-ElementRegex = Regexp.new('\A(' + Chem::Number2Element.inject([]){|ret, el| ret.push(el.to_s)}.sort.reverse.join("|") + ')', Regexp::IGNORECASE)
+ElementRegex   = Regexp.new('\A(Cl|Br|B|C|N|O|P|S|F|I|H)', Regexp::IGNORECASE)
+InorganicRegex = /\A\[([^\]]+)\]/
+NumberRegex    = /\A\d+/
+BackSlashRegex = /\\/
+OtherRegex     = /\A./
 
 def parse( line )
   @q = []
@@ -59,18 +60,18 @@ def parse( line )
   line.strip!
   until line.empty? do
     case line
-    when /\A\[([^\]]+)\]/
+    when InorganicRegex
       # [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+/
+    when NumberRegex
       @q.push [:NUMBER, $& ]
-    when /\\/
+    when BackSlashRegex
       @q.push [:BSLASH, :BSLASH]
-    when /\A./
+    when OtherRegex
       @q.push [$&, $&]
     else
       raise RuntimeError, 'must not happen'
@@ -78,13 +79,12 @@ def parse( line )
     line = $'
   end
   @q.push [ :EOL, nil ]
-#  p @q
   mol = Chem::SmilesMol.new
   construct(mol, do_parse)
   mol
 end
 
-..end smiles.ry modeval..id6e4480ccfa
+..end smiles.ry modeval..idae4de8f30f
 
 ##### racc 1.4.4 generates ###
 
@@ -333,10 +333,12 @@ module Chem
   
   class SmilesAtom
     include Atom
-    attr_accessor :bond, :element, :element, :chiral, :hydrogen_count, :charge, :smiles_pos, :is_aromatic
+    attr_accessor :bond, :element, :element, :chiral, :hydrogen_count, :charge, :is_aromatic, :smiles_pos
+
     def inspect
-      "{%s %s(%s)}" % [@bond, @element, smiles_pos ? smiles_pos.join : ""]
+      "{%s %s(%s)}" % [@bond, @element, smiles_pos ? smiles_pos.join("-") : ""]
     end
+
   end
   
   class SmilesBond
@@ -359,14 +361,14 @@ module Chem
       return if to.bond == '.'
       bond = SmilesBond.new
 
-      case to.bond
-      when '='
-        bond.v = 2
-      when '#'
-        bond.v = 3
-      else
-        bond.v = 1
-      end
+      bond.v = case to.bond
+               when '='
+                 2
+               when '#'
+                 3
+               else
+                 1
+               end
       @edges.push([bond, from, to])
     end
 

data/lib/chem/db/types/type_gd.rb

@@ -0,0 +1,35 @@
+
+module Chem
+
+  module Type
+    module GDType
+
+      def self.detect_file file
+        begin
+          require 'GD'
+        rescue LoadError
+          return false
+        end
+        ['.png', '.gif', '.jpg', '.jpeg', '.tiff'].include?(File.extname(file))
+      end
+
+      # ChemRuby will never parse PNG ;)
+      def self.parse file
+        raise NotImplementedError
+      end
+
+      def self.detect_type type
+        [:gd_png, :gd_gif, :gd_jpeg, :gd_tiff].include?(type)
+      end
+
+      def self.save mol, filename, params = {}
+        require 'chem/db/gd.rb'
+        GDWriter.save(mol, filename, params)
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::GDType
+
+end

data/lib/chem/db/types/type_gspan.rb

@@ -19,9 +19,9 @@ module Chem
         type == :gspan
       end
 
-      def self.save mol, filename
+      def self.save mol, filename, params = {}
         #      require 'chem/db/gspan.rb'
-        Chem::GSpan.save(mol, filename)
+        Chem::GSpan.save(mol, filename, params)
       end
     end
   end

data/lib/chem/db/types/type_kcf.rb

@@ -25,4 +25,23 @@ module Chem
 
   ChemTypeRegistry << Type::KCFType
 
+  module KCFRPairType
+
+    def self.detect_file file
+      File.extname(file) == '.kcf' && /A\d+/.match(file)
+    end
+
+    def self.parse file
+      require 'chem/db/kcf_rpair'
+      Chem::KCF::RPairMolecule.new(File.open(file))
+    end
+
+    def self.detect_type type
+      type == :kcf_rpair
+    end
+
+  end
+
+  ChemTypeRegistry << KCFRPairType
+
 end

data/lib/chem/db/types/type_kegg.rb

@@ -14,6 +14,7 @@ module Chem
       end
 
       def self.parse file
+        require 'chem/db/kegg'
         Chem::KEGG::KeggReactionParser.new file
       end
 
@@ -35,6 +36,7 @@ module Chem
       end
 
       def self.parse file
+        require 'chem/db/kegg'
         Chem::KEGG::KeggReactionMapParser.new file
       end
 

data/lib/chem/db/types/type_mdl.rb

@@ -20,7 +20,7 @@ module Chem
       end
 
       def self.save mol, filename, params = {}
-        # require 'chem/db/mdl.rb'
+        require 'chem/db/mdl.rb'
         mol.save_as_mdl(filename)
       end
     end

data/lib/chem/db/types/type_png.rb

@@ -5,6 +5,11 @@ module Chem
     module PNGType
 
       def self.detect_file file
+        begin
+          require 'RMagick'
+        rescue LoadError
+          return false
+        end
         ['.png', '.gif', '.jpg', '.jpeg', '.tiff'].include?(File.extname(file))
       end
 
@@ -18,7 +23,6 @@ module Chem
       end
 
       def self.save mol, filename, params = {}
-        require 'RMagick'
         require 'chem/db/rmagick.rb'
         RMagickWriter.save(mol, filename, params)
       end

data/lib/chem/db/types/type_rdf.rb

@@ -0,0 +1,22 @@
+
+module Chem
+
+  module Type
+
+    module RDFType
+      def self.detect_file file
+        File.extname(file) == '.rdf'
+      end
+
+      def self.parse file
+        require 'chem/db/mdl.rb'
+      end
+
+      def self.detect_type type
+        type == :rdf
+      end
+    end
+
+  end
+
+end