chemruby 0.9.3 → 1.1.9

data/ext/utils.c

@@ -0,0 +1,56 @@
+#include <ruby.h>
+#include "utils.h"
+
+int
+ntz(long l){
+  int n;
+  if(l == 0) return ARCH;
+  n = 1;
+  if(( l & 0x000FFFF) == 0) { n = n + 16 ; l = l >> 16; }
+  if(( l & 0x00000FF) == 0) { n = n +  8 ; l = l >>  8; }
+  if(( l & 0x000000F) == 0) { n = n +  4 ; l = l >>  4; }
+  if(( l & 0x0000003) == 0) { n = n +  2 ; l = l >>  2; }
+  return n - (l & 1);
+}
+
+int
+m_ntz(long *l, int n_bytes){
+  int i, n;
+  n = 0;
+  for(i = 0 ; i < n_bytes ; i++){
+    if(l[i] == 0){
+      n += ARCH;
+    }else{
+      return n + ntz(l[i]);
+    }
+  }
+  return n;
+}
+
+void *
+talloc(size_t size){
+  void * ptr;
+  ptr = malloc(size);
+  if(ptr == NULL){
+    rb_raise(rb_eNoMemError, "Cannot allocate memory");
+  }
+  return ptr;
+}
+
+void *
+trealloc(void *from, size_t size){
+  void * ptr;
+  ptr = realloc(from, size);
+  if(ptr == NULL){
+    rb_raise(rb_eNoMemError, "Cannot allocate memory");
+  }
+  return ptr;
+}
+
+void
+dump_long(long l, int n){
+  int i;
+  for(i = 0 ; i < n ; i++){
+    printf("%s", (l & (1 << i)) != 0 ? "@" : ".");
+  }
+}

data/ext/utils.h

@@ -0,0 +1,13 @@
+#include <stdio.h>
+
+#define ARCH 32
+
+#define NBYTES(width) ((width - 1 ) / ARCH + 1)
+#define BITON(mat, h, w, n_bytes)   (mat[h * n_bytes + w / ARCH] |=  (1 << (w % ARCH)))
+#define BITOFF(mat, h, w, n_bytes)  (mat[h * n_bytes + w / ARCH] &= ~(1 << (w % ARCH)))
+
+int ntz(long l);
+int m_ntz(long *l, int n_bytes);
+void * talloc(size_t size);
+void * trealloc(void *from, size_t size);
+void dump_long(long l, int n);

data/lib/chem.rb

@@ -1,7 +1,7 @@
 #
 # Chem module.  See documentation for the file chem.rb for an overview
 #
-# $Id: chem.rb 158 2006-02-09 07:16:48Z tanaka $
+# $Id: chem.rb 160 2006-02-14 06:49:37Z tanaka $
 #
 # == Introduction
 #
@@ -20,6 +20,7 @@
 
 
 require 'stringio'
+require 'graph'
 
 require 'chem/data'
 require 'chem/utils'
@@ -29,7 +30,17 @@ require 'chem/db'
 
 require 'tempfile'
 
+# Convension over Configuration
+
 module Chem
+  # read ~/.chemrc or...
+  if ENV["HOME"]
+    DefaultDataDir = File.join(ENV["HOME"], "data")
+  end
+
+  def self.data_dir
+    DefaultDataDir
+  end
 
   autoload   :MDL,   'chem/db/mdl.rb'
   autoload   :CDX,   'chem/db/cdx.rb'
@@ -38,11 +49,6 @@ module Chem
 
   module_function
 
-  # returns first entry
-  def find_first str
-    p str
-  end
-
   # format_class = Chem.autodetect("file.mol")
   #
   # Automatically detect file type and returns
@@ -70,12 +76,14 @@ module Chem
   end
 
   alias :parse_file :open_mol
+  alias :load       :open_mol
   module_function :parse_file
+  module_function :load
 
   # 
-  def self.save(array, filename)
+  def self.save(array, filename, params = {})
     format = autodetect filename
-    format.save(array, filename)
+    format.save(array, filename, params)
   end
 
   def parse_smiles smiles
@@ -115,6 +123,24 @@ module Chem
       format.save(self, filename, params)
     end
 
+    # Redirect methods to OpenBabel
+    def method_missing(m, *args)
+      unless @ob_mol.respond_to?(m)
+        super(m, *args)
+      end
+      @ob_mol.__send__(m, *args)
+    end
+
+  end
+
+  module Atom
+    def method_missing(m, *args)
+      if not @ob_atom.nil? and @ob_atom.respond_to?(m)
+        @ob_atom.__send__(m, *args)
+      else
+        super(m, *args)
+      end
+    end
   end
 
 end

data/lib/chem/db.rb

@@ -1,5 +1,11 @@
 
 #require 'chem/db/smiles'
+require 'chem/db/pubchem'
+require 'chem/utils/openbabel'
+require 'chem/utils/cdk'
+require 'chem/db/opsin'
+require 'chem/db/cml'
+
 
 module Chem
 
@@ -30,6 +36,8 @@ module Chem
 
 end
 
+require 'chem/db/vector'
+
 Chem::Db::load
 
 __END__

data/lib/chem/db/cansmi.rb

@@ -1,4 +1,4 @@
-# Author::     Nobuya Tanaka tanaka@chemruby.org
+# Author::     Nobuya Tanaka t@chemruby.org
 
 module Chem
 

data/lib/chem/db/cdx.rb

@@ -1,7 +1,7 @@
 #
 # cdx.rb - Cambridge Software cdx and cdxml file parser library
 #
-# Copyright (C) 2003 Nobuya Tanaka <tanaka@chemruby.org>
+# Copyright (C) 2005 Nobuya Tanaka <t@chemruby.org>
 #
 # Example:
 #   cdx_file = Chem.open_mol("hypericin.cdx")

data/lib/chem/db/cml.rb

@@ -0,0 +1,52 @@
+require 'rexml/document'
+
+module Chem
+
+  class CMLAtom
+
+    include Atom
+    attr_reader :node_id
+
+    def initialize(element, node_id)
+      @element = element
+      @node_id = node_id
+    end
+
+  end
+
+  class CMLBond
+
+    include Bond
+
+    def initialize(v)
+      @v = v
+    end
+
+  end
+
+  class CMLMolecule
+    include Molecule
+
+    def initialize(str)
+      @nodes = []
+      @edges = []
+      atom_refs = {}
+
+      xml = REXML::Document.new(str)
+      xml.elements.each("cml/molecule") do |molecule|
+        molecule.elements.each("atomArray/atom") do |atom_element|
+          atom = CMLAtom.new(atom_element.attributes["elementType"],
+                             atom_element.attributes["id"])
+          @nodes << atom
+          atom_refs[atom.node_id] = atom
+        end
+        molecule.elements.each("bondArray/bond") do |bond_element|
+          from, to = (bond_element.attributes["atomRefs2"]).split(" ")
+          valence  = bond_element.attributes["order"].to_i
+          @edges << [CMLBond.new(valence), atom_refs[from], atom_refs[to]]
+        end
+      end
+    end
+
+  end
+end

data/lib/chem/db/gd.rb

@@ -0,0 +1,64 @@
+# RMagick adaptor for chem/db/vector.rb
+
+require 'chem/db/vector'
+
+module Chem
+  class GDWriter
+
+    include Writer
+
+    # Constructor for GD Adaptor
+    # See chem/db/vector.rb for detail parameters
+    def initialize mol, params
+      params[:size]        ||= [350, 350]
+      params[:orig_point]  ||= [10, 10]
+      params[:margin]      ||= [10, 10]
+      @default_pointsize = (params[:pointsize] ? params[:pointsize] : 14)
+      params[:upside_down] = params[:upside_down] ? false : true
+      super
+    end
+
+    # Draws line
+    # This method may be invoked from chem/db/vector.rb
+    def line(from, to, color)
+      a_color = @img.colorAllocate(*to_256(color))
+      @img.line(from[0], from[1], to[0], to[1], a_color)
+    end
+
+    def self.save(mol, filename, params)
+      writer = self.new(mol, params)
+      writer.draw(filename, params)
+    end
+
+    def fill(nodes, color, params = {})
+      poly = GD::Polygon.new
+      nodes.each do |node|
+        poly.addPt(node[0], node[1])
+      end
+      @img.filledPolygon(poly, @img.colorAllocate(*to_256(color)))
+    end
+
+    def text(str, x, y, params = {})
+      font = GD::Font::LargeFont
+      a_color = nil
+      a_color = params[:color] ? @img.colorAllocate(*to_256(params[:color])) : @img.colorAllocate(0, 0, 0)
+      @img.string(font, x - font.width / 2.0, y - font.height / 2.0, str, a_color)
+    end
+    
+    def draw filename, params
+
+      x, y = params[:size]
+      x += params[:margin][0] * 2
+      y += params[:margin][0] * 2
+      
+      @img = GD::Image.new(x, y)
+      background_color = @img.colorAllocate(255, 255, 255)
+
+      # Vector#draw_body
+      draw_body
+      
+      @img.png(open(filename, "w"))
+    end
+
+  end
+end

data/lib/chem/db/gspan.rb

@@ -15,7 +15,7 @@ module Chem
   class GSpan
 
     FIRST_NODE = /\((\d+)\)/
-    REG_NODE = / (\d+) \((\d+)+.(\d+)\)/
+    REG_NODE   = /\s*(\d+)\s*\((\d*)(f|b)(\d+)\)/
 
     # Parse one-lined gSpan formatted string and return
     # molecule object.
@@ -45,7 +45,7 @@ module Chem
     # Save molecule as gSpan formatted file.
     # Example :
     #   Chem::GSpan.save(mols , "filename") # mols : an array of molecules
-    def self.save mols, filename
+    def self.save mols, filename, params = {}
       open(filename, "w") do |out|
         mols.each_with_index do |mol, mol_idx|
           out.puts "t # #{mol_idx} -1 #{mol.name}"

data/lib/chem/db/kcf_rpair.rb

@@ -0,0 +1,34 @@
+# This is stub
+module Chem
+
+  module KCF
+
+    class RPairMolecule
+      include Molecule
+
+      def initialize input
+        state = nil
+        input.each do |line|
+          case line[0..11]
+          when "            "
+            case state
+            when :alignment
+              idx, from, to = line.split
+              from
+            end
+          when "ENTRY       "
+          when "NAME        "
+          when "COMPOUND    "
+          when "TYPE        "
+          when "ALIGN       "
+            state = :alignment
+            p line[11..-1].strip.to_i
+          end
+        end
+      end
+
+    end
+
+  end
+
+end

data/lib/chem/db/kegg.rb

@@ -1,7 +1,7 @@
 #
 # = chem/db/kegg.rb - KEGG (Kyoto Encylopedia of Genes and Genomes)
 #
-# Author::	Nobuya Tanaka <tanaka@chemruby.org>
+# Author::	Nobuya Tanaka <t@chemruby.org>
 #
 # $Id:$
 #
@@ -9,8 +9,42 @@
 require 'chem/db/mdl'
 
 module Chem
+  class KEGGException < Exception
+  end
 
   module KEGG
+
+    CNUMREG = /C(\d\d\d\d\d)/
+    ECREG   = /EC([^.]+)\.([^.]+)\.([^.]+)\.([^.]+)/
+    @@kegg = {}
+
+    def self.[](kegg_id)
+      @@kegg[kegg_id] ||= case kegg_id
+                         when CNUMREG
+                         when ECREG
+                           EC.new($1, $2, $3, $4)
+                         else
+                           raise KEGGException, "Unknown KEGG ID '#{kegg_id}'"
+                         end
+    end
+
+    class Compound
+    end
+
+    class Reaction
+    end
+
+    module ReactionList
+    end
+
+    class EC
+
+      def initialize(num1, num2, num3, num4)
+        #puts Chem.data_dir
+      end
+
+    end
+
   class KeggDirectory
 
     attr_reader :dir

data/lib/chem/db/mdl.rb

@@ -2,18 +2,29 @@
 # chem/db/mdl.rb - MDL molfile format class
 #
 
+require 'date'
 
 module Chem
 
   module Molecule
 
     MDLCountLineFormat = "%3d%3d%3d%3d%3d%3d%3d%3d%3d  0999 V2000"
+    MDLHeaderLine2Format = "%2s%8s%02d%02d%02d%02d%02d"
 
-    def save_as_mdl filename
+    def save_as_mdl(filename)
       File.open(filename, "w") do |out|
+        now = DateTime.now
+        out.puts 
+        out.puts MDLHeaderLine2Format % [
+          "  ",
+          "ChemRuby",
+          now.month,
+          now.mday,
+          now.year % 2000,
+          now.hour,
+          now.min
+        ]
         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
@@ -21,6 +32,7 @@ module Chem
         edges.each do |edge, atom1, atom2|
           out.puts edge.to_mdl(nodes.index(atom1) + 1, nodes.index(atom2) + 1)
         end
+        out.puts "M  END"
       end
     end
 
@@ -30,7 +42,10 @@ module Chem
 
     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
+    def to_mdl(mapping = 0)
+      self.x ||= 0
+      self.y ||= 0
+      self.z ||= 0
       MDLAtomLineFormat % [x, y, z, element, 0, 0, 0, 0, 0, 0, 0, 0, 0, mapping, 0, 0]
     end
 
@@ -38,7 +53,7 @@ module Chem
 
   module Bond
 
-    def to_mdl from, to
+    def to_mdl(from, to)
       "%3d%3d%3d%3d      " % [from, to, v, 0]
     end
 
@@ -46,20 +61,20 @@ module Chem
 
   module Reaction
 
-    def to_mdl_rxn
-      return # fix me
-#      out = STDOUT
-      out.puts "$RXN"
-      out.puts
-      out.puts "ISIS     112620051015"
-      out.puts
-      out.puts "%3d%3d" % [@reactants.length, @products.length]
-      @reactants.each{ |mol| output_mdl_mol(mol, out)}
-      @products.each{ |mol| output_mdl_mol(mol, out)}
-    end
+#     def to_mdl_rxn
+#       return # fix me
+# #      out = STDOUT
+#       out.puts "$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
+    def output_mdl_mol(mol, out)
       out.puts "$MOL"
       mol.nodes.each do |node|
         out.puts node.to_mdl(10)
@@ -73,9 +88,7 @@ module Chem
 
     class MDLAtom
 
-      require 'chem/utils/transform'
       include Atom
-      include Chem::Transform::ThreeDimension
 
       Stereo = {
         0 => :not_stereo,
@@ -149,7 +162,7 @@ module Chem
         2 => :chain
       }
 
-      def initialize line  ; @line              = line                                       ; end
+      def initialize(line)  ; @line              = line                                       ; end
 
       def v                ; @v               ||= @line[6..8].to_i                           ; end
 
@@ -174,10 +187,29 @@ module Chem
       end
       alias name entry
 
-      def parse input
-        input.readline
-        @title = input.readline
-        raise MDLException if input.readline == nil
+      attr_reader :mol_name
+
+      def program_name ; @program_name ||= @header_line2[2..9] end
+
+      def date_time
+        year_last_two = @header_line2[14..15].to_i
+        year = year_last_two + (year_last_two > 80 ? 1900 : 2000)
+        @date ||= DateTime.new(
+                               year,
+                               @header_line2[10..11].to_i,
+                               @header_line2[12..13].to_i,
+                               @header_line2[16..17].to_i,
+                               @header_line2[18..19].to_i)
+      end
+
+      def dimensional_codes
+        @dimensional_codes ||=  @header_line2[20..21]
+      end
+
+      def parse(input)
+        @mol_name = input.readline.chop
+        @header_line2 = input.readline.chop
+        raise MDLException if @comment = input.readline == nil
         line = input.readline
         n_atom = line[0..2].to_i
         n_bond = line[3..5].to_i
@@ -224,12 +256,12 @@ module Chem
         @edges = []
       end
 
-      def self.parse_io input
+      def self.parse_io(input)
         mol = MdlMolecule.new
         mol.parse input
       end
 
-      def self.parse file
+      def self.parse(file)
         mol = MdlMolecule.new
         input = open(file)
         mol.parse input
@@ -239,18 +271,22 @@ module Chem
 
     class RxnAtom
       include Atom
-      attr_accessor :reactant, :product
+#      attr_accessor :reactant, :product
 
-      def reactant= rct
+      def reactant=(rct)
         @reactant = @representative = rct
       end
 
-      def method_missing name, *args
-        @representative.send(name, *args)
+      def method_missing(name, *args)
+        if @representative.respond_to?(name)
+          @representative.send(name, *args)
+        else
+          super(name, *args)
+        end
       end
       
 
-      def product= prd
+      def product=(prd)
         @product = prd
         @representative = prd unless @representative
       end
@@ -341,7 +377,7 @@ module Chem
       end
 
       private
-      def get_edge_hash mols, hash
+      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
@@ -350,7 +386,7 @@ module Chem
       end
 
       private 
-      def read_mol input, n, mols, atoms
+      def read_mol(input, n, mols, atoms)
         n.times do
           loop do
             line = input.readline # $MOL
@@ -366,13 +402,18 @@ module Chem
       end
 
       private
-      def parse_header input
+      def parse_header(input)
         4.times{|n| input.readline}
         input.readline.split.collect{|n| n.to_i}
       end
 
     end
 
+    module RDFParser
+      def initialize(input)
+      end
+    end
+
   end
 
 end