chemruby 0.9.3

data/lib/chem/utils/ullmann.rb

@@ -0,0 +1,134 @@
+#
+# = chem/utils/subgraph.rb - Subgraph isomorphism
+#
+# Author::	Nobuya Tanaka <tanaka@chemruby.org>
+#		
+# Copyright::	Copyright (c) 2001, 2005 ChemRuby project
+#
+# $Id: ullmann.rb 139 2006-02-07 07:39:20Z tanaka $
+#
+
+require 'subcomp'
+
+$ARC = 4 # for 32-bit computer
+
+module Graph
+
+  def adj_matrix
+    n_long = (nodes.length - 1) / 32 + 1
+    mat = Array.new(n_long * @nodes.length, 0)
+    nodes.each_with_index do |node, idx|
+      adjacent_to(node).each do |bond, node|
+        keta = nodes.index(node) / 32
+        mat[idx * n_long + keta] += 1 << (nodes.index(node) - keta * 32)
+      end
+    end
+    mat.pack("L*")
+  end
+
+  def match_by_adj_mat mat, len
+    m = Array.new("0xff", 100).pack("c*")
+    subcomp_match_by_ullmann(mat, len, self.adjacency_list, self.nodes.length, m)
+  end
+
+  def match_by_ullmann other, &block
+    if other.nodes.length == 1
+      self.nodes.find{|node| node.element == other.nodes[0].element}
+    end
+    subcomp_match_by_ullmann(adj_matrix, nodes.length, other.adjacency_list, other.nodes.length, other.matchable(self, &block))
+  end
+  alias match match_by_ullmann
+
+  # returns match correspondences without duplicate
+  def match_exhaustively other
+    correspond = {}
+    result = []
+    while true
+      match = self.match_by_ullmann(other) do |a, b|
+        a.element == b.element and not (correspond[a] and correspond[a].include? b)
+      end
+      break if not match
+      result.push(match)
+      match.each_with_index do |n, m|
+        (correspond[other.nodes[n]] ||=[]).push @nodes[m]
+      end
+    end
+    result
+  end
+
+  def matchable other, exlucde = {}
+    n_long = (other.nodes.length - 1) / 32 + 1
+    mat = Array.new(n_long * @nodes.length, 0)
+    @nodes.each_with_index do |node, index|
+      other.nodes.each_with_index do |n, idx|
+        if node.element == n.element
+          keta = idx / 32
+          mat[index * n_long + keta] += 1 << (idx - keta * 32)
+        end
+      end
+    end
+    mat.pack("L*")
+  end
+
+  #obsolete
+  def matchable_old other, exlucde = {}
+    n_long = (other.nodes.length - 1) / 32 + 1
+    row_unit = n_long * ( 32 / 8)
+    r = "\0" * 10000
+    if block_given?
+      @nodes.each_with_index do |node, index|
+        other.nodes.each_with_index do |o_node, idx|
+          if yield(node, o_node)
+            col_byte = idx / 8
+            col_bit  = idx - col_byte * 8
+            r[index * row_unit + col_byte] += (1 << col_bit)
+          end
+        end
+      end
+    else
+      @nodes.each_with_index do |node, index|
+        other.nodes.each_with_index do |o_node, idx|
+          if node.element == o_node.element or node.element == :R or o_node.element == :R
+            col_byte = idx / 8
+            col_bit  = idx - col_byte * 8
+            r[index * row_unit + col_byte] += (1 << col_bit)
+          end
+        end
+      end
+    end
+    r
+  end
+
+  def adjacency_list
+    ret = []
+    @nodes.each do |node|
+      r = []
+      self.adjacent_to(node).each do |bond, to|
+        r << @nodes.index(to)
+      end
+      ret << r
+    end
+    ret
+  end
+
+  # Obsolete!?
+  def connection
+    self_adj = []
+    @nodes.each do |node|
+      i = 0
+      self.adjacent_to(node).each do |bond, to|
+        i += 1<< @nodes.index(to)
+      end
+      self_adj << i
+    end
+    self_adj
+  end
+
+end
+
+module Chem
+  module Molecule
+    include Graph
+  end
+end
+

data/lib/graph.rb

@@ -0,0 +1,41 @@
+#
+# graph.rb - Graph
+#
+#   Copyright (C) 2003-2005 TANAKA Nobuya <tanaka@chemruby.net>
+#
+# $Id: graph.rb 61 2005-10-12 09:17:39Z tanaka $
+#
+
+
+require 'graph/morgan'
+require 'graph/cluster'
+
+module Graph
+
+  attr_accessor :nodes, :edges, :adjacencies
+
+  def each
+    @nodes.each do |atom|
+      yield atom
+    end
+  end
+
+  def adjacent_to(atom)
+    #       instance_eval "alias :tmp_adjacent_to :adjacent_to"
+    #       instance_eval "alias :adjacent_to :adjacencies"
+    if @adjacencies == nil
+      @adjacencies = {}
+      @edges.each do |bond, atom_a, atom_b|
+        (@adjacencies[atom_a] ||= []).push([bond, atom_b])
+        (@adjacencies[atom_b] ||= []).push([bond, atom_a])
+      end
+    end
+    @adjacencies[atom] ||= []
+    @adjacencies[atom]
+  end
+
+  def adjacencies(atom)
+    @adjacencies[atom] ||= []
+    @adjacencies[atom]
+  end
+end

data/lib/graph/cluster.rb

@@ -0,0 +1,20 @@
+
+module Graph
+
+  def clustering_coefficient
+    cc = {} # clustering coefficient
+    @nodes.each do |node|
+      c = 0
+      adj = adjacent_to(node)
+      adj_nodes = adj.collect{|e, n| n}
+      adj.each do |ed, nd|
+        adjacent_to(nd).each do |e, n|
+          c += 1 if adj_nodes.include?(n)
+        end
+      end
+      cc[node] = c
+    end
+    cc
+  end
+
+end

data/lib/graph/morgan.rb

@@ -0,0 +1,38 @@
+
+module Graph
+  def morgan
+    ec = {}  # extended connectivity
+    tec = {} # trial extended connectivity
+
+    @nodes.each{ |a| tec[a] = 1 }
+
+    k = 0
+    k2 = k + 1
+
+    while k2 > k
+      k = k2
+      @nodes.each{ |a| ec[a] = tec[a] }
+
+      @nodes.each do |a|
+        tec[a] = adjacent_to(a).inject(0){|ret, (b, n)| ret + ec[n]}
+      end
+      k2 = @nodes.collect{|a| tec[a]}.uniq.length
+    end
+
+    #      calc morgan tree
+    max = @nodes.max{|a, b| tec[a] <=> tec[b]}
+
+    queue = [ max ]
+    traversed = [ max ]
+
+    while from = queue.shift
+      adjacent_to(from).sort{|(b1, n), (b2, m)| tec[m] <=> tec[n]}.each do |bond, atom|
+        unless traversed.include?(atom)
+          queue.push(atom)
+          traversed.push(atom)
+        end
+      end
+    end
+    [ec, tec, traversed]
+  end
+end

data/sample/frequent_subgraph.rb

@@ -0,0 +1,46 @@
+
+$: << "/home/tanaka/proj/chemruby/lib/"
+$: << "/home/tanaka/proj/chemruby/ext/"
+
+require 'chem'
+
+# Load 
+puts "Load molecules"
+
+mols = []
+
+Dir.glob("mol/*.mol") do |file
+  mols.push Chem.open_mol(filename) if File.exist?(filename)
+  print "."
+end
+
+puts
+puts "Load completed!"
+
+# Calculate with gSpan
+
+filename = "temp/temp.gspan.#{Process.pid}.0"
+filename.succ! while File.exist?(filename)
+# KADOWAKi suggested to removed .fp extension
+#filename = filename + ".fp"
+Chem.save(mols, filename)
+
+system("gSpan #{filename} -o -s32")
+freqs = Chem.open_mol("#{filename}.fp")
+
+# Save Image
+
+puts
+puts "Now save images in temp/"
+
+
+mols.each_with_index do |mol, i|
+  m = mol.match_by_ullmann(freqs[10])
+  if m
+    m.each do |index|
+      mol.nodes[index].visible = true
+    end
+    # need rmagick or use pdf
+    mol.save(File.join("temp", "mol_#{i}.png"))
+  end
+end

data/sample/images/ex1.rb

@@ -0,0 +1,11 @@
+#
+# 1. open file with Chem.open_mol
+# 2. save the object with Molecule#save
+# 3. No step 3 !
+
+require 'chem'
+
+mol = Chem.open_mol("mol/atp.mol")
+
+mol.save("temp/ex1.png")
+

data/sample/images/ex2.rb

@@ -0,0 +1,4 @@
+require 'chem'
+
+mol = Chem.open_mol("mol/atp.mol")
+mol.save("temp/ex2.png", :size => [300, 150])

data/sample/images/ex3.rb

@@ -0,0 +1,5 @@
+require 'chem'
+
+mol = Chem.open_mol("mol/atp.mol")
+mol.nodes.each{|node| node.visible = true unless node.element == :C}
+mol.save("temp/ex3.png")

data/sample/images/ex4.rb

@@ -0,0 +1,17 @@
+require 'chem'
+
+mol = Chem.open_mol("mol/atp.mol")
+mol.nodes.each do |node|
+
+  node.visible = true unless node.element == :C
+
+  case node.element
+  when :O
+    node.color = [1, 0, 0]
+  when :N
+    node.color = [0, 0, 1]
+  end
+
+end
+
+mol.save("temp/ex4.png")

data/sample/images/ex5.rb

@@ -0,0 +1,10 @@
+require 'chem'
+
+mol = Chem.open_mol("mol/atp.mol")
+
+mol.nodes.each do |node|
+  node.visible = true unless node.element == :C
+end
+
+mol.save("temp/ex5.png", :size => [350, 350])
+

data/sample/images/mol/adenine.mol

@@ -0,0 +1,26 @@
+
+  -ISIS-  02070623312D
+
+ 10 11  0  0  0  0  0  0  0  0999 V2000
+   -0.6276   -3.3023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0872   -3.7152    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    0.8037   -3.3019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.8008   -2.4713    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0861   -1.2557    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9059   -1.1709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -0.6264   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0867   -2.0617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.3424   -3.7143    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+  8  9  1  0  0  0  0
+  1  2  1  0  0  0  0
+  8  1  2  0  0  0  0
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+  5  6  1  0  0  0  0
+  7  8  1  0  0  0  0
+  9  5  1  0  0  0  0
+  4  9  2  0  0  0  0
+  1 10  1  0  0  0  0
+M  END

data/sample/images/mol/atp.mol

@@ -0,0 +1,69 @@
+
+  -ISIS-  02070623502D
+
+ 31 33  0  0  0  0  0  0  0  0999 V2000
+    2.4776   -1.7290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6787   -1.6299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6694    0.2591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3254   -0.5277    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3200   -0.2785    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+    2.0257   -1.0363    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+    1.1912   -0.9888    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+    0.9734   -0.1896    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+    0.2042    0.1028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.4581    0.1598    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    5.1745    0.5731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    4.4563    1.8128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+ 28 30  2  0  0  0  0
+  5  6  1  0  0  0  0
+ 28 31  1  0  0  0  0
+M  END

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