chemruby 0.9.3 → 1.1.9

data/lib/chem/utils/graph_db.rb

@@ -1,146 +0,0 @@
-
-require 'chem'
-require 'dbm'
-
-module Graph
-
-  class SubGraphDB
-
-    # Create Database object
-    # @idx  : index database for @mat and @typ
-    #         also stores number of nodes.
-    # @mat  : adjacency matrix database
-    # @typ  : node type database
-    # @dbm  : property database
-    def initialize dbname, mode = "w"
-      @dbm = DBM.open("#{dbname}.dbm")
-      @idx = open("#{dbname}.idx", mode)
-      @mat = open("#{dbname}.mat", mode)
-      @typ = open("#{dbname}.typ", mode)
-    end
-
-    def self.open dbname, mode = "r"
-      if mode == "r"
-        SubGraphDB.new(dbname, mode)
-      else
-        self.new(dbname, mode)
-      end
-    end
-
-    def []= key, mol
-      adj = mol.adj_matrix
-      @idx.print [mol.nodes.length, @mat.tell, adj.length].pack("i*")
-      @mat.print adj
-      @typ.print mol.nodes.inject([]){ |ret, node| ret.push(node.atomic_number)}.pack("i*")
-    end
-
-    # Closes database
-    def close
-      @dbm.close
-      @idx.close
-      @mat.close
-      @typ.close
-    end
-
-    # Searches molecule from database
-    # Example:
-    # db = SubGraphDB.open("somewhere/dbname")
-    # db.search(SMILES("CCCC"))
-    def search mol
-      @idx.rewind
-      i = 1
-      until @idx.eof?
-        n_nodes, mat, len_matrix = @idx.read(4 * 3).unpack("i*")
-        m = [0xff].pack("c") * 100
-        open("test.bin", "w").puts m
-
-        matrix = read_mat(mat, len_matrix)
-        #SubGraphDB.show(m, mol.nodes.length, n_nodes)
-        if SubGraphDB.match(matrix, n_nodes, mol.adjacency_list, mol.nodes.length, m)
-          puts "C%05d" % i
-        end
-        i += 1
-      end
-    end
-
-    private
-    def read_mat idx, len_matrix
-      @mat.seek(idx)
-      @mat.read(len_matrix)
-    end
-
-  end
-
-end
-
-__END__
-require 'chem/utils/subgraph/subcomp'
-
-module Chem
-  def self.open_db db_name
-    GraphDB.new(db_name)
-  end
-end
-
-class GraphDB
-
-#   def self.open db_name
-#     self.new(db_name)
-#   end
-
-#   def initialize db_name, mode="w"
-#     if mode == "a"
-#       @idx = File.open("#{db_name}.idx", "r+")
-#     else
-#       @idx = File.open("#{db_name}.idx", mode)
-#     end
-#     @typ = File.open("#{db_name}.typ", mode)
-#     @dat = File.open("#{db_name}.dat", mode)
-#     @num = File.open("#{db_name}.num", mode)
-#     @typ.print("NodeType ISAM")
-#     @dat.print("Adjacency ISAM")
-#   end
-
-  def insert mol
-    n_bytes = mol.nodes.length / ($ARC * 8.0)
-
-#     @typ.flush
-#     @dat.flush
-#     @idx.flush
-
-#     record_num = @idx.tell
-#     @idx.print [@typ.tell, @dat.tell].pack("ii")
-
-#     @typ.print [mol.nodes.length, mol.edges.length].pack("ii")
-#     @dat.print [n_bytes.ceil].pack("i")
-
-#     @typ.print mol.nodes.collect { |node|
-#        Chem::Element2Number[node.element]
-#     }.pack("i*")
-
-#     mol.nodes.each do |k|
-#       atom_type = mol.atoms[k].setup_graph(i)
-#       @typ.print [atom_type].pack("i")
-#     end
-
-
-#     @dat.print [n_bytes.ceil].pack("i")
-#     j = 0
-#     mol.atoms.keys.sort.each do |k|
-#       0.upto(n_bytes.ceil - 1) do |o|
-#         i = 0
-#         mol.atoms[k].set_neighbor
-#         0.upto($ARC * 8 - 1) do |m|
-#           i += mol.atoms[k].neighbor.include?(mol.atoms[m + 8 * $ARC * o + 1]) ? 2**m : 0
-#         end
-#         @dat.print [i].pack("L")
-#       end
-#       j += 1
-#     end
-#     #p mol.adjacency_list
-#     mol.connection.each do |c|
-#       puts "%040b" % c
-#     end
-    #record_num
-  end
-end

data/test/test_sssr.rb

@@ -1,18 +0,0 @@
-# $Id: test_sssr.rb 65 2005-10-25 17:17:36Z tanaka $
-
-require 'chem/utils/sssr'
-
-require 'test/all'
-require 'test/ctab_test'
-
-class SssrTest < Test::Unit::TestCase
-
-  def setup
-  end
-
-  def test_coronen
-    coronen = Chem.open_mol($data_dir + '/A_21/coronen.mol')
-    coronen.find_sssr
-  end
-
-end

data/test/test_subcomp.rb

@@ -1,37 +0,0 @@
-# $Id: test_subcomp.rb 101 2006-01-06 22:26:49Z tanaka $
-
-require 'test/unit'
-require 'test/all'
-
-require 'chem'
-
-class SubcompTest < Test::Unit::TestCase
-
-  def setup
-    @mol = Chem.open_mol($data_dir + 'hypericin.mol')
-  end
-
-#   def test_mol
-#     mol = Chem.open_mol($data_dir + 'hypericin.mol')
-#     #assert_equal(mol.nodes.length, mol.match_by_ullmann(mol).length)
-#   end
-
-#   def test_match_by_atom
-#     mol2 = Chem.parse_smiles("CCCBrCC")
-#     mol = Chem.parse_smiles("CCBr")
-#     assert_equal(mol.nodes.length, mol.match_by_ullmann(mol2).length);
-#   end
-
-  def test_search
-    @mol.match_by_ullmann(@mol)
-  end
-
-#   def test_exhaustive
-#     cyclopropane = SMILES("C1CCC1")
-#     match = cyclopropane.match_by_ullmann(cyclopropane)
-#     assert_equal([0, 1, 2, 3], match)
-#     match = cyclopropane.match_exhaustively(cyclopropane)
-#   end
-
-end
-