chemruby 0.9.3

data/lib/chem/db/tinker.rb

@@ -0,0 +1,77 @@
+#
+#   tinker.rb - TINKER
+#
+# http://dasher.wustl.edu/tinker/
+#
+#
+
+module Chem
+
+  module TINKER
+
+    class TinkerAtom
+
+      include Atom
+
+      attr_reader :x, :y, :z, :element, :connection
+      def initialize ff, x, y, z, connection
+        @x, @y, @z = x.to_f, y.to_f, z.to_f
+        @element = ff[0..0]
+        @connection = []
+        connection.each do |n|
+          @connection.push(n)
+        end
+      end
+    end
+
+    class TinkerBond
+
+      include Bond
+      
+      attr_accessor :b, :e, :v, :q
+      def initialize b, e
+        @b, @e = b, e
+      end
+    end
+
+    class TinkerMol
+      attr_reader :atoms, :bonds
+
+      def initialize
+        @atoms = {}
+        @bonds = []
+      end
+
+      def construct
+        @atoms.each_value do |a|
+          a.connection.each do |c|
+            raise "unknown atom number %s" % @atoms.inspect if !@atoms.has_key?(c)
+            bond = TinkerBond.new(a, @atoms[c])
+            @bonds.push(bond)
+          end
+        end
+      end
+
+    end
+
+    class TinkerReader
+
+      attr_reader :mol
+
+      def initialize input
+        puts input.readline
+        @mol = TinkerMol.new
+        input.each_line do |line|
+          number, ff, x, y, z, unknown, ary = line.split
+          atom = TinkerAtom.new(ff, x, y, z, ary)
+          @mol.atoms[number] = atom
+        end
+
+        @mol.construct
+      end
+
+    end
+
+  end
+
+end

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

@@ -0,0 +1,9 @@
+
+module Chem
+  module Molecule
+    def to_cansmi
+      require 'chem/db/cansmi.rb'
+      self.to_cansmi
+    end
+  end
+end

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

@@ -0,0 +1,24 @@
+
+module Chem
+
+  module Type
+    module CdxType
+
+      def self.detect_file file
+        File.extname(file) == '.cdx'
+      end
+
+      def self.parse file
+        #      require 'chem/db/cdx.rb'
+        mol = CDX::CDX.new
+        mol.open file
+      end
+
+      def self.detect_type type
+        type == :cdx
+      end
+    end
+  end
+
+  ChemTypeRegistry << Type::CdxType
+end

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

@@ -0,0 +1,31 @@
+
+
+module Chem
+
+  module Type
+    module GSpanType
+
+      def self.detect_file file
+        File.extname(file) == '.fp'
+      end
+
+      def self.parse file
+        # autoloaded
+        # require 'chem/db/gspan.rb'
+        Chem.parse_gspan(file)
+      end
+
+      def self.detect_type type
+        type == :gspan
+      end
+
+      def self.save mol, filename
+        #      require 'chem/db/gspan.rb'
+        Chem::GSpan.save(mol, filename)
+      end
+    end
+  end
+
+  ChemTypeRegistry << Type::GSpanType
+
+end

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

@@ -0,0 +1,28 @@
+
+module Chem
+
+  module Type
+    module KCFType
+
+      # Returns true if extension of file is .kcf and
+      # file name starts C-number
+      def self.detect_file file
+        File.extname(file) == '.kcf' && /C\d+/.match(file)
+      end
+
+      # Parse file as KCF
+      def self.parse file
+        require 'chem/db/kcf'
+        Chem::KEGG::KCF.new(File.open(file))
+      end
+
+      def self.detect_type type
+        type == :kcf
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::KCFType
+
+end

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

@@ -0,0 +1,26 @@
+module Chem
+
+  module Type
+    
+    module KCFGlycanType
+
+      def self.detect_file file
+        File.extname(file) == '.kcf' && /G\d+/.match(file)
+      end
+
+      def self.parse file
+        require 'chem/db/kcf_glycan'
+        mol = Chem::KEGG::KCFGlycan.new File.open(file)
+      end
+
+      def self.detect_type type
+        type == :kcf_glycan
+      end
+
+    end
+
+  end
+
+  ChemTypeRegistry << Type::KCFGlycanType
+
+end

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

@@ -0,0 +1,92 @@
+
+module Chem
+
+  module Type
+
+    module KeggReactionType
+
+      def self.detect_file filename
+        if File.basename(filename) == "reaction"
+          File.open(filename) do |file|
+            return true if /ENTRY       /.match(file.readline)
+          end
+        end
+      end
+
+      def self.parse file
+        Chem::KEGG::KeggReactionParser.new file
+      end
+
+      def self.detect_type type
+        type == :kegg_reaction
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::KeggReactionType
+
+  module Type
+
+    module KeggReactionMapType
+
+      def self.detect_file filename
+        return true if File.basename(filename) == 'reaction_mapformula.lst'
+      end
+
+      def self.parse file
+        Chem::KEGG::KeggReactionMapParser.new file
+      end
+
+      def self.detect_type type
+        type == :kegg_rxn_map
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::KeggReactionMapType
+
+  module Type
+    module KeggReactionLstType
+
+      def self.detect_file filename
+        return true if File.basename(filename) == 'reaction.lst'
+      end
+
+      def self.parse file
+        require 'chem/db/kegg.rb'
+        Chem::KEGG::KeggReactionLstParser.new file
+      end
+
+      def self.detect_type type
+        type == :kegg_rxn_lst
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::KeggReactionLstType
+
+  module Type
+    module KeggGlycanType
+
+      def self.detect_file filename
+        return true if File.basename(filename) == "glycan"
+      end
+
+      def self.parse file
+        require 'chem/db/kegg.rb'
+        Chem::KEGG::KeggGlycanParser.new file
+      end
+
+      def self.detect_type type
+        type == :kegg_glycan
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::KeggGlycanType
+
+end

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

@@ -0,0 +1,31 @@
+
+module Chem
+
+  module Type
+    module MdlMolType
+
+      def self.detect_file file
+        File.extname(file) == '.mol'
+      end
+
+      def self.parse file
+        # autloaded
+        require 'chem/db/mdl.rb'
+        mol = Chem::MDL::MdlMolecule.new
+        mol.open file
+      end
+
+      def self.detect_type type
+        type == :mdl
+      end
+
+      def self.save mol, filename, params = {}
+        # require 'chem/db/mdl.rb'
+        mol.save_as_mdl(filename)
+      end
+    end
+  end
+
+  ChemTypeRegistry << Type::MdlMolType
+
+end

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

@@ -0,0 +1,33 @@
+
+module Chem
+
+  module Type
+
+    module PDFType
+
+      def self.detect_file file
+        File.extname(file) == '.pdf'
+      end
+
+      # ChemRuby will never parse PDF ;)
+      def self.parse file
+        raise NotImplementedError
+      end
+
+      def self.detect_type type
+        type == :pdf
+      end
+
+      def self.save mol, filename, params = {}
+        require 'chem/db/pdf.rb'
+        open(filename, "w") do |out|
+          mol.save_as_pdf(out, params)
+        end
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::PDFType
+
+end

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

@@ -0,0 +1,31 @@
+
+module Chem
+
+  module Type
+    module PNGType
+
+      def self.detect_file file
+        ['.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
+        type == :png
+      end
+
+      def self.save mol, filename, params = {}
+        require 'RMagick'
+        require 'chem/db/rmagick.rb'
+        RMagickWriter.save(mol, filename, params)
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::PNGType
+
+end

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

@@ -0,0 +1,25 @@
+
+module Chem
+
+  module Type
+    module MdlRxnType
+
+      def self.detect_file file
+        File.extname(file) == '.rxn'
+      end
+
+      def self.parse file
+        mol = MdlReaction.new
+        mol.open_rxn file
+      end
+
+      def self.detect_type type
+        type == :rxn
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::MdlRxnType
+
+end

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

@@ -0,0 +1,25 @@
+
+module Chem
+
+  module Type
+    module SdfType
+
+      def self.detect_file file
+        File.extname(file) == '.sdf'
+      end
+
+      def self.parse file
+        require 'chem/db/sdf.rb'
+        MDL::SdfParser.parse file
+      end
+
+      def self.detect_type type
+        type == :sdf
+      end
+
+    end
+  end
+
+  ChemTypeRegistry << Type::SdfType
+
+end