chemruby 0.9.3

data/lib/chem/db/molconnz.rb

@@ -0,0 +1,12 @@
+#!/usr/local/bin/ruby
+
+molconn = open(ARGV.shift, "r")
+molconn.readline
+molconn.readline
+while !molconn.eof?
+  line = molconn.readline
+  if /-1/ !~ line
+    num, code, element, *connection = line.split(',')
+    puts connection.join(' ')
+  end
+end

data/lib/chem/db/mopac.rb

@@ -0,0 +1,88 @@
+#
+# chem/mopac.rb - MOPAC7 format class
+#
+
+require 'chem/molecule'
+require 'scanf'
+
+module Chem
+  module Mopac7
+    class MopacReader
+      def initialize entry
+        ea = entry.split("\n")
+        n_line = 0
+        0.upto(ea.length) do |n|
+          n_line = n if /SCF FIELD WAS ACHIEVED/ =~ ea[n]
+        end
+        n_atom = 0
+        n_line.upto(ea.length) do |n|
+          line = ea[n]
+          if /FINAL HEAT OF FORMATION =\s+(\d+.\d+) KCAL/ =~ line
+            @heat_of_formation = $1.to_f
+          elsif /TOTAL ENERGY/ =~ line
+            @total_energy = line.scanf("TOTAL ENERGY            =%f")
+          elsif /ELECTRONIC ENERGY/ =~ line
+            @electronic_energy = line.scanf("ELECTRONIC ENERGY       =%f")
+          elsif /CORE-CORE REPULSION/ =~ line
+            @core_core_repulstion = line.scanf("CORE-CORE REPULSION     =%f")
+          elsif /GRADIENT NORM/ =~ line
+            @gradient_norm = line.scanf("GRADIENT NORM           =%f")
+          elsif /IONIZATION POTENTIAL/ =~ line
+            @ionization_potential = line.scanf("IONIZATION POTENTIAL    =%f")
+          elsif /NO. OF FILLED LEVELS/ =~ line
+            @no_of_filled_levels = line.scanf("NO. OF FILLED LEVELS    =%d")
+          elsif /MOLECULAR WEIGHT/ =~ line
+            @molecular_weight = line.scanf("MOLECULAR WEIGHT        =%f")
+          elsif /    ATOM   CHEMICAL  BOND LENGTH    BOND ANGLE     TWIST ANGLE/ =~ line
+            Range.new(n+4, ea.length).each do |l|
+              if '' == ea[l]
+                n_atom = l - n - 4
+                break
+              end
+              if /^      1/ =~ ea[l]
+                ea[l].scanf("%d%s")
+              elsif /^      2/ =~ ea[l]
+                ea[l].scanf("%d%s%f*%d")
+              elsif /^      3/ =~ ea[l]
+                ea[l].scanf("%d%s%f*%f*%d%d")
+              else
+                ea[l].scanf("%d%s%f*%f*%f*%d%d%d")
+              end
+            end
+          elsif /INTERATOMIC DISTANCES/ =~ line
+            @distances = {}
+            reduced = 0
+            first = n + 3 + 1
+
+            while n_atom - reduced> 0
+              Range.new(first, first + n_atom - reduced - 1).each do |l|
+                ary =  ea[l].scanf("%s%d"+"%f"* (l - first + 1))
+                1.upto(l - first + 1) do |ll|
+                  @distances[[ary[1], ll + reduced]] = ary[ll + 1]
+                  @distances[[ll + reduced, ary[1]]] = ary[ll + 1]
+                end
+              end
+              first = first + n_atom - reduced + 3
+              reduced = reduced + 6
+            end
+#             1.upto(n_atom) do |nn|
+#               print "%3d" % nn
+#               1.upto(n_atom) do |mm|
+#                 print " %3f" % @distances[[nn, mm]] if @distances[[nn, mm]]
+#               end
+#               puts
+#             end
+          elsif /MOLECULAR POINT GROUP/ =~ line
+            @symmetry = line.scanf("MOLECULAR POINT GROUP   :%s")
+          elsif /EIGENVECTORS/
+            
+          end
+        end
+      end
+      def MopacReader.open_out file
+        MopacReader.new(File.open(file, 'r').gets(nil))
+      end
+    end
+  end
+end
+

data/lib/chem/db/msi.rb

@@ -0,0 +1,107 @@
+#!/usr/local/bin/ruby
+
+require 'chem/molecule'
+require 'scanf'
+
+module Chem
+
+  # parser for msi file
+  # MSI : Molecular Simulation Inc. 
+  module MSI
+
+    module MSIObject
+
+      attr_accessor :parent, :child, :prop
+
+      def initialize n = 0
+        @prop = {}
+        @n = n
+      end
+
+      def child= child
+        @child = child
+        child.parent = self
+      end
+
+    end
+
+    class MSIFile
+      include MSIObject
+    end
+
+    class Model < Molecule
+      include MSIObject
+    end
+
+    class MSIAtom < Atom
+
+      include MSIObject
+
+      def b
+        @prop['Atom1']
+      end
+
+      def e
+        @prop['Atom2']
+      end
+
+    end
+
+    class MSIBond < Bond
+      include MSIObject
+    end
+
+    class MSIReader
+
+      def MSIReader.open input
+        MSIReader.new(input)
+      end
+
+      def model
+        @top
+      end
+
+      def initialize input
+        @objects = {}
+        @input = input
+      end
+
+      def read
+        current = MSIFile.new
+        @top = current
+        @input.each_line do |l|
+          if /\((\d+) (\S+)/ =~ l
+            case $2
+            when 'Model'
+              current.child = Model.new($1)
+              current = current.child
+            when 'Atom'
+              current.child = MSIAtom.new($1)
+              current = current.child
+            when 'Bond'
+              current.child = MSIBond.new($1)
+              current = current.child
+            end
+            @objects[$1.to_i] = current
+          elsif /\(A (\S) (\S+) (.+)\)/ =~ (l)
+            case $1
+            when 'C'
+              current.prop[$2] = $3
+            when 'I'
+              current.prop[$2] = $3.to_i
+            when 'O'
+              current.prop[$2] = @objects[$3.to_i]
+            when 'D'
+              current.prop[$2] = $3.scanf("(%f %f %f")
+            end
+          elsif /\s+\)/ =~ l
+            current = current.parent
+          end
+        end
+      end
+
+    end
+
+  end
+end
+

data/lib/chem/db/pdb_dic.rb

@@ -0,0 +1,115 @@
+require 'chem/molecule'
+
+module Chem
+  class PdbDic
+    class PdbDicAtom < Atom
+      attr_reader :atom_id, :neighbor
+      def initialize atom_id
+        @bonds = []
+        @neighbor = []
+        @atom_id = atom_id
+        set_element
+      end
+      def set_element
+        # Heuristically set element. Any idea?
+        case @atom_id.gsub(/(\d|[*'\"])/, '').upcase
+        when /S/
+          @element = 'S'
+        when 'B'
+          @elmenet = 'B'
+        when /^BR/
+          @element = 'Br'
+        when /^MO/
+          @element = 'MO'
+        when /^W/
+          @element = 'W'
+        when /^I/
+          @element = 'I'
+        when /CL/
+          @element = 'Cl'
+        when /^A?B?C/
+          @element = 'C'
+        when /^A?B?H/
+          @element = 'H'
+        when /^A?N/
+          @element = 'N'
+        when /^A?O/
+          @element = 'O'
+        when /^A?P/
+          @element = 'P'
+        when /^F/
+          @element = 'F'
+        else
+          puts @atom_id
+        end
+      end
+    end
+    class PdbDicBond < Bond
+      attr_accessor :v
+    end
+    class PdbDicMolecule < Molecule
+      attr_reader :atoms, :bonds
+      def initialize
+        @atoms = {}
+        @bonds = []
+      end
+    end
+
+    attr_reader :mols
+    def initialize file, &block
+      @mols = {}
+      parse(file, &block)
+    end
+
+    def parse file, &block
+      i = 0
+      @input = File.open(file, 'r')
+      res = nil
+      while !@input.eof?
+        line = @input.readline
+        case line
+        when /^RESIDUE/
+          mol = PdbDicMolecule.new
+          res = line.split[1]
+          @mols[res] = mol
+#           if line.split[1] == 'ACY'
+#             puts 'Found ACY'
+#             exit
+#           end
+#          puts "'%s'" % line[0..5]
+        when /^CONECT/
+          atom = mol.atoms[line[11..15].strip] ||= PdbDicAtom.new(line[11..15].strip)
+          line[20..-1].chop.split.each do |atom_id|
+            if ! mol.atoms[atom_id]
+              atom2 = PdbDicAtom.new(atom_id)
+              mol.atoms[atom_id] = atom2
+              bond = PdbDicBond.new
+              bond.b = atom
+              bond.e = atom2
+              bond.v = 1
+              mol.bonds.push(bond)
+            end
+          end
+        when "\n"
+          mol.bonds.each do |bond|
+            bond.b.neighbor.push(bond.e) if ! bond.b.neighbor.include?(bond.e)
+            bond.e.neighbor.push(bond.b) if ! bond.e.neighbor.include?(bond.b)
+          end
+#          i += 1
+          if block
+            yield res, mol
+          end
+          return if i >= 100
+        else
+#          puts line
+        end
+      end
+    end
+    def PdbDic.each file, &block
+      PdbDic.new(file, &block)
+    end
+    def PdbDic.open(file, &block)
+      PdbDic.new(file, &block)
+    end
+  end
+end

data/lib/chem/db/pdf.rb

@@ -0,0 +1,131 @@
+
+require 'chem/db/vector'
+
+module Chem
+  class PDFWriter
+
+    include Writer
+
+    PDFHeader = <<EOL
+%PDF-1.3
+1 0 obj
+<< /Type /Catalog
+/Outlines 2 0 R
+/Pages 3 0 R
+>>
+endobj
+2 0 obj
+<< /Type /Outlines
+/Count 0
+>>
+endobj
+3 0 obj
+<< /Type /Pages
+/Kids [ 4 0 R]
+/Count 1
+>>
+endobj
+4 0 obj
+<< /Type /Page
+/Parent 3 0 R
+EOL
+
+    PDFMiddle = <<EOL
+/Contents 5 0 R
+/Resources << /ProcSet 6 0 R
+/Font << /F1 7 0 R >>
+>>
+>>
+endobj
+5 0 obj
+EOL
+
+    PDFFooter = <<EOL
+endstream
+endobj
+6 0 obj
+[ /PDF /Text ]
+endobj
+7 0 obj
+<< /Type /Font
+/Subtype /Type1
+/Name /F1
+/BaseFont /Helvetica
+/Encoding /MacRomanEncoding
+>>
+endobj
+xref
+0 8
+0000000000 65535 f
+0000000009 00000 n
+0000000074 00000 n
+0000000120 00000 n
+0000000179 00000 n
+0000000364 00000 n
+0000000466 00000 n
+0000000496 00000 n
+trailer
+<< /Size 8
+/Root 1 0 R
+>>
+startxref
+625
+%%EOF
+EOL
+
+    def initialize mol, params
+      params[:size]        ||= [180, 200]
+      params[:orig_point]  ||= [0, 0]
+      params[:margin]      ||= [10, 10]
+      @default_pointsize = (params[:pointsize] ? params[:pointsize] : 14)
+      super
+    end
+
+    def line(from, to, color)
+      @vect << color.join(' ') + " RG"
+      @vect << "#{from[0]} #{from[1]} m"
+      @vect << "#{to[0]} #{to[1]} l"
+      @vect << "S"
+    end
+
+    def fill(nodes, color)
+      @vect << "0 w"                       # setline width
+      @vect << color.join(' ') + " RG"     # set setrgbcolor
+      @vect << "%d %d m" % [nodes[0][0], nodes[0][1]]
+      nodes[1..-1].each do |vect|
+        @vect << "%d %d l" % [vect[0], vect[1]]
+      end
+      @vect << "b"
+      @vect << "1 w"                       # setline width
+    end
+
+    def text(str, x, y, params = {})
+      @vect << "BT"
+      @vect << "/F1 #{@params[:font]} Tf"
+      @vect << "1 0 0 1 #{x - @params[:font] * 0.4} #{y - @params[:font] * 0.4} Tm"
+      @vect << "(#{str}) Tj"
+      @vect << "ET"
+    end
+
+    def save out
+      @out = out
+      @params[:font] ||= 12.0
+      @params[:orig_point] ||= [0, 0]
+      @vect = ["q"]
+      @vect << "1 0 0 1 #{@params[:orig_point][0]} #{@params[:orig_point][1]} cm"
+      @out.puts(PDFHeader)
+      @out.puts "/MediaBox [ 0 0 %d %d]" % @params[:size]
+      @out.puts PDFMiddle
+
+      draw_body
+
+      @vect << "Q"
+      str = @vect.join("\n")
+
+      @out.puts "<< /Length #{str.length} >> stream"
+      @out.puts str
+      @out.puts PDFFooter
+    end
+
+  end
+end