Class: Chem::CDX::CDX

Inherits:

Object

• Object
• Chem::CDX::CDX

Includes:

Molecule

Defined in:

lib/chem/db/cdx.rb

Constant Summary

Constants included from Molecule

Molecule::DESCRIPTORNAME, Molecule::ELEMNUM, Molecule::EpsHeader, Molecule::MDLCountLineFormat, Molecule::MDLHeaderLine2Format

Instance Attribute Summary

Attributes included from Molecule

#cdk2atom, #cdk_mol, #name, #ob_mol, #source

Attributes included from Graph

#adjacencies, #edges, #nodes

Class Method Summary

• .cdx_create_object(object_type, str) ⇒ Object
• .open(filename) ⇒ Object

Instance Method Summary

• #cdxml_create_object(object_type, att) ⇒ Object
• #cdxml_open(filename) ⇒ Object
• #each ⇒ Object
• #initialize ⇒ CDX constructor

  A new instance of CDX.

• #make_p ⇒ Object
• #objects ⇒ Object
• #open(filename) ⇒ Object
• #pool ⇒ Object
• #push_mol(mol) ⇒ Object
• #recurse_cdxml(element, parent) ⇒ Object
• #set_id(id) ⇒ Object
• #to_bin ⇒ Object
• #to_xml ⇒ Object

Methods included from Molecule

#-, #adjacent_index, #assign_2d_geometry, #bit_mat, #box_size, #breadth_first_search, #canonical_ring, #cdk_BCUT, #cdk_CPSA, #cdk_RotatableBondsCount, #cdk_calc_descriptor, #cdk_calc_descriptors, #cdk_find_all_rings, #cdk_fingerprint, #cdk_gasteiger_marsili_partial_charges, #cdk_generate_2D, #cdk_generate_randomly, #cdk_generate_vicinity, #cdk_hose_code, #cdk_hueckel, #cdk_mcs, #cdk_properties, #cdk_rule_of_file, #cdk_save_as, #cdk_setup, #cdk_sssr, #cdk_wiener_numbers, #cdk_xlogp, #composition, #connected?, #deep_dup, #delete, #delete_bond, #depth_first_search, #divide, #f_dfs, #find_smallest_ring, #find_sssr, #fingerprint, #generate_pubchem_subskey, #hilight, #induced_sub, #match, #match_by_ullmann, #method_missing, #molecular_weight, #n_hydrogen, #ob_export_as, #ob_save_as, #oxidation_number, #pubchem_subskeys, #remove_hydrogens!, #save, #save_as_mdl, #save_as_pdf, #subset_in_composition?, #to_cansmi, #to_eps, #to_inchi, #to_sybyl, #typ_str, #use_open_babel

Methods included from Graph

#adjacent_to, #clustering_coefficient, #morgan, #terminal_nodes

Constructor Details

#initialize ⇒ CDX

Returns a new instance of CDX.

# File 'lib/chem/db/cdx.rb', line 1328

def initialize
  @mols = Array.new
  @end_object = [0x0000].pack('s')

  @object_pool = {}
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Chem::Molecule

Class Method Details

.cdx_create_object(object_type, str) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1231

def self.cdx_create_object object_type, str
  case object_type
  when :CDXCoordinate
    return CDXCoordinate.new(str.unpack('l')[0])
  when :CDXPoint2D
    xy = str.unpack("V2")
    return CDXPoint2D.new(xy[1], xy[0])
  when :CDXPoint3D#fix me
    return 'fix me'
  when :CDXRectangle
    bound = str.unpack("V4")
    return CDXRectangle.new(bound[1], bound[0], bound[3], bound[2])
  when :CDXBoolean
    return CDXBoolean.new(str[0] == 0 ? false : true)
  when :CDXBooleanImplied
    return CDXBooleanImplied.new(str[0] == 0 ? false : true)
  when :CDXColorTable # fix me
    ct = CDXColorTable.new
    kaisu = str.unpack("v")[0]
    start = 2
    1.upto(kaisu) do |n|
      rgb = str[start, 6].unpack("v3")
      ct.push(rgb[0], rgb[1], rgb[2])
      start += 6
    end
    return ct
  when :CDXCurvePoints #fix me
    return 'fix me'
  when :CDXCurvePoints3D #fix me
    return 'fix me'
  when :CDXElementList #fix me
    return 'fix me'
  when :CDXFontTable #fix me
    font_table = CDXFontTable.new
    font_table.platform = str[0..1].unpack('v')[0]
    n = str[2..3].unpack('v')[0]
    start = 4
    n.times do |n|
      font = Font_class.new
      font.font_id = str[start, 2].unpack('v')[0]
      font.charset = str[start+2, 2].unpack('v')[0]
      font.length = str[start+4, 2].unpack('v')[0]
      font.name = str[start+6, font.length].unpack('a*')[0]
      #          p font.name
      start += 6 + font.length
      font_table.push_font(font)
    end
    return font_table
  when :CDXFormula #fix me
    return 'fix me'
  when :INT8
    return Int8.new(str.unpack('c')[0])
  when :UINT32
    return Uint32.new(str.unpack("V")[0])
  when :INT32
    return Int32.new(str.unpack("V")[0])
  when :UINT16
    return Uint16.new(str.unpack("v")[0])
  when :INT16
    return Int16.new(str.unpack("s")[0])
  when :UINT8
    return Uint8.new(str.unpack('C')[0])
  when :FLOAT64
    return Float64.new(str.unpack('d')[0])# fix me
  when :CDXObjectIDArray
    return CDXObjectIDArray.new(str.unpack('V*'))
  when :CDXObjectIDArrayWithCounts #fix me
    return 'fix me'
  when :CDXObjectID
    return CDXObjectID.new(str.unpack('L')[0])
  when :CDXRepresentsProperty #fix me
    return 'fix me'
  when :CDXString
    cdxstring = CDXString.new
    n = str[0..1].unpack('v')[0]
    n.times do |nn|
      start = 2 + 10 * nn
      cdxstring.push_style(str[start, 10].unpack('v5'))
    end
    cdxstring.push_string(str[(2+10*n)..-1].unpack('a*')[0])
    return cdxstring
  when :CDXFontStyle# fix me
    return CDXFontStyle.new(str[0, 10].unpack('v4'))
  when :CDXDate# fix me
    return 'fix me'
  when :CDXLineStarts# fix me
    return 'fix me'
  when :INT16ListWithCounts# fix me
    return 'fix me'
  when :Unformatted
    return Unformatted.new(str.unpack('H*')[0].upcase)
  else
    p object_type
    return str
  end
end

.open(filename) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1215

def self.open filename
  CDX.new filename
end

Instance Method Details

#cdxml_create_object(object_type, att) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1384

def cdxml_create_object object_type, att
  case object_type
  when :CDXStyle
    p att
  when :CDXObject
    p att
  when :CDXCoordinate
    return CDXCoordinate.new(att.to_i)
  when :CDXPoint2D
    return CDXPoint2D.new(att.split[0].to_i * 65536, att.split[1].to_i * 65536)
  when :CDXPoint3D#fix me
    return 'fix me'
  when :CDXRectangle
    bound = att.split
    return CDXRectangle.new(bound[0].to_i * 65536, bound[0].to_i * 65536, bound[3].to_i * 65536, bound[2].to_i * 65536)
  when :CDXBoolean
    return CDXBoolean.new(att == "yes")
  when :CDXBooleanImplied
    return CDXBooleanImplied.new(att == "yes")
    #       when :CDXColorTable # fix me
    #         ct = CDXColorTable.new
    #         p ct
    #         1.upto(kaisu) do |n|
    #           rgb = str[start, 6].unpack("v3")
    #           ct.push(rgb[0], rgb[1], rgb[2])
    #           start += 6
    #         end
    #         return ct
    #       when :CDXCurvePoints #fix me
    #         return 'fix me'
    #       when :CDXCurvePoints3D #fix me
    #         return 'fix me'
    #       when :CDXElementList #fix me
    #         return 'fix me'
    #       when :CDXFontTable #fix me
    #         font_table = CDXFontTable.new
    #         font_table.platform = str[0..1].unpack('v')[0]
    #         n = str[2..3].unpack('v')[0]
    #         start = 4
    #         font_class = Struct.new("Font", :font_id, :charset, :length, :name)
    #         n.times do |n|
    #           font = font_class.new
    #           font.font_id = str[start, 2].unpack('v')[0]
    #           font.charset = str[start+2, 2].unpack('v')[0]
    #           font.length = str[start+4, 2].unpack('v')[0]
    #           font.name = str[start+6, font.length].unpack('a*')[0]
    # #          p font.name
    #           start += 6 + font.length
    #           font_table.push_font(font)
    #         end
    #         return font_table
    #       when :CDXFormula #fix me
    #         return 'fix me'
  when :INT8
    return Int8.new(att.to_i)
  when :UINT32
    return Uint32.new(att.to_i)
  when :INT32
    return Int32.new(att.to_i)
  when :UINT16
    return Uint16.new(att.to_i)
  when :INT16
    return Int16.new(att.to_i)
  when :UINT8
    return Uint8.new(att.to_i)
  when :FLOAT64
    return Float64.new(att.to_i)
  when :CDXObjectIDArray
    return CDXObjectIDArray.new(att.split.collect{|i| i.to_i})
    #       when :CDXObjectIDArrayWithCounts #fix me
    #         return 'fix me'
  when :CDXObjectID
    return CDXObjectID.new(att.to_i)
    #       when :CDXRepresentsProperty #fix me
    #         return 'fix me'
  when :CDXString# may be fix me
    cdxstring = CDXString.new
    cdxstring.push_string(att)
    return cdxstring
    #         n = str[0..1].unpack('v')[0]
    #         n.times do |nn|
    #           start = 2 + 10 * nn
    #           cdxstring.push_style(str[start, 10].unpack('v5'))
    #         end
    #         cdxstring.push_string(str[(2+10*n)..-1].unpack('a*')[0])
    #         return cdxstring
    #       when :CDXFontStyle# fix me
    #         return CDXFontStyle.new(str[0, 10].unpack('v4'))
    #       when :CDXDate# fix me
    #         return 'fix me'
    #       when :CDXLineStarts# fix me
    #         return 'fix me'
    #       when :INT16ListWithCounts# fix me
    #         return 'fix me'
  when :Unformatted
    return Unformatted.new(att)
  else
    p object_type
    return "cdxml_create_object not supported data type! please fix me!"
  end
end

#cdxml_open(filename) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1335

def cdxml_open(filename)
  require 'rexml/document'

  @object_id = 0
  @objects = parent = CDXObject.new('CDXML', @object_id)
  @object_id += 1

  file = File.new(filename, "r")
  doc = REXML::Document.new(file)
  doc.elements.each do |element|
    parent.objects[@object_id] = recurse_cdxml(element, parent)
  end
  #      p parent
end

#each ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1350

def each
  # must return each mol
end

#make_p ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1184

def make_p
  @objects = CDXObject.new('CDXML', 0)
  object_id = 1
  cdxstring = CDXString.new
  cdxstring.push_string("test.cdxml")
  @objects.properties["Name"] = cdxstring
  page = CDXObject.new('page', object_id)
  @objects.objects[object_id] = page
  object_id += 1
  atomlist = {}
  @mols.last.atoms.each do |atom|
    #      1.upto(10) do |number|
    n = CDXObject.new('n', object_id)
    atomlist[atom] = n
    n.properties['Z'] = Int16.new(object_id)
    n.properties['p'] = CDXPoint2D.new((atom.x + 30) * 10 * 65536, (atom.y + 30) * 10 * 65536)
    n.properties['AS'] = Int16.new(1)
    n.properties['Element'] = Int16.new(atom.atomic_number)
    page.objects[object_id] = n
    object_id += 1
  end
  @mols.last.bonds.each do |bond|
    b = CDXObject.new('b', object_id)
    b.properties['E'] = CDXObjectID.new(atomlist[bond.e].object_id)
    b.properties['B'] = CDXObjectID.new(atomlist[bond.b].object_id)
    b.properties['Order'] = Int16.new(bond.v)
    page.objects[object_id] = b
    object_id += 1
  end
end

#objects ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1223

def objects
  @objects
end

#open(filename) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1486

def open(filename)
  input = File.open(filename, 'r')
  input.read(8)
  input.read(4)
  input.read(16)

  @objects = parent = CDXObject.new('CDXML', 0)
  parent.parent = parent

  sp = 0
  while !input.eof? do
    tag = input.read(2).unpack("v")[0]
    if tag == 0
      sp -= 1
      parent = parent.parent
    elsif (tag & 0x8000) == 0 # Property
      num = input.read(2).unpack("v")[0]
      bytes = input.read(num)
      puts "null number %04x " % tag if Cdx_value2name[tag] == nil
      STDOUT.flush
      parent.properties[Cdx_value2name[tag][0]] =
        CDX.cdx_create_object(Cdx_value2name[tag][1], bytes)
    elsif tag == nil
      next
    else                   # Object
      id = input.read(4).unpack('V')[0]
      object = CDXObject.new(Cdx_value2name[tag][0], id)
      object.name = Cdx_value2name[tag][0]
      @object_pool[id] = object
      parent.objects[id] = object
      object.parent = parent
      parent = object
    end
  end
  self
end

#pool ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1227

def pool
  @object_pool
end

#push_mol(mol) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1168

def push_mol mol
  @mols.push(mol)
end

#recurse_cdxml(element, parent) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1354

def recurse_cdxml element, parent
  obj = CDXObject.new(element.name, 0)
  case element.name
  when 'color'#fix me
  when 's'#fix me
    obj.properties['']
  when 'font'#fix me
  else
    element.attributes.each do |key, att|
      if 'id' == key
        obj.object_id = att.to_i
      else
        #            puts "%s %s" % [key, $cdx_name2value[key].inspect]
        obj.properties[key] = cdxml_create_object(Cdx_value2name[Cdx_name2value[key]][1], att)
      end
    end
  end
  element.elements.each do |el|
    if el.attributes['id']
      object_id = el.attributes['id']# fix me
    else
      object_id =  @object_id
      @object_id += 1
    end
    obj.objects[@object_id] = recurse_cdxml(el, obj)
    @object_id += 1
  end
  obj
end

#set_id(id) ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1180

def set_id id
  return [id].pack('V')
end

#to_bin ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1172

def to_bin
  return Bin_header + @objects.to_bin
end

#to_xml ⇒ Object

# File 'lib/chem/db/cdx.rb', line 1176

def to_xml
  return Xml_header + @objects.to_xml
end