Class: Chem::CDX::CDX
Constant Summary
Constants included
from Molecule
Molecule::EpsHeader, Molecule::MDLCountLineFormat
Instance Attribute Summary
Attributes included from Molecule
#name, #source
Attributes included from Graph
#adjacencies, #edges, #nodes
Class Method Summary
collapse
Instance Method Summary
collapse
Methods included from Molecule
#-, #assign_2d_geometry, #breadth_first_search, #canonical_ring, #composition, #connected?, #deep_dup, #delete, #delete_bond, #depth_first_search, #divide, #find_smallest_ring, #find_sssr, #induced_sub, #molecular_weight, #n_hydrogen, #oxidation_number, #save, #save_as_mdl, #save_as_pdf, #search_pubchem, #subset_in_composition?, #to_cansmi, #to_eps, #to_sybyl, #trim
Methods included from Graph
#adj_matrix, #adjacency_list, #adjacent_to, #clustering_coefficient, #connection, #match_by_adj_mat, #match_by_ullmann, #match_exhaustively, #matchable, #matchable_old, #morgan
Constructor Details
#initialize ⇒ CDX
Returns a new instance of CDX.
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# File 'lib/chem/db/cdx.rb', line 1328
def initialize
@mols = Array.new
@end_object = [0x0000].pack('s')
@object_pool = {}
end
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Class Method Details
.cdx_create_object(object_type, str) ⇒ Object
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# 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 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 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 return 'fix me'
when :CDXCurvePoints3D return 'fix me'
when :CDXElementList return 'fix me'
when :CDXFontTable 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]
start += 6 + font.length
font_table.push_font(font)
end
return font_table
when :CDXFormula 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]) when :CDXObjectIDArray
return CDXObjectIDArray.new(str.unpack('V*'))
when :CDXObjectIDArrayWithCounts return 'fix me'
when :CDXObjectID
return CDXObjectID.new(str.unpack('L')[0])
when :CDXRepresentsProperty 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 return CDXFontStyle.new(str[0, 10].unpack('v4'))
when :CDXDate return 'fix me'
when :CDXLineStarts return 'fix me'
when :INT16ListWithCounts return 'fix me'
when :Unformatted
return Unformatted.new(str.unpack('H*')[0].upcase)
else
p object_type
return str
end
end
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.open(filename) ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1215
def self.open filename
CDX.new filename
end
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Instance Method Details
#cdxml_create_object(object_type, att) ⇒ Object
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# 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 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 :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 :CDXObjectID
return CDXObjectID.new(att.to_i)
when :CDXString cdxstring = CDXString.new
cdxstring.push_string(att)
return cdxstring
when :Unformatted
return Unformatted.new(att)
else
p object_type
return "cdxml_create_object not supported data type! please fix me!"
end
end
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#cdxml_open(filename) ⇒ Object
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# 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
end
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#each ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1350
def each
end
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#make_p ⇒ Object
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# 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|
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
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#objects ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1223
def objects
@objects
end
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#open(filename) ⇒ Object
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# 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 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 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
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#pool ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1227
def pool
@object_pool
end
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#push_mol(mol) ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1168
def push_mol mol
@mols.push(mol)
end
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#recurse_cdxml(element, parent) ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1354
def recurse_cdxml element, parent
obj = CDXObject.new(element.name, 0)
case element.name
when 'color' when 's' obj.properties['']
when 'font' else
element.attributes.each do |key, att|
if 'id' == key
obj.object_id = att.to_i
else
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'] else
object_id = @object_id
@object_id += 1
end
obj.objects[@object_id] = recurse_cdxml(el, obj)
@object_id += 1
end
obj
end
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#set_id(id) ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1180
def set_id id
return [id].pack('V')
end
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#to_bin ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1172
def to_bin
return Bin_header + @objects.to_bin
end
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#to_xml ⇒ Object
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# File 'lib/chem/db/cdx.rb', line 1176
def to_xml
return Xml_header + @objects.to_xml
end
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