Class: ChemScanner::ChemDraw::FragmentNode

Inherits:
BaseNode
  • Object
show all
Defined in:
lib/chem_scanner/chem_draw/node/fragment_node.rb

Overview

CDX Node parser

Constant Summary

Constants included from BaseValue

BaseValue::ARROW_NOGO_CROSS, BaseValue::CDXML_ARROW_TYPE, BaseValue::CDXML_ATOM_EXTERNAL_CONNECTION_TYPE, BaseValue::CDXML_CDX_POINT, BaseValue::CDXML_GRAPHIC_TYPE, BaseValue::CDXML_LINE_TYPE, BaseValue::CDXML_NODE_TYPE, BaseValue::CDXML_ORBITAL_TYPE, BaseValue::CDXML_OVAL_TYPE, BaseValue::TEXT_ATTRIBUTES

Instance Attribute Summary collapse

Attributes inherited from BaseNode

#id, #parser, #parser_type, #polygon

Instance Method Summary collapse

Methods inherited from BaseNode

#assign_center, #bounding_box, #cdx_read, #cdxml_read, #center_x, #center_y, #get_tempid, #pre_parse_node, #read, #set_cdx, #set_cdxml

Methods included from BaseValue

#binary_chunks, #cdx_styles, #cdx_text, #cdxml_text, #do_unhandled, #point_2d, #point_3d, #polygon_from_bb, #read_bounding_box, #read_ids, #read_int, #read_type, #read_value

Constructor Details

#initialize(parser, parser_type, id) ⇒ FragmentNode 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 17

def initialize(parser, parser_type, id)
  super(parser, parser_type, id)

  @num_hydrogens = -1
  @atnum = -1
  @spin = 0
  @charge = 0
  @iso = 0
  @color = 0
  @type = -1
  @ext_type = -1
  @alias_text = ""
  @warning = false
  @warning_data = ""
  @is_alias = false

  @nested_fragment = {}
  @nested_text = {}
  @expanded = false
  @is_polymer = false
end

Instance Attribute Details

#alias_text ⇒ Object

Returns the value of attribute alias_text.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def alias_text
  @alias_text
end

#atnum ⇒ Object

Returns the value of attribute atnum.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def atnum
  @atnum
end

#charge ⇒ Object

Returns the value of attribute charge.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def charge
  @charge
end

#color ⇒ Object

Returns the value of attribute color.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def color
  @color
end

#expanded ⇒ Object

Returns the value of attribute expanded.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def expanded
  @expanded
end

#ext_type ⇒ Object

Returns the value of attribute ext_type.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def ext_type
  @ext_type
end

#fragment ⇒ Object

Returns the value of attribute fragment.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def fragment
  @fragment
end

#is_alias ⇒ Object

Returns the value of attribute is_alias.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def is_alias
  @is_alias
end

#is_polymer ⇒ Object

Returns the value of attribute is_polymer.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def is_polymer
  @is_polymer
end

#iso ⇒ Object

Returns the value of attribute iso.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def iso
  @iso
end

#nested_fragment ⇒ Object

Returns the value of attribute nested_fragment.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def nested_fragment
  @nested_fragment
end

#nested_text ⇒ Object

Returns the value of attribute nested_text.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def nested_text
  @nested_text
end

#num_hydrogens ⇒ Object

Returns the value of attribute num_hydrogens.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def num_hydrogens
  @num_hydrogens
end

#point ⇒ Object

Returns the value of attribute point.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def point
  @point
end

#spin ⇒ Object

Returns the value of attribute spin.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def spin
  @spin
end

#type ⇒ Object

Returns the value of attribute type.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def type
  @type
end

#warning ⇒ Object

Returns the value of attribute warning.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def warning
  @warning
end

#warning_data ⇒ Object

Returns the value of attribute warning_data.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def warning_data
  @warning_data
end

#x ⇒ Object

Returns the value of attribute x.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def x
  @x
end

#y ⇒ Object

Returns the value of attribute y.



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 12

def y
  @y
end

Instance Method Details

#clone ⇒ Object 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 121

def clone
  cloned = self.class.new(@parser, @parser_type, nil)
  cloned.num_hydrogens = @num_hydrogens
  cloned.atnum = @atnum
  cloned.spin = @spin
  cloned.charge = @charge
  cloned.iso = @iso
  cloned.color = @color
  cloned.type = @type
  cloned.alias_text = @alias_text
  cloned.warning = @warning
  cloned.warning_data = @warning_data
  cloned.is_alias = @is_alias
  cloned.expanded = @expanded

  cloned.nested_fragment = {}
  cloned.nested_text = {}
  @nested_fragment.each { |k, v| cloned.nested_fragment[k] = v }
  @nested_text.each { |k, v| cloned.nested_text[k] = v }

  cloned
end

#has_nil_coord? ⇒ Boolean 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 104

def has_nil_coord?
  (@x.nil? || @y.nil?) && @polygon.nil?
end

#leftbottom ⇒ Object 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 96

def leftbottom
  @polygon.nil? ? point : @polygon.bounding_box.leftbottom
end

#parse_node(tag, nid, data) ⇒ Object

rubocop:disable Methods/PerceivedComplexity



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 40

def parse_node(tag, nid, data)
  ref = @props_ref[tag]
  ref = ref.nil? ? @obj_ref[tag] : ref

  case ref
  when "Node_Element" then @atnum = read_value(tag, data)
  when "Atom_Radical" then @spin = read_value(tag, data)
  when "Atom_Isotope" then @iso = read_value(tag, data)
  when "Fragment"
    frag = Fragment.new(@parser, @parser_type, nid)
    frag.read
    @nested_fragment[nid] = frag
  when "Atom_GenericNickname"
    nickname = send("#{@parser_type}_text", data)
    @generic_nickname = nickname.first[:text] unless nickname.empty?
  when "Node_Type"
    @type = read_type(tag, data, CDXML_NODE_TYPE)
    @is_alias = ALIAS_VALUES.include?(@type)
  when "2DPosition" then @x, @y = read_value(tag, data)
  when "Atom_Charge" then @charge = read_value(tag, data)
  when "Text"
    @text = Text.new(@parser, @parser_type, nid, true)
    # NOTE: MUST read first in order to maintain CDX reader
    @text.read
    @polygon = @text.polygon

    @nested_text[@text.id] = @text
  when "ChemicalWarning"
    @warning = true
    @warning_data = @parser_type == "cdxml" ? data.text : data
  when "Atom_NumHydrogens" then @num_hydrogens = read_value(tag, data)
  when "ForegroundColor" then @color = read_value(tag, data)
  when "Atom_ExternalConnectionType"
    @ext_type = read_type(tag, data, CDXML_ATOM_EXTERNAL_CONNECTION_TYPE)
  else do_unhandled(tag)
  end
end

#post_parse_node ⇒ Object

rubocop:enable Methods/PerceivedComplexity



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 79

def post_parse_node
  @point = Geometry::Point.new(@x, @y)

  if !@text.nil? && !@text.value.empty?
    @alias_text = @text.value
    return
  end

  interpreter = ChemScanner::Interpreter
  if !@generic_nickname.nil? &&
      interpreter.rgroup_atom?(@generic_nickname)
    @is_alias = true
    @type = 7
    @alias_text = @generic_nickname
  end
end

#righttop ⇒ Object 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 100

def righttop
  @polygon.nil? ? point : @polygon.bounding_box.righttop
end

#set_expanded ⇒ Object 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 112

def set_expanded
  @expanded = true
end

#set_is_polymer ⇒ Object 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 116

def set_is_polymer
  @is_alias = true
  @is_polymer = true
end

#set_type(type) ⇒ Object 



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# File 'lib/chem_scanner/chem_draw/node/fragment_node.rb', line 108

def set_type(type)
  @type = type
end