Class: ChemScanner::Interpreter::Atom

Inherits:
Object
  • Object
show all
Defined in:
lib/chem_scanner/interpreter/element/atom.rb

Overview

Atom class

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(node, rw_mol) ⇒ Atom

Returns a new instance of Atom.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 10

def initialize(node, rw_mol)
  @rw_mol = rw_mol

  @node = node

  @type = node.type
  @ext_type = node.ext_type
  @atnum = node.atnum
  @num_hydrogens = node.num_hydrogens
  @charge = node.charge
  @iso = node.iso
  @x = node.x || 0
  @y = node.y || 0
  @point = node.point

  @is_alias = node.is_alias
  @alias_text = node.alias_text.strip
  @warning = node.warning
  @warning_data = node.warning_data

  @is_polymer = node.is_polymer
end

Instance Attribute Details

#alias_text ⇒ Object

Returns the value of attribute alias_text.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 7

def alias_text
  @alias_text
end

#charge ⇒ Object

Returns the value of attribute charge.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 7

def charge
  @charge
end

#ext_type ⇒ Object (readonly)

Returns the value of attribute ext_type.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 8

def ext_type
  @ext_type
end

#is_alias ⇒ Object

Returns the value of attribute is_alias.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 7

def is_alias
  @is_alias
end

#is_polymer ⇒ Object (readonly)

Returns the value of attribute is_polymer.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 8

def is_polymer
  @is_polymer
end

#point ⇒ Object (readonly)

Returns the value of attribute point.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 8

def point
  @point
end

#type ⇒ Object (readonly)

Returns the value of attribute type.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 8

def type
  @type
end

#warning ⇒ Object (readonly)

Returns the value of attribute warning.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 8

def warning
  @warning
end

#warning_data ⇒ Object (readonly)

Returns the value of attribute warning_data.



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 8

def warning_data
  @warning_data
end

Instance Method Details

#clone ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 80

def clone
  cnode = @node.clone
  clone = self.class.new(cnode, @rw_mol)
  clone.process

  clone
end

#get_idx ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 53

def get_idx
  get_rd_atom.get_idx
end

#get_rd_atom ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 49

def get_rd_atom
  @rw_mol.get_atom_with_bookmark(@node.id)
end

#id ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 57

def id
  @node.id
end

#inspect ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 61

def inspect
  (
    "#<Atom: id=#{@node.id}, " +
      "type: #{@type}, " +
      "external_type: #{@ext_type}, " +
      "atnum: #{@atnum}, " +
      "num_hydrogens: #{@num_hydrogens}, " +
      "charge: #{charge}, " +
      "iso: #{@iso}, " +
      "x: #{@x}, " +
      "y: #{@y}, " +
      "is_alias: #{is_alias}, " +
      "is_polymer: #{is_polymer}, " +
      "alias_text: #{alias_text}, " +
      "warning_data: #{@warning_data}, " +
      "warning: #{@warning} >"
  )
end

#process ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 33

def process
  # Set default to Carbon
  @atnum.negative? && @atnum = 6
  @rw_mol.add_atom(RDKitChem::Atom.new(@atnum), false)
  rd_atom = @rw_mol.get_last_atom
  @rw_mol.set_atom_bookmark(rd_atom, @node.id)

  @num_hydrogens >= 0 && rd_atom.set_num_explicit_hs(@num_hydrogens)
  rd_atom.set_formal_charge(@charge)
  rd_atom.set_isotope(@iso)
  conf = @rw_mol.get_conformer(0)
  conf.set_atom_pos(rd_atom.get_idx, RDKitChem::Point3D.new(@x, @y, 0))

  process_alias
end

#set_2d(coord_x, coord_y) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 88

def set_2d(coord_x, coord_y)
  @x = coord_x
  @y = coord_y

  conf = @rw_mol.get_conformer(0)
  conf.set_atom_pos(get_idx, RDKitChem::Point3D.new(@x, @y, 0))
end

#set_formal_charge(charge) ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 96

def set_formal_charge(charge)
  @charge = charge
  rd_atom = get_rd_atom
  rd_atom.set_formal_charge(charge)
end

#set_polymer ⇒ Object 



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# File 'lib/chem_scanner/interpreter/element/atom.rb', line 102

def set_polymer
  @is_alias = true
  @is_polymer = true
end