Table of Contents

Class: atom bkchem/atom.py

Class ATOM --------------------------------------------------

Base Classes   
meta_enabled
area_colored
point_drawable
text_like
child
Methods   
__get_charge
__get_drawn
__get_font_size
__get_molecule
__get_multiplicity
__get_name
__get_parent
__get_pos
__get_show
__get_show_hydrogens
__get_type
__get_valency
__get_x
__get_xml_text
__get_y
__get_z
__init__
__set_charge
__set_font_size
__set_molecule
__set_multiplicity
__set_name
__set_pos
__set_show
__set_show_hydrogens
__set_type
__set_valency
__set_x
__set_xml_text
__set_y
__set_z
__str__
_set_mark_helper
_set_name
atoms_bound_to
bbox
create_mark
decide_pos
delete
draw
find_place_for_mark
focus
generate_marks_from_cheminfo
get_charge_from_marks
get_formula_dict
get_free_valency
get_ftext
get_occupied_valency
get_package
get_text
get_xy
get_xyz
lift
move
move_to
read_package
redraw
reposition_marks
scale_font
select
set_mark
set_name
set_valency_from_name
split_element_and_charge
toggle_center
transform
unfocus
unselect
update_after_valency_change
update_font
  __get_charge 
__get_charge ( self )

charge

  __get_drawn 
__get_drawn ( self )

is the atoms drawn? on the paper or just virtual

drawn

  __get_font_size 
__get_font_size ( self )

font_size (override of text_like.xml_text)

  __get_molecule 
__get_molecule ( self )

molecule

  __get_multiplicity 
__get_multiplicity ( self )

multiplicity

  __get_name 
__get_name ( self )

name

  __get_parent 
__get_parent ( self )

parent

  __get_pos 
__get_pos ( self )

pos

  __get_show 
__get_show ( self )

show

  __get_show_hydrogens 
__get_show_hydrogens ( self )

show_hydrogens

  __get_type 
__get_type ( self )

type

  __get_valency 
__get_valency ( self )

valency

  __get_x 
__get_x ( self )

x

  __get_xml_text 
__get_xml_text ( self )

xml_text (override of text_like.xml_text)

  __get_y 
__get_y ( self )

y

  __get_z 
__get_z ( self )

z

  __init__ 
__init__ (
        self,
        paper,
        xy=(),
        package=None,
        molecule=None,
        )

  __set_charge 
__set_charge ( self,  charge )

  __set_font_size 
__set_font_size ( self,  font_size )

  __set_molecule 
__set_molecule ( self,  mol )

  __set_multiplicity 
__set_multiplicity ( self,  multiplicity )

  __set_name 
__set_name ( self,  name )

  __set_pos 
__set_pos ( self,  pos )

  __set_show 
__set_show ( self,  show )

  __set_show_hydrogens 
__set_show_hydrogens ( self,  show_hydrogens )

  __set_type 
__set_type ( self,  type )

  __set_valency 
__set_valency ( self,  val )

  __set_x 
__set_x ( self,  x )

  __set_xml_text 
__set_xml_text ( self,  xml_text )

  __set_y 
__set_y ( self,  y )

  __set_z 
__set_z ( self,  z )

  __str__ 
__str__ ( self )

  _set_mark_helper 
_set_mark_helper (
        self,
        mark,
        sign=1,
        )

  _set_name 
_set_name (
        self,
        name,
        interpret=1,
        check_valency=1,
        )

  atoms_bound_to 
atoms_bound_to ( self )

just link to molecule.atoms_bound_to()

  bbox 
bbox ( self )

  create_mark 
create_mark (
        self,
        mark='radical',
        angle='auto',
        draw=1,
        )

creates the mark, does not care about the chemical meaning of this

  decide_pos 
decide_pos ( self )

  delete 
delete ( self )

  draw 
draw ( self )

draws atom with respect to its properties

  find_place_for_mark 
find_place_for_mark ( self,  mark )

  focus 
focus ( self )

  generate_marks_from_cheminfo 
generate_marks_from_cheminfo ( self )

  get_charge_from_marks 
get_charge_from_marks ( self )

  get_formula_dict 
get_formula_dict ( self )

returns formula as dictionary that can be passed to functions in periodic_table

  get_free_valency 
get_free_valency ( self,  strict=0 )

returns free valency of atom.

  get_ftext 
get_ftext ( self )

  get_occupied_valency 
get_occupied_valency ( self )

  get_package 
get_package ( self,  doc )

  get_text 
get_text ( self )

  get_xy 
get_xy ( self )

  get_xyz 
get_xyz ( self,  real=0 )

returns atoms coordinates, default are screen coordinates, real!=0 changes it to real coordinates (these two are usually different for imported molecules)

  lift 
lift ( self )

  move 
move (
        self,
        dx,
        dy,
        dont_move_marks=0,
        )

moves object with his selector (when present)

  move_to 
move_to (
        self,
        x,
        y,
        dont_move_marks=0,
        )

  read_package 
read_package ( self,  package )

  redraw 
redraw ( self,  suppress_reposition=0 )

  reposition_marks 
reposition_marks ( self )

  scale_font 
scale_font ( self,  ratio )

scales font of atom. does not redraw !!

  select 
select ( self )

  set_mark 
set_mark (
        self,
        mark='radical',
        toggle=1,
        angle='auto',
        )

sets the mark and takes care of toggling and charge and multiplicity changes

  set_name 
set_name (
        self,
        name,
        interpret=1,
        check_valency=1,
        )

  set_valency_from_name 
set_valency_from_name ( self )

  split_element_and_charge 
split_element_and_charge ( self,  txt )

returns tuple of (element, charge) or None if the text does not match this pattern

  toggle_center 
toggle_center ( self,  mode=0 )

toggles the centering of text between center-first and center-last(mode=0) or sets it strictly - mode=-1, mode=1

  transform 
transform ( self,  tr )

  unfocus 
unfocus ( self )

  unselect 
unselect ( self )

  update_after_valency_change 
update_after_valency_change ( self )

  update_font 
update_font ( self )


Table of Contents

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