def add_atom_to( self, a1, bond_to_use=None, pos=None):
"""adds new atom bound to atom id with bond, the position of new atom can be specified in pos or is
decided calling find_place(), if x, y is specified and matches already existing atom it will be
used instead of creating new one """
if pos != None:
x, y = pos
else:
if bond_to_use:
x, y = self.find_place( a1, Screen.any_to_px( self.paper.standard.bond_length), added_order=bond_to_use.order)
else:
x, y = self.find_place( a1, Screen.any_to_px( self.paper.standard.bond_length))
a2 = None # the new atom
if pos:
# try if the coordinates are the same as of another atom
for at in self.atoms:
if abs( at.x - x) < 2 and abs( at.y - y) < 2 and not at == a1:
a2 = at
break
if not a2:
a2 = self.create_new_atom( x, y)
b = bond_to_use or bond( self.paper.standard, order=1, type='n')
self.add_edge( a1, a2, e=b)
b.molecule = self
b.draw()
return a2, b
def on_begin( self, scaling=None):
self.paper.unselect_all()
if self.paper.get_paper_property( 'crop_svg'):
if len( self.paper.find_all()) <= 1: # background only
Store.log( _('There is nothing to export. If you want to export an empty paper disable cropping of the drawing in the File/Properties menu.'), message_type="error")
return 0
x1, y1, x2, y2 = self.paper.get_cropping_bbox()
dx = x2-x1
dy = y2-y1
scalex, scaley = scaling or self.get_scaling( dx, dy)
if not scalex:
# the setting of scaling was canceled
return 0
self.transformer = transform.transform()
self.transformer.set_move( -x1, -y1)
self.transformer.set_scaling_xy( scalex, scaley)
else:
dx = Screen.mm_to_px( self.paper._paper_properties['size_x'])
dy = Screen.mm_to_px( self.paper._paper_properties['size_y'])
scalex, scaley = scaling or self.get_scaling( dx, dy)
if not scalex:
# the setting of scaling was canceled
return 0
self.transformer = transform.transform()
self.transformer.set_scaling_xy( scalex, scaley)
x1, y1, x2, y2 = self.transformer.transform_4( (0, 0, dx, dy))
self.pagesize = tuple( map( round, (x2-x1, y2-y1)))
self.attrs['text_to_curves'] = False
self.converter = self.converter_class( **self.attrs)
return 1
def on_begin( self):
self.paper.unselect_all()
scale = 720.0/self.paper.winfo_fpixels( '254m')
if self.paper.get_paper_property( 'crop_svg'):
margin = self.paper.get_paper_property('crop_margin')
items = list( self.paper.find_all())
items.remove( self.paper.background)
if not items:
Store.log( _('There is nothing to export. If you want to export an empty paper disable cropping of the drawing in the File/Properties menu.'), message_type="error")
return 0
x1, y1, x2, y2 = self.paper.list_bbox( items)
self.transformer = transform.transform()
self.transformer.set_move( -x1+margin, -y1+margin)
self.transformer.set_scaling( scale)
dx = x2-x1 +2*margin
dy = y2-y1 +2*margin
else:
self.transformer = transform.transform()
self.transformer.set_scaling( scale)
dx = Screen.mm_to_px( self.paper._paper_properties['size_x'])
dy = Screen.mm_to_px( self.paper._paper_properties['size_y'])
self.canvas = self.init_canvas( pagesize=(scale*dx, scale*dy))
self.converter = self.converter_class()
return 1
def on_begin( self, scaling=None):
self.paper.unselect_all()
if self.paper.get_paper_property( 'crop_svg'):
if len( self.paper.find_all()) <= 1: # background only
Store.log( _('There is nothing to export. If you want to export an empty paper disable cropping of the drawing in the File/Properties menu.'), message_type="error")
return 0
x1, y1, x2, y2 = self.paper.get_cropping_bbox()
dx = x2-x1
dy = y2-y1
scalex, scaley = scaling or self.get_scaling( dx, dy)
if not scalex:
# the setting of scaling was canceled
return 0
self.transformer = transform.transform()
self.transformer.set_move( -x1, -y1)
self.transformer.set_scaling_xy( scalex, scaley)
else:
dx = Screen.mm_to_px( self.paper._paper_properties['size_x'])
dy = Screen.mm_to_px( self.paper._paper_properties['size_y'])
scalex, scaley = scaling or self.get_scaling( dx, dy)
if not scalex:
# the setting of scaling was canceled
return 0
self.transformer = transform.transform()
self.transformer.set_scaling_xy( scalex, scaley)
x1, y1, x2, y2 = self.transformer.transform_4( (0, 0, dx, dy))
self.pagesize = tuple( map( round, (x2-x1, y2-y1)))
self.attrs['text_to_curves'] = False
self.converter = self.converter_class( **self.attrs)
return 1
def add_atom_to(self, a1, bond_to_use=None, pos=None):
"""adds new atom bound to atom id with bond, the position of new atom can be specified in pos or is
decided calling find_place(), if x, y is specified and matches already existing atom it will be
used instead of creating new one """
if pos != None:
x, y = pos
else:
if bond_to_use:
x, y = self.find_place(a1,
Screen.any_to_px(
self.paper.standard.bond_length),
added_order=bond_to_use.order)
else:
x, y = self.find_place(
a1, Screen.any_to_px(self.paper.standard.bond_length))
a2 = None # the new atom
if pos:
# try if the coordinates are the same as of another atom
for at in self.atoms:
if abs(at.x - x) < 2 and abs(at.y - y) < 2 and not at == a1:
a2 = at
break
if not a2:
a2 = self.create_new_atom(x, y)
b = bond_to_use or bond(self.paper.standard, order=1, type='n')
self.add_edge(a1, a2, e=b)
b.molecule = self
b.draw()
return a2, b
def add_plus_mark( self, o, page):
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.atom.area_color),
stroke_width=Screen.px_to_cm( 1))
style_name = self.get_appropriate_style_name( s)
# we must process oval first - it would otherwise cover the lines
for i in o.items:
if self.paper.type( i) == "oval":
x, y, x2, y2 = map( Screen.px_to_cm, self.paper.coords( i))
size = Screen.px_to_cm( o.size)
dom_extensions.elementUnder( page, 'draw:ellipse',
(( 'svg:x', '%fcm' % x),
( 'svg:y', '%fcm' % y),
( 'svg:width', '%fcm' % size),
( 'svg:height', '%fcm' % size),
( 'draw:style-name', style_name)))
for i in o.items:
if self.paper.type( i) == "line":
coords = self.paper.coords( i)
# because some weird bug in tcl/tk i had to hack the coordinates in marks.py
# the hack is reversed here in order to get the coords back
# I also reduce the size of the mark a little
#if o.items.index( i) == 1:
# coords[0] += 0
# coords[2] += -1
#elif o.items.index( i) == 2:
# coords[1] += 0
# coords[3] += -1
# end of hack
coords = map( Screen.px_to_cm, coords)
self.create_oo_line( coords, page, style_name)
def add_arrow( self, a, page):
for item in a.items:
# polygons (arrow heads, etc.)
if self.paper.type( item) == "polygon":
a_color = self.paper.itemcget( item, "fill")
l_color = self.paper.itemcget( item, "outline")
l_width = float( self.paper.itemcget( item, "width"))
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( l_color),
fill_color=self.paper.any_color_to_rgb_string( a_color),
stroke_width=Screen.px_to_cm( l_width))
style_name = self.get_appropriate_style_name( s)
ps = geometry.coordinate_flat_list_to_xy_tuples( self.paper.coords( item))
points = [map( Screen.px_to_cm, p) for p in ps]
self.create_oo_polygon( points, page, style_name)
# polylines - standard arrows
elif self.paper.type( item) == "line":
line_pin = a._pins.index( self.paper.itemcget( item, 'arrow'))
end_pin, start_pin = None,None
if line_pin==1 or line_pin==3:
end_pin = 1
if line_pin==2 or line_pin==3:
start_pin = 1
l_color = self.paper.itemcget( item, "fill")
l_width = float( self.paper.itemcget( item, "width"))
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( l_color),
marker_end=end_pin,
marker_start=start_pin,
stroke_width=Screen.px_to_cm( l_width))
style_name = self.get_appropriate_style_name( s)
ps = geometry.coordinate_flat_list_to_xy_tuples( self.paper.coords( item))
points = [map( Screen.px_to_cm, p) for p in ps]
if self.paper.itemcget( item, "smooth") == "0":
self.create_oo_polyline( points, page, style_name)
else:
self.create_oo_bezier( points, page, style_name)
def add_plus_mark(self, o, page):
s = graphics_style(
stroke_color=self.paper.any_color_to_rgb_string(o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string(o.atom.area_color),
stroke_width=Screen.px_to_cm(1))
style_name = self.get_appropriate_style_name(s)
# we must process oval first - it would otherwise cover the lines
for i in o.items:
if self.paper.type(i) == "oval":
x, y, x2, y2 = map(Screen.px_to_cm, self.paper.coords(i))
size = Screen.px_to_cm(o.size)
dom_extensions.elementUnder(page, 'draw:ellipse',
(('svg:x', '%fcm' % x),
('svg:y', '%fcm' % y),
('svg:width', '%fcm' % size),
('svg:height', '%fcm' % size),
('draw:style-name', style_name)))
for i in o.items:
if self.paper.type(i) == "line":
coords = self.paper.coords(i)
# because some weird bug in tcl/tk i had to hack the coordinates in marks.py
# the hack is reversed here in order to get the coords back
# I also reduce the size of the mark a little
#if o.items.index( i) == 1:
# coords[0] += 0
# coords[2] += -1
#elif o.items.index( i) == 2:
# coords[1] += 0
# coords[3] += -1
# end of hack
coords = map(Screen.px_to_cm, coords)
self.create_oo_line(coords, page, style_name)
def add_arrow( self, a, page):
for item in a.items:
# polygons (arrow heads, etc.)
if self.paper.type( item) == "polygon":
a_color = self.paper.itemcget( item, "fill")
l_color = self.paper.itemcget( item, "outline")
l_width = float( self.paper.itemcget( item, "width"))
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( l_color),
fill_color=self.paper.any_color_to_rgb_string( a_color),
stroke_width=Screen.px_to_cm( l_width))
style_name = self.get_appropriate_style_name( s)
ps = geometry.coordinate_flat_list_to_xy_tuples( self.paper.coords( item))
points = [map( Screen.px_to_cm, p) for p in ps]
self.create_oo_polygon( points, page, style_name)
# polylines - standard arrows
elif self.paper.type( item) == "line":
line_pin = a._pins.index( self.paper.itemcget( item, 'arrow'))
end_pin, start_pin = None,None
if line_pin==1 or line_pin==3:
end_pin = 1
if line_pin==2 or line_pin==3:
start_pin = 1
l_color = self.paper.itemcget( item, "fill")
l_width = float( self.paper.itemcget( item, "width"))
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( l_color),
marker_end=end_pin,
marker_start=start_pin,
stroke_width=Screen.px_to_cm( l_width))
style_name = self.get_appropriate_style_name( s)
ps = geometry.coordinate_flat_list_to_xy_tuples( self.paper.coords( item))
points = [map( Screen.px_to_cm, p) for p in ps]
if self.paper.itemcget( item, "smooth") == "0":
self.create_oo_polyline( points, page, style_name)
else:
self.create_oo_bezier( points, page, style_name)
def on_begin(self):
self.paper.unselect_all()
scale = 720.0 / self.paper.winfo_fpixels('254m')
if self.paper.get_paper_property('crop_svg'):
margin = self.paper.get_paper_property('crop_margin')
items = list(self.paper.find_all())
items.remove(self.paper.background)
if not items:
Store.log(_(
'There is nothing to export. If you want to export an empty paper disable cropping of the drawing in the File/Properties menu.'
),
message_type="error")
return 0
x1, y1, x2, y2 = self.paper.list_bbox(items)
self.transformer = transform.transform()
self.transformer.set_move(-x1 + margin, -y1 + margin)
self.transformer.set_scaling(scale)
dx = x2 - x1 + 2 * margin
dy = y2 - y1 + 2 * margin
else:
self.transformer = transform.transform()
self.transformer.set_scaling(scale)
dx = Screen.mm_to_px(self.paper._paper_properties['size_x'])
dy = Screen.mm_to_px(self.paper._paper_properties['size_y'])
self.canvas = self.init_canvas(pagesize=(scale * dx, scale * dy))
self.converter = self.converter_class()
return 1
def switch_to_type( self, type):
if type in "wha" and self.type not in "wha":
# get the standard width only if the changes is not within the "wha" group
self.wedge_width = Screen.any_to_px( self.paper.standard.wedge_width)
elif type not in "wha" and self.type in "wha":
# when both are outside the 'wha' do the similar
self.bond_width = Screen.any_to_px( self.paper.standard.bond_width)
self.type = type
def switch_to_type( self, type):
if type in "wha" and self.type not in "wha":
# get the standard width only if the changes is not within the "wha" group
self.wedge_width = Screen.any_to_px( self.paper.standard.wedge_width)
elif type not in "wha" and self.type in "wha":
# when both are outside the 'wha' do the similar
self.bond_width = Screen.any_to_px( self.paper.standard.bond_width)
self.type = type
def read_standard_values( self, standard, old_standard=None):
meta_enabled.read_standard_values( self, standard, old_standard=old_standard)
# wedge width
if not old_standard or (standard.wedge_width != old_standard.wedge_width):
self.wedge_width = Screen.any_to_px( standard.wedge_width)
# line width
if not old_standard or (standard.line_width != old_standard.line_width):
self.line_width = Screen.any_to_px( standard.line_width)
# bond width
if not old_standard or (standard.bond_width != old_standard.bond_width):
if hasattr( self, 'bond_width'):
self.bond_width = misc.signum( self.bond_width) * Screen.any_to_px( standard.bond_width)
else:
self.bond_width = Screen.any_to_px( standard.bond_width)
def add_radical_mark(self, o, page):
s = graphics_style(
stroke_color=self.paper.any_color_to_rgb_string(o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string(o.atom.line_color),
stroke_width=Screen.px_to_cm(0.1))
style_name = self.get_appropriate_style_name(s)
for i in o.items:
x, y, x2, y2 = map(Screen.px_to_cm, self.paper.coords(i))
size = Screen.px_to_cm(o.size)
dom_extensions.elementUnder(
page, 'draw:ellipse',
(('svg:x', '%fcm' % x), ('svg:y', '%fcm' % y),
('svg:width', '%fcm' % size), ('svg:height', '%fcm' % size),
('draw:style-name', style_name)))
def add_radical_mark( self, o, page):
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
stroke_width=Screen.px_to_cm( 0.1))
style_name = self.get_appropriate_style_name( s)
for i in o.items:
x, y, x2, y2 = map( Screen.px_to_cm, self.paper.coords( i))
size = Screen.px_to_cm( o.size)
dom_extensions.elementUnder( page, 'draw:ellipse',
(( 'svg:x', '%fcm' % x),
( 'svg:y', '%fcm' % y),
( 'svg:width', '%fcm' % size),
( 'svg:height', '%fcm' % size),
( 'draw:style-name', style_name)))
def read_standard_values( self, standard, old_standard=None):
meta_enabled.read_standard_values( self, standard, old_standard=old_standard)
# wedge width
if not old_standard or (standard.wedge_width != old_standard.wedge_width):
self.wedge_width = Screen.any_to_px( standard.wedge_width)
# line width
if not old_standard or (standard.line_width != old_standard.line_width):
self.line_width = Screen.any_to_px( standard.line_width)
# bond width
if not old_standard or (standard.bond_width != old_standard.bond_width):
if hasattr( self, 'bond_width'):
self.bond_width = misc.signum( self.bond_width) * Screen.any_to_px( standard.bond_width)
else:
self.bond_width = Screen.any_to_px( standard.bond_width)
def add_polyline(self, o, page):
s = graphics_style(stroke_color=self.paper.any_color_to_rgb_string(
o.line_color),
stroke_width=Screen.px_to_cm(o.line_width))
style_name = self.get_appropriate_style_name(s)
points = [map(Screen.px_to_cm, p.get_xy()) for p in o.points]
self.create_oo_polyline(points, page, style_name)
def read_package( self, package, atom):
typ = package.getAttribute( 'type')
cls = globals().get( typ, None)
if cls:
auto = 0 #package.getAttribute( 'auto') != None and package.getAttribute( 'auto')) or 0
x, y, z = Screen.read_xml_point( package)
size = package.getAttribute( 'size') and float( package.getAttribute( 'size')) or None
if size:
m = cls( atom, x, y, size=size, auto=int(auto))
else:
m = cls( atom, x, y, auto=int(auto))
# class specific attributes
for (attr, typ) in m.meta__save_attrs.items():
val = package.getAttribute( attr)
if val != '':
if typ == bool:
value = bool( data.booleans.index( val))
elif typ == int:
value = int( val)
else:
value = val
setattr( m, attr, value)
if hasattr( m, "_after_read_package"):
m._after_read_package()
return m
else:
raise ValueError("no such mark type %s" % typ)
def add_polygon( self, o, page):
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.area_color),
stroke_width=Screen.px_to_cm( o.line_width))
style_name = self.get_appropriate_style_name( s)
points = [map( Screen.px_to_cm, p.get_xy()) for p in o.points]
self.create_oo_polygon( points, page, style_name)
def read_package(self, package):
"""reads the dom element package and sets internal state according to it"""
if package.getAttribute('id'):
self.id = package.getAttribute('id')
pos = package.getElementsByTagName('point')[0]
x, y, z = Screen.read_xml_point(pos)
self.set_xy(x, y)
ft = package.getElementsByTagName('ftext')
try:
self.xml_ftext = reduce(operator.add, [
e.nodeValue
for e in ft[0].childNodes if isinstance(e, dom.Text)
], '')
except IndexError:
self.xml_ftext = "?"
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int(fnt.getAttribute('size'))
self.font_family = fnt.getAttribute('family')
if fnt.getAttribute('color'):
self.line_color = fnt.getAttribute('color')
if package.getAttribute('background-color'):
self.area_color = package.getAttribute('background-color')
def read_standard_values(self, standard, old_standard=None):
meta_enabled.read_standard_values(self,
standard,
old_standard=old_standard)
if not old_standard or (standard.line_width !=
old_standard.line_width):
self.line_width = Screen.any_to_px(standard.line_width)
def get_package(self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
a = doc.createElement('text')
a.setAttribute('id', self.id)
if self.area_color != '':
a.setAttribute('background-color', self.area_color)
if self.font_size != self.paper.standard.font_size \
or self.font_family != self.paper.standard.font_family \
or self.line_color != self.paper.standard.line_color:
font = dom_extensions.elementUnder(
a,
'font',
attributes=(('size', str(self.font_size)), ('family',
self.font_family)))
if self.line_color != self.paper.standard.line_color:
font.setAttribute('color', self.line_color)
x, y = Screen.px_to_text_with_unit((self.x, self.y))
dom_extensions.elementUnder(a,
'point',
attributes=(('x', x), ('y', y)))
ftext = dom_extensions.elementUnder(a, 'ftext')
ftext.appendChild(doc.createTextNode(self.xml_ftext))
return a
def get_transformed_template(self, n, coords, type="empty", paper=None):
"""type is type of connection - 'bond', 'atom1'(for single atom), 'atom2'(for atom with more than 1 bond), 'empty'"""
pap = paper or Store.app.paper
pap.onread_id_sandbox_activate() # must be here to mangle the ids
current = molecule(pap, package=self.templates[n])
pap.onread_id_sandbox_finish(apply_to=[current]) # id mangling
current.name = ""
self._scale_ratio = 1
trans = transform()
# type empty - just draws the template - no conection
if type == "empty":
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1 = coords
bond_length = Screen.any_to_px(Store.app.paper.standard.bond_length)
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
trans.set_move(-xt2, -yt2)
trans.set_scaling(bond_length / math.sqrt((xt1 - xt2) ** 2 + (yt1 - yt2) ** 2))
trans.set_move(x1, y1)
# type atom
elif type == "atom1" or type == "atom2":
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1, x2, y2 = coords
trans.set_move(-xt2, -yt2)
trans.set_scaling(
math.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2) / math.sqrt((xt1 - xt2) ** 2 + (yt1 - yt2) ** 2)
)
trans.set_rotation(math.atan2(xt1 - xt2, yt1 - yt2) - math.atan2(x1 - x2, y1 - y2))
trans.set_move(x2, y2)
# type bond
elif type == "bond":
if not (current.t_bond_first and current.t_bond_second):
warn("this template is not capable to be added to bond - sorry.")
return None
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
xt1, yt1 = current.t_bond_first.get_xy()
xt2, yt2 = current.t_bond_second.get_xy()
x1, y1, x2, y2 = coords
self._scale_ratio = math.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2) / math.sqrt(
(xt1 - xt2) ** 2 + (yt1 - yt2) ** 2
) # further needed for bond.bond_width transformation
trans.set_move(-xt1, -yt1)
trans.set_rotation(math.atan2(xt1 - xt2, yt1 - yt2) - math.atan2(x1 - x2, y1 - y2))
trans.set_scaling(self._scale_ratio)
trans.set_move(x1, y1)
self.transform_template(current, trans)
# remove obsolete info from template
if type == "atom1":
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
elif type == "atom2":
current.t_atom.x = x1
current.t_atom.y = y1
current.t_atom = None
current.t_bond_first = None
current.t_bond_second = None
# return ready template
return current
def add_electronpair_mark( self, o, page):
i = o.items[0]
width = float( self.paper.itemcget( i, 'width'))
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
stroke_width=Screen.px_to_cm( width))
style_name = self.get_appropriate_style_name( s)
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, style_name)
def add_electronpair_mark( self, o, page):
i = o.items[0]
width = float( self.paper.itemcget( i, 'width'))
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
stroke_width=Screen.px_to_cm( width))
style_name = self.get_appropriate_style_name( s)
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, style_name)
def expand( self):
"""expands the group and returns list of atoms that new drawing afterwords"""
if self.group_type == "builtin":
names = Store.gm.get_template_names()
if self.symbol in names:
a2 = self.neighbors[0]
x1, y1 = a2.get_xy()
x2, y2 = self.get_xy()
self.group_graph = Store.gm.get_transformed_template( names.index( self.symbol), (x1,y1,x2,y2), type='atom1')
replacement = self.group_graph.next_to_t_atom
else:
print "unknown group %s" % a.symbol
return None
elif self.group_type == "chain":
self.group_graph = self.molecule.create_graph()
p = PT.formula_dict( self.symbol)
n = p['C']
last = None
for i in range( n):
v = self.group_graph.add_vertex()
v.x, v.y = None, None
if last:
self.group_graph.add_edge( last, v)
last = v
replacement = self.group_graph.vertices[0]
replacement.x = self.x
replacement.y = self.y
elif self.group_type == "implicit":
if not self.group_graph:
self.set_name( self.symbol, occupied_valency=self.occupied_valency)
for v in self.group_graph.vertices:
v.x, v.y = None, None
v.show = v.symbol != 'C'
assert self.connecting_atom != None
replacement = self.connecting_atom
replacement.x = self.x
replacement.y = self.y
self.molecule.eat_molecule( self.group_graph)
self.molecule.move_bonds_between_atoms( self, replacement)
self.molecule.delete_vertex( self)
if self.occupied_valency:
oasa.coords_generator.calculate_coords( self.molecule, bond_length=-1)
else:
# if the group is the only vertex of the molecule we must set the bond_length explicitly
# and the move the whole molecule
replacement.x = None
replacement.y = None
x, y = self.x, self.y
oasa.coords_generator.calculate_coords( self.molecule, bond_length=Screen.any_to_px( self.paper.standard.bond_length))
dx = x - replacement.x
dy = y - replacement.y
[a.move( dx, dy) for a in self.group_graph.vertices]
return self.group_graph.vertices
def add_bond( self, b, page):
"""adds bond item to page"""
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.line_width))
style_name = self.get_appropriate_style_name( s)
l_group = page
# items to export
line_items, items = b.get_exportable_items()
# the export itself
if b.type in 'nhd':
for i in items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, style_name)
elif b.type == 'o':
for i in items:
x, y, x2, y2 = map( Screen.px_to_cm, self.paper.coords( i))
size = Screen.px_to_cm( x2-x)
dom_extensions.elementUnder( page, 'draw:ellipse',
(( 'svg:x', '%fcm' % x),
( 'svg:y', '%fcm' % y),
( 'svg:width', '%fcm' % size),
( 'svg:height', '%fcm' % size),
( 'draw:style-name', style_name)))
elif b.type == 'b':
# bold bonds width is determined by the wedge_width
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.wedge_width))
b_style_name = self.get_appropriate_style_name( s)
for i in items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, b_style_name)
elif b.type == 'w':
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
fill_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.line_width))
style_name = self.get_appropriate_style_name( s)
for i in items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
point_array = []
for i in range( 0, len( coords), 2):
point_array.append( (coords[i], coords[i+1]))
self.create_oo_polygon( point_array, page, style_name)
elif b.type == 'a':
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.line_width))
style_name = self.get_appropriate_style_name( s)
for i in items:
coords = self.paper.coords( i)
points = []
for j in range( 0, len( coords), 2):
points.append( ( Screen.px_to_cm( coords[j]), Screen.px_to_cm(coords[j+1])))
self.create_oo_polyline( points, page, style_name)
# line_items
for i in line_items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, style_name)
def add_bond( self, b, page):
"""adds bond item to page"""
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.line_width))
style_name = self.get_appropriate_style_name( s)
l_group = page
# items to export
line_items, items = b.get_exportable_items()
# the export itself
if b.type in 'nhd':
for i in items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, style_name)
elif b.type == 'o':
for i in items:
x, y, x2, y2 = map( Screen.px_to_cm, self.paper.coords( i))
size = Screen.px_to_cm( x2-x)
dom_extensions.elementUnder( page, 'draw:ellipse',
(( 'svg:x', '%fcm' % x),
( 'svg:y', '%fcm' % y),
( 'svg:width', '%fcm' % size),
( 'svg:height', '%fcm' % size),
( 'draw:style-name', style_name)))
elif b.type == 'b':
# bold bonds width is determined by the wedge_width
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.wedge_width))
b_style_name = self.get_appropriate_style_name( s)
for i in items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, b_style_name)
elif b.type == 'w':
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
fill_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.line_width))
style_name = self.get_appropriate_style_name( s)
for i in items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
point_array = []
for i in range( 0, len( coords), 2):
point_array.append( (coords[i], coords[i+1]))
self.create_oo_polygon( point_array, page, style_name)
elif b.type == 'a':
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( b.line_color),
stroke_width=Screen.px_to_cm( b.line_width))
style_name = self.get_appropriate_style_name( s)
for i in items:
coords = self.paper.coords( i)
points = []
for j in range( 0, len( coords), 2):
points.append( ( Screen.px_to_cm( coords[j]), Screen.px_to_cm(coords[j+1])))
self.create_oo_polyline( points, page, style_name)
# line_items
for i in line_items:
coords = map( Screen.px_to_cm, self.paper.coords( i))
self.create_oo_line( coords, page, style_name)
def add_oval( self, o, page):
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.area_color),
stroke_width=Screen.px_to_cm( o.line_width))
style_name = self.get_appropriate_style_name( s)
x, y, x2, y2 = map( Screen.px_to_cm, o.coords)
dom_extensions.elementUnder( page, 'draw:ellipse',
(( 'svg:x', '%fcm' % x),
( 'svg:y', '%fcm' % y),
( 'svg:width', '%fcm' % (x2-x)),
( 'svg:height', '%fcm' % (y2-y)),
( 'draw:style-name', style_name)))
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
if package.getAttribute( 'id'):
self.id = package.getAttribute( 'id')
pnt = package.getElementsByTagName( 'point')[0]
self.x, self.y, z = Screen.read_xml_point( pnt)
if package.getAttribute( 'font_size'):
self.font_size = int( package.getAttribute( 'font_size'))
if package.getAttribute( 'color'):
self.line_color = package.getAttribute( 'color')
if package.getAttribute( 'background-color'):
self.area_color = package.getAttribute( 'background-color')
def add_oval( self, o, page):
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.area_color),
stroke_width=Screen.px_to_cm( o.line_width))
style_name = self.get_appropriate_style_name( s)
x, y, x2, y2 = map( Screen.px_to_cm, o.coords)
dom_extensions.elementUnder( page, 'draw:ellipse',
(( 'svg:x', '%fcm' % x),
( 'svg:y', '%fcm' % y),
( 'svg:width', '%fcm' % (x2-x)),
( 'svg:height', '%fcm' % (y2-y)),
( 'draw:style-name', style_name)))
def read_package(self, package):
"""reads the dom element package and sets internal state according to it"""
if package.getAttribute('id'):
self.id = package.getAttribute('id')
pnt = package.getElementsByTagName('point')[0]
self.x, self.y, z = Screen.read_xml_point(pnt)
if package.getAttribute('font_size'):
self.font_size = int(package.getAttribute('font_size'))
if package.getAttribute('color'):
self.line_color = package.getAttribute('color')
if package.getAttribute('background-color'):
self.area_color = package.getAttribute('background-color')
def get_package(self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
pack = doc.createElement('circle')
x1, y1, x2, y2 = Screen.px_to_text_with_unit(
self.paper.screen_to_real_coords(self.coords))
dom_extensions.setAttributes(
pack,
(('x1', x1), ('y1', y1), ('x2', x2), ('y2', y2),
('area_color', self.area_color), ('line_color', self.line_color),
('width', str(self.line_width))))
return pack
def oasa_mol_to_bkchem_mol(mol, paper):
m = molecule.molecule(paper)
if None in reduce(operator.add, [[a.x, a.y] for a in mol.atoms], []):
calc_position = 0
else:
calc_position = 1
minx = None
maxx = None
miny = None
maxy = None
# atoms
for a in mol.vertices:
a2 = oasa_atom_to_bkchem_atom(a, paper, m)
m.insert_atom(a2)
if calc_position:
# data for rescaling
if not maxx or a2.x > maxx:
maxx = a2.x
if not minx or a2.x < minx:
minx = a2.x
if not miny or a2.y < miny:
miny = a2.y
if not maxy or a2.y > maxy:
maxy = a2.y
# bonds
bond_lengths = []
for b in mol.edges:
b2 = oasa_bond_to_bkchem_bond(b, paper)
aa1, aa2 = b.vertices
atom1 = m.atoms[mol.vertices.index(aa1)]
atom2 = m.atoms[mol.vertices.index(aa2)]
m.add_edge(atom1, atom2, b2)
b2.molecule = m
if calc_position:
bond_lengths.append(
math.sqrt((b2.atom1.x - b2.atom2.x)**2 +
(b2.atom1.y - b2.atom2.y)**2))
# rescale
if calc_position:
bl = sum(bond_lengths) / len(bond_lengths)
scale = Screen.any_to_px(paper.standard.bond_length) / bl
movex = (maxx + minx) / 2
movey = (maxy + miny) / 2
trans = transform3d.transform3d()
trans.set_move(-movex, -movey, 0)
trans.set_scaling(scale)
trans.set_move(320, 240, 0)
for a in m.atoms:
a.x, a.y, a.z = trans.transform_xyz(a.x, a.y, a.z)
return m
def get_package( self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
pack = doc.createElement( 'circle')
x1, y1, x2, y2 = Screen.px_to_text_with_unit( self.paper.screen_to_real_coords( self.coords))
dom_extensions.setAttributes( pack, (('x1', x1),
('y1', y1),
('x2', x2),
('y2', y2),
('area_color', self.area_color),
('line_color', self.line_color),
('width', str( self.line_width))))
return pack
def get_package(self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
pls = doc.createElement('plus')
pls.setAttribute('id', self.id)
x, y = Screen.px_to_text_with_unit((self.x, self.y))
dom_extensions.elementUnder(pls, 'point', (('x', x), ('y', y)))
pls.setAttribute('font_size', str(self.font_size))
if self.line_color != '#000':
pls.setAttribute('color', self.line_color)
if self.area_color != '#ffffff':
pls.setAttribute('background-color', self.area_color)
return pls
def oasa_mol_to_bkchem_mol( mol, paper):
m = molecule.molecule( paper)
if None in reduce( operator.add, [[a.x, a.y] for a in mol.atoms], []):
calc_position = 0
else:
calc_position = 1
minx = None
maxx = None
miny = None
maxy = None
# atoms
for a in mol.vertices:
a2 = oasa_atom_to_bkchem_atom( a, paper, m)
m.insert_atom( a2)
if calc_position:
# data for rescaling
if not maxx or a2.x > maxx:
maxx = a2.x
if not minx or a2.x < minx:
minx = a2.x
if not miny or a2.y < miny:
miny = a2.y
if not maxy or a2.y > maxy:
maxy = a2.y
# bonds
bond_lengths = []
for b in mol.edges:
b2 = oasa_bond_to_bkchem_bond( b, paper)
aa1, aa2 = b.vertices
atom1 = m.atoms[ mol.vertices.index( aa1)]
atom2 = m.atoms[ mol.vertices.index( aa2)]
m.add_edge( atom1, atom2, b2)
b2.molecule = m
if calc_position:
bond_lengths.append( math.sqrt( (b2.atom1.x-b2.atom2.x)**2 + (b2.atom1.y-b2.atom2.y)**2))
# rescale
if calc_position:
bl = sum( bond_lengths) / len( bond_lengths)
scale = Screen.any_to_px( paper.standard.bond_length) / bl
movex = (maxx+minx)/2
movey = (maxy+miny)/2
trans = transform3d.transform3d()
trans.set_move( -movex, -movey, 0)
trans.set_scaling( scale)
trans.set_move( 320, 240, 0)
for a in m.atoms:
a.x, a.y, a.z = trans.transform_xyz( a.x, a.y, a.z)
return m
def get_package( self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
pls = doc.createElement('plus')
pls.setAttribute( 'id', self.id)
x, y = Screen.px_to_text_with_unit( (self.x, self.y))
dom_extensions.elementUnder( pls, 'point', (('x', x),
('y', y)))
pls.setAttribute('font_size', str( self.font_size))
if self.line_color != '#000':
pls.setAttribute( 'color', self.line_color)
if self.area_color != '#ffffff':
pls.setAttribute( 'background-color', self.area_color)
return pls
def read_package(self, package):
"""reads the dom element package and sets internal state according to it"""
a = ['no', 'yes']
on_off = ['off', 'on']
self.id = package.getAttribute('id')
# marks
for m in package.getElementsByTagName('mark'):
mrk = marks.mark.read_package(m, self)
self.marks.add(mrk)
# position
self.pos = package.getAttribute('pos')
position = package.getElementsByTagName('point')[0]
# reading of coords regardless of their unit
x, y, z = Screen.read_xml_point(position)
if z != None:
self.z = z * self.paper.real_to_screen_ratio()
# needed to support transparent handling of molecular size
x, y = self.paper.real_to_screen_coords((x, y))
self.x = x
self.y = y
ft = package.getElementsByTagName('ftext')
if ft:
self.set_name(
reduce(operator.add, [
e.nodeValue
for e in ft[0].childNodes if isinstance(e, dom.Text)
], '').encode('utf-8'))
else:
raise TypeError, "not text atom"
# font and fill color
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int(fnt.getAttribute('size'))
self.font_family = fnt.getAttribute('family')
if fnt.getAttribute('color'):
self.line_color = fnt.getAttribute('color')
# background color
if package.getAttributeNode('background-color'):
self.area_color = package.getAttribute('background-color')
# number
if package.getAttribute('show_number'):
self.show_number = bool(
data.booleans.index(package.getAttribute('show_number')))
if package.getAttribute('number'):
self.number = package.getAttribute('number')
def add_orbital( self, o, page):
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.atom.area_color),
stroke_width=Screen.px_to_cm( 1.0))
style_name = self.get_appropriate_style_name( s)
i = 0
points = []
for c in o._get_my_curve( num_points=50):
if not i:
x = c
i = 1
else:
points.append( map( Screen.px_to_cm, (x, c)))
i = 0
self.create_oo_polygon( points, page, style_name)
def add_orbital( self, o, page):
s = graphics_style( stroke_color=self.paper.any_color_to_rgb_string( o.atom.line_color),
fill_color=self.paper.any_color_to_rgb_string( o.atom.area_color),
stroke_width=Screen.px_to_cm( 1.0))
style_name = self.get_appropriate_style_name( s)
i = 0
points = []
for c in o._get_my_curve( num_points=50):
if not i:
x = c
i = 1
else:
points.append( map( Screen.px_to_cm, (x, c)))
i = 0
self.create_oo_polygon( points, page, style_name)
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
a = ['no','yes']
on_off = ['off','on']
self.id = package.getAttribute( 'id')
# marks
for m in package.getElementsByTagName( 'mark'):
mrk = marks.mark.read_package( m, self)
self.marks.add( mrk)
# position
self.pos = package.getAttribute( 'pos')
position = package.getElementsByTagName( 'point')[0]
# reading of coords regardless of their unit
x, y, z = Screen.read_xml_point( position)
if z != None:
self.z = z* self.paper.real_to_screen_ratio()
# needed to support transparent handling of molecular size
x, y = self.paper.real_to_screen_coords( (x, y))
self.x = x
self.y = y
ft = package.getElementsByTagName('ftext')
if ft:
self.set_name(''.join(e.nodeValue for e in ft[0].childNodes
if isinstance(e, dom.Text)))
else:
raise TypeError("Not text atom.")
# font and fill color
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int( fnt.getAttribute( 'size'))
self.font_family = fnt.getAttribute( 'family')
if fnt.getAttribute( 'color'):
self.line_color = fnt.getAttribute( 'color')
# background color
if package.getAttributeNode( 'background-color'):
self.area_color = package.getAttribute( 'background-color')
# number
if package.getAttribute( 'show_number'):
self.show_number = bool( data.booleans.index( package.getAttribute( 'show_number')))
if package.getAttribute( 'number'):
self.number = package.getAttribute( 'number')
def read_package(self, package):
"""reads the dom element package and sets internal state according to it"""
a = ['no', 'yes']
on_off = ['off', 'on']
self.id = package.getAttribute('id')
self.pos = package.getAttribute('pos')
position = package.getElementsByTagName('point')[0]
# reading of coords regardless of their unit
x, y, z = Screen.read_xml_point(position)
if z is not None:
self.z = z * self.paper.real_to_screen_ratio()
# needed to support transparent handling of molecular size
x, y = self.paper.real_to_screen_coords((x, y))
self.x = x
self.y = y
self.symbol = package.getAttribute("name")
# font and fill color
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int(fnt.getAttribute('size'))
self.font_family = fnt.getAttribute('family')
if fnt.getAttribute('color'):
self.line_color = fnt.getAttribute('color')
# background color
if package.getAttributeNode('background-color'):
self.area_color = package.getAttribute('background-color')
# marks
for m in package.getElementsByTagName('mark'):
mrk = marks.mark.read_package(m, self)
self.marks.add(mrk)
# number
if package.getAttribute('show_number'):
self.show_number = bool(
data.booleans.index(package.getAttribute('show_number')))
if package.getAttribute('number'):
self.number = package.getAttribute('number')
# free_sites
if package.getAttribute('free_sites'):
self.free_sites = int(package.getAttribute('free_sites'))
def get_package( self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
a = doc.createElement('text')
a.setAttribute( 'id', self.id)
if self.area_color != '':
a.setAttribute( 'background-color', self.area_color)
if self.font_size != self.paper.standard.font_size \
or self.font_family != self.paper.standard.font_family \
or self.line_color != self.paper.standard.line_color:
font = dom_extensions.elementUnder( a, 'font', attributes=(('size', str( self.font_size)), ('family', self.font_family)))
if self.line_color != self.paper.standard.line_color:
font.setAttribute( 'color', self.line_color)
x, y = Screen.px_to_text_with_unit( (self.x, self.y))
dom_extensions.elementUnder( a, 'point', attributes=(('x', x),('y', y)))
ftext = dom_extensions.elementUnder( a, 'ftext')
ftext.appendChild( doc.createTextNode( self.xml_ftext))
return a
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
a = ['no','yes']
on_off = ['off','on']
self.id = package.getAttribute( 'id')
self.pos = package.getAttribute( 'pos')
position = package.getElementsByTagName( 'point')[0]
# reading of coords regardless of their unit
x, y, z = Screen.read_xml_point( position)
if z != None:
self.z = z* self.paper.real_to_screen_ratio()
# needed to support transparent handling of molecular size
x, y = self.paper.real_to_screen_coords( (x, y))
self.x = x
self.y = y
self.group_type = package.getAttribute( "group-type")
if self.group_type in ("implicit","explicit"):
#read the graph once
pass
self.symbol = package.getAttribute( "name")
# font and fill color
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int( fnt.getAttribute( 'size'))
self.font_family = fnt.getAttribute( 'family')
if fnt.getAttribute( 'color'):
self.line_color = fnt.getAttribute( 'color')
# background color
if package.getAttributeNode( 'background-color'):
self.area_color = package.getAttribute( 'background-color')
# marks
for m in package.getElementsByTagName( 'mark'):
mrk = marks.mark.read_package( m, self)
self.marks.add( mrk)
# number
if package.getAttribute( 'show_number'):
self.show_number = bool( data.booleans.index( package.getAttribute( 'show_number')))
if package.getAttribute( 'number'):
self.number = package.getAttribute( 'number')
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
if package.getAttribute( 'id'):
self.id = package.getAttribute( 'id')
pos = package.getElementsByTagName( 'point')[0]
x, y, z = Screen.read_xml_point( pos)
self.set_xy( x, y)
ft = package.getElementsByTagName('ftext')
try:
self.xml_ftext = reduce( operator.add, [e.nodeValue for e in ft[0].childNodes if isinstance( e, dom.Text)], '')
except IndexError:
self.xml_ftext = "?"
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int( fnt.getAttribute( 'size'))
self.font_family = fnt.getAttribute( 'family')
if fnt.getAttribute( 'color'):
self.line_color = fnt.getAttribute( 'color')
if package.getAttribute( 'background-color'):
self.area_color = package.getAttribute( 'background-color')
def write_to_file(self, name):
#{"v BKChemu bond.type":"v ChemDraw hodnota atributu Display elementu b"}
bondType = {
"w": "WedgeBegin",
"h": "WedgedHashBegin",
"a": "Wavy",
"b": "Bold",
"d": "Dash",
"o": "Dash"
}
#{"arrow.type v BKChemu":["graphic/ArrowType","arrow/ArrowheadHead","arrow/ ArrowheadTail","arrow/ArrowheadType"]}
#"retro":["RetroSynthetic","Full","","Angle"] - nefunguje, potrebuje dalsi povinne atributy
arrowType = {
"equilibrium": ["Equilibrium", "HalfLeft", "HalfLeft", "Solid"],
"equilibrium2": ["Equilibrium", "HalfLeft", "HalfLeft", "Solid"],
"normal": ["FullHead", "Full", "", "Solid"],
"electron": ["HalfHead", "HalfLeft", "", "Solid"]
}
colors = [
"#ffffff", "#000000", "#ff0000", "#ffff00", "#00ff00", "#00ffff",
"#0000ff", "#ff00ff"
]
fonts = ["Arial", "Times New Roman"]
out = dom.Document()
root = out.createElement("CDXML")
out.appendChild(root)
elem01 = out.createElement("colortable")
root.appendChild(elem01)
elem03 = out.createElement("fonttable")
root.appendChild(elem03)
elem1 = out.createElement("page")
root.appendChild(elem1)
PaperX = int(Screen.mm_to_px(self.paper.get_paper_property("size_x")))
PaperY = int(Screen.mm_to_px(self.paper.get_paper_property("size_y")))
elem1.setAttribute("BoundingBox",
"%d %d %d %d" % (0, 0, PaperX, PaperY))
elem1.setAttribute("Width", str(PaperX))
elem1.setAttribute("Height", str(PaperY))
elem1.setAttribute("DrawingSpace", "poster")
for mol in self.paper.molecules:
elem2 = out.createElement("fragment")
elem1.appendChild(elem2)
for atom in mol.atoms:
elem3 = out.createElement("n")
elem2.appendChild(elem3)
elem3.setAttribute("id", re.sub("atom", "", atom.id))
elem3.setAttribute("p", "%f %f" % (atom.x, atom.y))
elem3.setAttribute("NumHydrogens", "%d" % atom.free_valency)
if atom.symbol != "C" or atom.show:
elem4 = out.createElement("t")
elem3.appendChild(elem4)
elem6 = out.createElement("s")
elem6.setAttribute("size", str(atom.font_size))
elem6.setAttribute("face", "96")
elem4.appendChild(elem6)
text4 = re.sub("<.*?>", "", atom.xml_ftext)
if text4:
symbol = out.createTextNode(text4)
elem6.appendChild(symbol)
else:
symbol = out.createTextNode(atom.xml_ftext)
elem6.appendChild(symbol)
NewColor = self.paper.any_color_to_rgb_string(
atom.line_color)
if NewColor not in colors:
colors.append(NewColor)
for color in colors:
if color == NewColor:
ShowColor = str(colors.index(color) + 2)
elem4.setAttribute("color", ShowColor)
elem6.setAttribute("color", ShowColor)
NewFont = atom.font_family
if NewFont not in fonts:
fonts.append(NewFont)
for font in fonts:
if font == NewFont:
FontId = str(fonts.index(font) + 3)
elem6.setAttribute("font", FontId)
for bond in mol.bonds:
elem5 = out.createElement("b")
elem2.appendChild(elem5)
elem5.setAttribute("B", re.sub("atom", "", bond.atom1.id))
elem5.setAttribute("E", re.sub("atom", "", bond.atom2.id))
for bondB, bondC in bondType.items():
if bond.type == bondB:
elem5.setAttribute("Display", bondC)
elif bond.type == "h" and bond.equithick == 1:
elem5.setAttribute("Display", "Hash")
NewColor = self.paper.any_color_to_rgb_string(bond.line_color)
if NewColor not in colors:
colors.append(NewColor)
for color in colors:
if color == NewColor:
ShowColor = str(colors.index(color) + 2)
elem5.setAttribute("color", ShowColor)
#print int( self.paper.any_color_to_rgb_string( bond.line_color)[1:3], 16)
if bond.order > 1:
elem5.setAttribute("Order", "%d" % bond.order)
#print bond.type,bond.equithick,bond.simple_double
for text in self.paper.texts:
elem7 = out.createElement("t")
elem1.appendChild(elem7)
elem7.setAttribute("id", re.sub("text", "", text.id))
elem7.setAttribute("p", "%f %f" % (text.x, text.y))
elem7.setAttribute(
"BoundingBox",
"%d %d %d %d" % (text.bbox()[0], text.bbox()[1],
text.bbox()[2], text.bbox()[3]))
minidoc = dom.parseString("<a>%s</a>" %
text.xml_ftext.encode('utf-8'))
textik = {"i": 2, "b": 1, "sub": 32, "sup": 64}
def get_text(el):
texts = []
for ch in el.childNodes:
if isinstance(ch, dom.Text):
parents = []
par = ch.parentNode
while not isinstance(par, dom.Document):
parents.append(str(par.nodeName))
par = par.parentNode
texts.append((ch.nodeValue, parents))
else:
texts += get_text(ch)
return texts
texts2 = get_text(minidoc.childNodes[0])
for text2 in texts2:
elem001 = out.createElement("s")
elem7.appendChild(elem001)
elem001.setAttribute("size", str(text.font_size))
text001 = out.createTextNode(text2[0])
elem001.appendChild(text001)
def LogOR(xs):
if len(xs) == 0:
return 0
else:
return xs[0] | LogOR(xs[1:])
Faces = []
for xxx in text2[1]:
for P, F in textik.items():
if P == xxx:
Faces.append(F)
Face = LogOR(Faces)
if Face != 0:
elem001.setAttribute("face", str(Face))
NewFont = text.font_family
if NewFont not in fonts:
fonts.append(NewFont)
for font in fonts:
if font == NewFont:
FontId = str(fonts.index(font) + 3)
elem001.setAttribute("font", FontId)
NewColor = self.paper.any_color_to_rgb_string(text.line_color)
if NewColor not in colors:
colors.append(NewColor)
for color in colors:
if color == NewColor:
ShowColor = str(colors.index(color) + 2)
elem001.setAttribute("color", ShowColor)
elem7.setAttribute("color", ShowColor)
for plus in self.paper.pluses:
elem9 = out.createElement("graphic")
elem1.appendChild(elem9)
elem9.setAttribute("SymbolType", "Plus")
elem9.setAttribute("BoundingBox", "%f %f %f %f" % plus.bbox())
elem9.setAttribute("GraphicType", "Symbol")
elem9.setAttribute("id", re.sub("plus", "", plus.id))
#print plus.bbox()
NewColor = self.paper.any_color_to_rgb_string(plus.line_color)
if NewColor not in colors:
colors.append(NewColor)
for color in colors:
if color == NewColor:
ShowColor = str(colors.index(color) + 2)
elem9.setAttribute("color", ShowColor)
for arrow in self.paper.arrows:
arrowPoints = [p.get_xy() for p in arrow.points]
elem10 = out.createElement("graphic")
elem1.appendChild(elem10)
elem10.setAttribute("GraphicType", "Line")
for arrowB, arrowC in arrowType.items():
if arrow.type == arrowB:
elem10.setAttribute("ArrowType", arrowC[0])
NewColor = self.paper.any_color_to_rgb_string(arrow.line_color)
if NewColor not in colors:
colors.append(NewColor)
for color in colors:
if color == NewColor:
ShowColor = str(colors.index(color) + 2)
elem10.setAttribute("color", ShowColor)
elem11 = out.createElement("arrow")
elem1.appendChild(elem11)
for arrowB, arrowC in arrowType.items():
if arrow.type == arrowB:
elem11.setAttribute("ArrowheadHead", arrowC[1])
elem11.setAttribute("ArrowheadTail", arrowC[2])
elem11.setAttribute("ArrowheadType", arrowC[3])
elem11.setAttribute(
"Head3D",
str(arrowPoints[-1][0]) + " " + str(arrowPoints[-1][1]))
elem11.setAttribute(
"Tail3D",
str(arrowPoints[0][0]) + " " + str(arrowPoints[0][1]))
elem11.setAttribute(
"BoundingBox",
"%f %f %f %f" % (arrowPoints[-1][0], arrowPoints[-1][1],
arrowPoints[0][0], arrowPoints[0][1]))
elem11.setAttribute("color", ShowColor)
#print arrow
#print arrow.type
for color in colors:
elem02 = out.createElement("color")
elem01.appendChild(elem02)
red = str(int(color[1:3], 16) / 255.0)
green = str(int(color[3:5], 16) / 255.0)
blue = str(int(color[5:7], 16) / 255.0)
elem02.setAttribute("r", red)
elem02.setAttribute("g", green)
elem02.setAttribute("b", blue)
FontId = 3
for font in fonts:
elem04 = out.createElement("font")
elem03.appendChild(elem04)
elem04.setAttribute("id", str(FontId))
FontId += 1
elem04.setAttribute("name", font)
with open(name, 'wb') as f:
f.write(out.toxml('utf-8'))
def read_standard_values( self, standard, old_standard=None):
meta_enabled.read_standard_values( self, standard, old_standard=old_standard)
if not old_standard or (standard.line_width != old_standard.line_width):
self.line_width = Screen.any_to_px( standard.line_width)
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
a = ['no','yes']
on_off = ['off','on']
self.id = package.getAttribute( 'id')
# marks (we read them here because they influence the charge)
for m in package.getElementsByTagName( 'mark'):
mrk = marks.mark.read_package( m, self)
self.marks.add( mrk)
self.pos = package.getAttribute( 'pos')
position = package.getElementsByTagName( 'point')[0]
# reading of coords regardless of their unit
x, y, z = Screen.read_xml_point( position)
if z is not None:
self.z = z* self.paper.real_to_screen_ratio()
# needed to support transparent handling of molecular size
x, y = self.paper.real_to_screen_coords( (x, y))
self.x = x
self.y = y
ft = package.getElementsByTagName('ftext')
if ft:
self.set_name(''.join([e.toxml('utf-8') for e in ft[0].childNodes]),
check_valency=0,
interpret=0)
else:
self.set_name( package.getAttribute( 'name'), check_valency=0)
# charge
self.charge = package.getAttribute('charge') and int( package.getAttribute('charge')) or 0
# hydrogens
if package.getAttribute( 'hydrogens'):
self.show_hydrogens = package.getAttribute('hydrogens')
else:
self.show_hydrogens = 0
# font and fill color
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int( fnt.getAttribute( 'size'))
self.font_family = fnt.getAttribute( 'family')
if fnt.getAttribute( 'color'):
self.line_color = fnt.getAttribute( 'color')
# show
if package.getAttribute( 'show'):
self.show = package.getAttribute( 'show')
else:
self.show = (self.symbol!='C')
# background color
if package.getAttributeNode( 'background-color'):
self.area_color = package.getAttribute( 'background-color')
# multiplicity
if package.getAttribute( 'multiplicity'):
self.multiplicity = int( package.getAttribute( 'multiplicity'))
# valency
if package.getAttribute( 'valency'):
self.valency = int( package.getAttribute( 'valency'))
# number
if package.getAttribute( 'show_number'):
self.show_number = bool( data.booleans.index( package.getAttribute( 'show_number')))
if package.getAttribute( 'number'):
self.number = package.getAttribute( 'number')
# free_sites
if package.getAttribute( 'free_sites'):
self.free_sites = int( package.getAttribute( 'free_sites'))
def expand(self):
"""expands the group and returns list of atoms that new drawing afterwords"""
if self.group_type == "builtin":
names = Store.gm.get_template_names()
if self.symbol in names:
a2 = self.neighbors[0]
x1, y1 = a2.get_xy()
x2, y2 = self.get_xy()
self.group_graph = Store.gm.get_transformed_template(
names.index(self.symbol), (x1, y1, x2, y2), type='atom1')
replacement = self.group_graph.next_to_t_atom
else:
print("unknown group %s" % a.symbol)
return None
elif self.group_type == "chain":
self.group_graph = self.molecule.create_graph()
p = PT.formula_dict(self.symbol)
n = p['C']
last = None
for i in range(n):
v = self.group_graph.add_vertex()
v.x, v.y = None, None
if last:
self.group_graph.add_edge(last, v)
last = v
replacement = self.group_graph.vertices[0]
replacement.x = self.x
replacement.y = self.y
elif self.group_type == "implicit":
if not self.group_graph:
self.set_name(self.symbol,
occupied_valency=self.occupied_valency)
for v in self.group_graph.vertices:
v.x, v.y = None, None
v.show = v.symbol != 'C'
assert self.connecting_atom is not None
replacement = self.connecting_atom
replacement.x = self.x
replacement.y = self.y
self.molecule.eat_molecule(self.group_graph)
self.molecule.move_bonds_between_atoms(self, replacement)
self.molecule.delete_vertex(self)
if self.occupied_valency:
oasa.coords_generator.calculate_coords(self.molecule,
bond_length=-1)
else:
# if the group is the only vertex of the molecule we must set the bond_length explicitly
# and the move the whole molecule
replacement.x = None
replacement.y = None
x, y = self.x, self.y
oasa.coords_generator.calculate_coords(
self.molecule,
bond_length=Screen.any_to_px(self.paper.standard.bond_length))
dx = x - replacement.x
dy = y - replacement.y
[a.move(dx, dy) for a in self.group_graph.vertices]
return self.group_graph.vertices
def read_package(self, package):
"""reads the dom element package and sets internal state according to it"""
x, y, z = Screen.read_xml_point(package)
self.x, self.y = self.paper.real_to_screen_coords((x, y))
def y(self, y): self._y = Screen.any_to_px( y)
def construct_dom_tree( self, top_levels):
"""constructs the SVG dom from all top_levels"""
# the constants
border_size = self.paper.get_paper_property( 'crop_margin')
# converter
px_to_cm_txt = lambda x: Screen.px_to_text_with_unit( x, unit="cm", round_to=5)
px_to_mm_txt = lambda x: Screen.px_to_text_with_unit( x, unit="mm", round_to=5)
# the code
self._id = 0
doc = self.document
self.top = dom_extensions.elementUnder( doc, "svg", attributes=(("xmlns", "http://www.w3.org/2000/svg"),
("version", "1.0")))
if self.full_size:
sx = self.paper.get_paper_property( 'size_x')
sy = self.paper.get_paper_property( 'size_y')
dom_extensions.setAttributes( self.top, (("width", '%fmm' % sx),
("height", '%fmm' % sy),
('viewBox', '0 0 %d %d' % (Screen.mm_to_px(sx), Screen.mm_to_px(sy)))))
else:
items = list( self.paper.find_all())
items.remove( self.paper.background)
x1, y1, x2, y2 = self.paper.list_bbox( items)
w = px_to_mm_txt( x2 -x1 +2*border_size)
h = px_to_mm_txt( y2 -y1 +2*border_size)
bx2, by2 = x2-x1+2*border_size, y2-y1+2*border_size
dom_extensions.setAttributes( self.top, (("width", w),
("height", h),
("viewBox",'0 0 %d %d' % ( bx2, by2))))
self.group = dom_extensions.elementUnder( self.top, 'g',
(('font-size', '12pt'),
('font-family', 'Helvetica'),
('stroke-linecap', 'round')))
if not self.full_size:
self.group.setAttribute( 'transform', 'translate(%d,%d)' % (-x1+border_size, -y1+border_size))
# sort the top_levels according to paper.stack
cs = []
for c in self.paper.stack:
if c in top_levels:
cs.append( c)
for o in cs:
if o.object_type == 'molecule':
for b in o.bonds:
self.add_bond( b)
for a in o.atoms:
self.add_atom( a)
elif o.object_type == 'arrow':
self.add_arrow( o)
elif o.object_type == 'text':
self.add_text( o)
elif o.object_type == 'plus':
self.add_plus( o)
elif o.object_type in data.vector_graphics_types:
if o.object_type == 'rect':
self.add_rect( o)
elif o.object_type == 'oval':
self.add_oval( o)
elif o.object_type == 'polygon':
self.add_polygon( o)
elif o.object_type == 'polyline':
self.add_polyline( o)
def done(self, button):
"""called on dialog exit"""
self.dialog.deactivate()
if button != _('OK'):
pass
else:
#print self.marks.get()
# apply changes
for o in self.items:
change = 0
# ATOM
if o.object_type == 'atom':
a = self.atom_show.index(Pmw.SELECT)
if a != 2:
o.show = a
change = 1
# positionning
a = self.atom_pos.index(Pmw.SELECT)
if a != 2:
o.pos = ('center-first', 'center-last')[a]
change = 1
if self.atom_charge.get():
a = int(self.atom_charge.get())
if hasattr(o, 'charge') and o.charge != a:
o.charge = a
change = 1
# hydrogens
a = int(self.atom_show_h.index(Pmw.SELECT))
if a != 2:
o.show_hydrogens = a
change = 1
# font is in common now
# BOND
elif o.object_type == 'bond':
# width is in common now
# bond_width
d = Screen.any_to_px(self.bond_dist.getvalue())
if d:
if d != abs(o.bond_width):
o.bond_width = d * misc.signum(o.bond_width)
change = 1
# wedge_width
d = Screen.any_to_px(self.wedge_width.getvalue())
if d:
if d != o.wedge_width:
o.wedge_width = d
change = 1
# ratio
ratio = self.double_length_ratio.getvalue()
if ratio:
ratio = float(self.double_length_ratio.getvalue())
if ratio != o.double_length_ratio:
o.double_length_ratio = ratio
change = 1
# ARROW - most is in common now
elif o.object_type == 'arrow':
if self.arrow_start_changed:
o.set_pins(start=self.arrow_start.get())
change = 1
if self.arrow_end_changed:
o.set_pins(end=self.arrow_end.get())
change = 1
if self.spline_changed:
o.spline = self.spline.get()
change = 1
# TEXT - all is in common now
# PLUS - all is in common now
# VECTOR - all is in common now
# COMMON PROPERTIES
# LINE COLOR
if hasattr(o, 'line_color') and self.line_color.color:
if self.line_color.color != o.line_color:
o.line_color = self.line_color.color
change = 1
# AREA COLOR
if hasattr(o, 'area_color') and self.area_color.color:
if self.area_color.color != o.area_color:
o.area_color = self.area_color.color
change = 1
# LINE WIDTH
if hasattr(o, 'line_width'):
w = Screen.any_to_px(self.line_width.getvalue())
if w:
if w != o.line_width:
o.line_width = w
change = 1
# FONT
if hasattr(o, 'font_family'):
if self.font_size.get():
a = int(self.font_size.get())
o.font_size = a
change = 1
if self.font_family.getcurselection(
) and self.font_family.getcurselection(
)[0] != self.used_family:
a = self.font_family.getcurselection()[0]
o.font_family = a
change = 1
# APPLY THE CHANGES
if change:
o.redraw()
self.changes_made = 1
self.cleanup()
def get_transformed_template(self, n, coords, type='empty', paper=None):
"""type is type of connection - 'bond', 'atom1'(for single atom), 'atom2'(for atom with more than 1 bond), 'empty'"""
pap = paper or Store.app.paper
pap.onread_id_sandbox_activate() # must be here to mangle the ids
current = molecule(pap, package=self.templates[n])
pap.onread_id_sandbox_finish(apply_to=[current]) # id mangling
current.name = ''
self._scale_ratio = 1
trans = transform()
# type empty - just draws the template - no conection
if type == 'empty':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1 = coords
bond_length = Screen.any_to_px(
Store.app.paper.standard.bond_length)
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
trans.set_move(-xt2, -yt2)
trans.set_scaling(bond_length / math.sqrt((xt1 - xt2)**2 +
(yt1 - yt2)**2))
trans.set_move(x1, y1)
#type atom
elif type == 'atom1' or type == 'atom2':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1, x2, y2 = coords
trans.set_move(-xt2, -yt2)
trans.set_scaling(
math.sqrt((x1 - x2)**2 + (y1 - y2)**2) /
math.sqrt((xt1 - xt2)**2 + (yt1 - yt2)**2))
trans.set_rotation(
math.atan2(xt1 - xt2, yt1 - yt2) -
math.atan2(x1 - x2, y1 - y2))
trans.set_move(x2, y2)
#type bond
elif type == 'bond':
if not (current.t_bond_first and current.t_bond_second):
warn(
"this template is not capable to be added to bond - sorry."
)
return None
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
xt1, yt1 = current.t_bond_first.get_xy()
xt2, yt2 = current.t_bond_second.get_xy()
x1, y1, x2, y2 = coords
self._scale_ratio = math.sqrt(
(x1 - x2)**2 + (y1 - y2)**2) / math.sqrt(
(xt1 - xt2)**2 + (yt1 - yt2)**
2) # further needed for bond.bond_width transformation
trans.set_move(-xt1, -yt1)
trans.set_rotation(
math.atan2(xt1 - xt2, yt1 - yt2) -
math.atan2(x1 - x2, y1 - y2))
trans.set_scaling(self._scale_ratio)
trans.set_move(x1, y1)
self.transform_template(current, trans)
#remove obsolete info from template
if type == 'atom1':
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
elif type == 'atom2':
current.t_atom.x = x1
current.t_atom.y = y1
current.t_atom = None
current.t_bond_first = None
current.t_bond_second = None
#return ready template
return current
def construct_dom_tree(self, top_levels):
"""Construct the SVG dom from all top_levels.
"""
# the constants
border_size = self.paper.get_paper_property('crop_margin')
# converter
px_to_cm_txt = lambda x: Screen.px_to_text_with_unit(
x, unit="cm", round_to=5)
px_to_mm_txt = lambda x: Screen.px_to_text_with_unit(
x, unit="mm", round_to=5)
# the code
self._id = 0
doc = self.document
self.top = dom_extensions.elementUnder(
doc,
"svg",
attributes=(("xmlns", "http://www.w3.org/2000/svg"), ("version",
"1.0")))
if self.full_size:
sx = self.paper.get_paper_property('size_x')
sy = self.paper.get_paper_property('size_y')
dom_extensions.setAttributes(
self.top, (("width", '%fmm' % sx), ("height", '%fmm' % sy),
('viewBox', '0 0 %d %d' %
(Screen.mm_to_px(sx), Screen.mm_to_px(sy)))))
else:
items = list(self.paper.find_all())
items.remove(self.paper.background)
x1, y1, x2, y2 = self.paper.list_bbox(items)
w = px_to_mm_txt(x2 - x1 + 2 * border_size)
h = px_to_mm_txt(y2 - y1 + 2 * border_size)
bx2, by2 = x2 - x1 + 2 * border_size, y2 - y1 + 2 * border_size
dom_extensions.setAttributes(
self.top, (("width", w), ("height", h),
("viewBox", '0 0 %d %d' % (bx2, by2))))
self.group = dom_extensions.elementUnder(self.top, 'g',
(('font-size', '12pt'),
('font-family', 'Helvetica'),
('stroke-linecap', 'round')))
if not self.full_size:
self.group.setAttribute(
'transform',
'translate(%d,%d)' % (-x1 + border_size, -y1 + border_size))
# sort the top_levels according to paper.stack
cs = []
for c in self.paper.stack:
if c in top_levels:
cs.append(c)
for o in cs:
if o.object_type == 'molecule':
for b in o.bonds:
self.add_bond(b)
for a in o.atoms:
self.add_atom(a)
elif o.object_type == 'arrow':
self.add_arrow(o)
elif o.object_type == 'text':
self.add_text(o)
elif o.object_type == 'plus':
self.add_plus(o)
elif o.object_type in data.vector_graphics_types:
if o.object_type == 'rect':
self.add_rect(o)
elif o.object_type == 'oval':
self.add_oval(o)
elif o.object_type == 'polygon':
self.add_polygon(o)
elif o.object_type == 'polyline':
self.add_polyline(o)
def _set_y( self, y): self._y = Screen.any_to_px( y)
def _set_x( self, x): self._x = Screen.any_to_px( x)
def write_to_file( self, name):
#{"v BKChemu bond.type":"v ChemDraw hodnota atributu Display elementu b"}
bondType={"w":"WedgeBegin",
"h":"WedgedHashBegin",
"a":"Wavy",
"b":"Bold",
"d":"Dash",
"o":"Dash"
}
#{"arrow.type v BKChemu":["graphic/ArrowType","arrow/ArrowheadHead","arrow/ ArrowheadTail","arrow/ArrowheadType"]}
#"retro":["RetroSynthetic","Full","","Angle"] - nefunguje, potrebuje dalsi povinne atributy
arrowType={"equilibrium":["Equilibrium","HalfLeft","HalfLeft","Solid"],
"equilibrium2":["Equilibrium","HalfLeft","HalfLeft","Solid"],
"normal":["FullHead","Full","","Solid"],
"electron":["HalfHead","HalfLeft","","Solid"]
}
colors=["#ffffff","#000000","#ff0000","#ffff00","#00ff00","#00ffff","#0000ff","#ff00ff"]
fonts=["Arial","Times New Roman"]
out=dom.Document()
root=out.createElement("CDXML")
out.appendChild(root)
elem01=out.createElement("colortable")
root.appendChild(elem01)
elem03=out.createElement("fonttable")
root.appendChild(elem03)
elem1=out.createElement("page")
root.appendChild(elem1)
PaperX=int(Screen.mm_to_px( self.paper.get_paper_property("size_x") ) )
PaperY=int(Screen.mm_to_px( self.paper.get_paper_property("size_y") ) )
elem1.setAttribute("BoundingBox","%d %d %d %d" % (0,0,PaperX,PaperY) )
elem1.setAttribute("Width",str(PaperX) )
elem1.setAttribute("Height",str(PaperY) )
elem1.setAttribute("DrawingSpace","poster")
for mol in self.paper.molecules:
elem2=out.createElement("fragment")
elem1.appendChild(elem2)
for atom in mol.atoms:
elem3=out.createElement("n")
elem2.appendChild(elem3)
elem3.setAttribute("id",re.sub("atom","",atom.id) )
elem3.setAttribute("p","%f %f" %(atom.x,atom.y) )
elem3.setAttribute("NumHydrogens","%d" % atom.free_valency)
if atom.symbol != "C" or atom.show:
elem4=out.createElement("t")
elem3.appendChild(elem4)
elem6=out.createElement("s")
elem6.setAttribute("size",str(atom.font_size) )
elem6.setAttribute("face","96")
elem4.appendChild(elem6)
text4 = re.sub( "<.*?>", "", atom.xml_ftext)
if text4:
symbol=out.createTextNode(text4)
elem6.appendChild(symbol)
else:
symbol=out.createTextNode(atom.xml_ftext)
elem6.appendChild(symbol)
NewColor=self.paper.any_color_to_rgb_string( atom.line_color)
if NewColor not in colors:
colors.append (NewColor)
for color in colors:
if color==NewColor:
ShowColor=str(colors.index(color)+2)
elem4.setAttribute("color",ShowColor)
elem6.setAttribute("color",ShowColor)
NewFont=atom.font_family
if NewFont not in fonts:
fonts.append(NewFont)
for font in fonts:
if font==NewFont:
FontId=str(fonts.index(font)+3)
elem6.setAttribute("font",FontId)
for bond in mol.bonds:
elem5=out.createElement("b")
elem2.appendChild(elem5)
elem5.setAttribute("B",re.sub("atom","",bond.atom1.id) )
elem5.setAttribute("E",re.sub("atom","",bond.atom2.id) )
for bondB, bondC in bondType.items():
if bond.type==bondB:
elem5.setAttribute("Display",bondC)
elif bond.type=="h" and bond.equithick==1:
elem5.setAttribute("Display","Hash")
NewColor=self.paper.any_color_to_rgb_string( bond.line_color)
if NewColor not in colors:
colors.append (NewColor)
for color in colors:
if color==NewColor:
ShowColor=str(colors.index(color)+2)
elem5.setAttribute("color",ShowColor)
#print int( self.paper.any_color_to_rgb_string( bond.line_color)[1:3], 16)
if bond.order > 1:
elem5.setAttribute("Order","%d" % bond.order )
#print bond.type,bond.equithick,bond.simple_double
for text in self.paper.texts:
elem7=out.createElement("t")
elem1.appendChild(elem7)
elem7.setAttribute("id",re.sub("text","",text.id))
elem7.setAttribute("p","%f %f" % (text.x,text.y))
elem7.setAttribute("BoundingBox","%d %d %d %d" % (text.bbox()[0],text.bbox()[1],text.bbox()[2],text.bbox()[3]) )
minidoc = dom.parseString( "<a>%s</a>" % text.xml_ftext.encode('utf-8'))
textik={"i":2,
"b":1,
"sub":32,
"sup":64
}
def get_text( el):
texts = []
for ch in el.childNodes:
if isinstance( ch, dom.Text):
parents = []
par = ch.parentNode
while not isinstance( par, dom.Document):
parents.append( str(par.nodeName))
par = par.parentNode
texts.append((ch.nodeValue, parents))
else:
texts += get_text( ch)
return texts
texts2= get_text(minidoc.childNodes[0])
for text2 in texts2:
elem001=out.createElement("s")
elem7.appendChild(elem001)
elem001.setAttribute("size", str(text.font_size))
text001=out.createTextNode(text2[0])
elem001.appendChild(text001)
def LogOR(xs):
if len(xs) == 0:
return 0
else:
return xs[0] | LogOR (xs[1:])
Faces=[]
for xxx in text2[1]:
for P, F in textik.items():
if P==xxx:
Faces.append(F)
Face=LogOR(Faces)
if Face!=0:
elem001.setAttribute("face",str(Face) )
NewFont=text.font_family
if NewFont not in fonts:
fonts.append(NewFont)
for font in fonts:
if font==NewFont:
FontId=str(fonts.index(font)+3)
elem001.setAttribute("font",FontId)
NewColor=self.paper.any_color_to_rgb_string(text.line_color)
if NewColor not in colors:
colors.append (NewColor)
for color in colors:
if color==NewColor:
ShowColor=str(colors.index(color)+2)
elem001.setAttribute("color",ShowColor)
elem7.setAttribute("color",ShowColor)
for plus in self.paper.pluses:
elem9=out.createElement("graphic")
elem1.appendChild(elem9)
elem9.setAttribute("SymbolType","Plus")
elem9.setAttribute("BoundingBox","%f %f %f %f" % plus.bbox())
elem9.setAttribute("GraphicType","Symbol")
elem9.setAttribute("id",re.sub("plus","",plus.id))
#print plus.bbox()
NewColor=self.paper.any_color_to_rgb_string(plus.line_color)
if NewColor not in colors:
colors.append (NewColor)
for color in colors:
if color==NewColor:
ShowColor=str(colors.index(color)+2)
elem9.setAttribute("color",ShowColor)
for arrow in self.paper.arrows:
arrowPoints=[p.get_xy() for p in arrow.points]
elem10=out.createElement("graphic")
elem1.appendChild(elem10)
elem10.setAttribute("GraphicType","Line")
for arrowB, arrowC in arrowType.items():
if arrow.type==arrowB:
elem10.setAttribute("ArrowType",arrowC[0])
NewColor=self.paper.any_color_to_rgb_string(arrow.line_color)
if NewColor not in colors:
colors.append (NewColor)
for color in colors:
if color==NewColor:
ShowColor=str(colors.index(color)+2)
elem10.setAttribute("color",ShowColor)
elem11=out.createElement("arrow")
elem1.appendChild(elem11)
for arrowB, arrowC in arrowType.items():
if arrow.type==arrowB:
elem11.setAttribute("ArrowheadHead",arrowC[1])
elem11.setAttribute("ArrowheadTail",arrowC[2])
elem11.setAttribute("ArrowheadType",arrowC[3])
elem11.setAttribute("Head3D",str(arrowPoints[-1][0])+" "+str(arrowPoints[-1][1]))
elem11.setAttribute("Tail3D",str(arrowPoints[0][0])+" "+str(arrowPoints[0][1]))
elem11.setAttribute("BoundingBox","%f %f %f %f" % (arrowPoints[-1][0],arrowPoints[-1][1],arrowPoints[0][0],arrowPoints[0][1]) )
elem11.setAttribute("color",ShowColor)
#print arrow
#print arrow.type
for color in colors:
elem02=out.createElement("color")
elem01.appendChild(elem02)
red=str(int(color[1:3],16)/255.0)
green=str(int(color[3:5],16)/255.0)
blue=str(int(color[5:7],16)/255.0)
elem02.setAttribute("r",red)
elem02.setAttribute("g",green)
elem02.setAttribute("b",blue)
FontId=3
for font in fonts:
elem04=out.createElement("font")
elem03.appendChild(elem04)
elem04.setAttribute("id",str(FontId) )
FontId+=1
elem04.setAttribute("name",font)
with open(name, 'wb') as f:
f.write(out.toxml('utf-8'))
