def _where_to_draw_from_and_to( self, b):
def fix_bbox( a):
x, y = a.x, a.y
data = self._vertex_to_bbox.get( a, None)
if data:
(ox, oy), bbox = data
dx = x - ox
dy = y - oy
bbox = [bbox[0]+dx,bbox[1]+dy,bbox[2]+dx,bbox[3]+dy]
return bbox
return None
# at first check if the bboxes are not overlapping
atom1, atom2 = b.vertices
x1, y1 = atom1.x, atom1.y
x2, y2 = atom2.x, atom2.y
bbox1 = fix_bbox( atom1)
bbox2 = fix_bbox( atom2)
if bbox1 and bbox2 and geometry.do_rectangles_intersect( bbox1, bbox2):
return None
# then we continue with computation
if bbox1:
x1, y1 = geometry.intersection_of_line_and_rect( (x1,y1,x2,y2), bbox1, round_edges=0)
if bbox2:
x2, y2 = geometry.intersection_of_line_and_rect( (x1,y1,x2,y2), bbox2, round_edges=0)
if geometry.point_distance( x1, y1, x2, y2) <= 1.0:
return None
else:
return (x1, y1, x2, y2)
def _where_to_draw_from_and_to(self, b):
def fix_bbox(a):
x, y = a.x, a.y
data = self._vertex_to_bbox.get(a, None)
if data:
(ox, oy), bbox = data
dx = x - ox
dy = y - oy
bbox = [bbox[0] + dx, bbox[1] + dy, bbox[2] + dx, bbox[3] + dy]
return bbox
return None
# at first check if the bboxes are not overlapping
atom1, atom2 = b.vertices
x1, y1 = atom1.x, atom1.y
x2, y2 = atom2.x, atom2.y
bbox1 = fix_bbox(atom1)
bbox2 = fix_bbox(atom2)
if bbox1 and bbox2 and geometry.do_rectangles_intersect(bbox1, bbox2):
return None
# then we continue with computation
if bbox1:
x1, y1 = geometry.intersection_of_line_and_rect((x1, y1, x2, y2),
bbox1,
round_edges=0)
if bbox2:
x2, y2 = geometry.intersection_of_line_and_rect((x1, y1, x2, y2),
bbox2,
round_edges=0)
if geometry.point_distance(x1, y1, x2, y2) <= 1.0:
return None
else:
return (x1, y1, x2, y2)
def _draw_vertex( self, v):
pos = sum( [(a.x < v.x) and -1 or 1 for a in v.neighbors if abs(a.x-v.x)>0.2])
if 'show_symbol' in v.properties_:
show_symbol = v.properties_['show_symbol']
else:
show_symbol = (v.symbol != "C" or v.degree == 0 or self.show_carbon_symbol)
if show_symbol:
x = v.x
y = v.y
text = v.symbol
hs = ""
if self.show_hydrogens_on_hetero or v.properties_.get( 'show_hydrogens', False):
if v.free_valency == 1:
hs = "H"
elif v.free_valency > 1:
hs = "H<sub>%d</sub>" % v.free_valency
if not hs:
pos = -1
if pos <= 0:
text += hs
else:
text = hs + text
# charge
charge = ""
if v.charge == 1:
charge = "<sup>+</sup>"
elif v.charge == -1:
charge = "<sup>−</sup>"
elif v.charge > 1:
charge = "<sup>%d+</sup>" % v.charge
elif v.charge < -1:
charge = "<sup>%d−</sup>" % abs( v.charge)
if charge:
if self._is_there_place( v, v.x+3, v.y-2) or v.charge < 0:
# we place negative charge regardless of available place
# otherwise minus might be mistaken for a bond
text += charge
charge = ""
# coloring
if self.color_atoms:
color = self.atom_colors.get( v.symbol, (0,0,0))
else:
color = (0,0,0)
center_letter = pos <= 0 and 'first' or 'last'
bbox = self._draw_text( (x,y), text, center_letter=center_letter, color=color)
self._vertex_to_bbox[v] = ((x,y), geometry.expand_rectangle( bbox, self.space_around_atom))
# sometimes charge is done here, if it wasn't done before
if charge:
assert v.charge > 0
# if charge was not dealt with we change its appearance from 2+ to ++
charge = v.charge * "+"
if self._is_there_place( v, v.x, v.y-10):
angle = 1.5*math.pi
elif self._is_there_place( v, v.x, v.y+10):
angle = 0.5*math.pi
else:
angle = self._find_place_around_atom( v)
self.context.set_font_size( self.subscript_size_ratio * self.font_size)
xbearing, ybearing, width, height, x_advance, y_advance = self.context.text_extents( charge)
x0 = v.x + 40*math.cos( angle)
y0 = v.y + 40*math.sin( angle)
line = (v.x,v.y,x0,y0)
charge_bbox = [x0-0.5*width,y0-0.5*height,x0+0.5*width,y0+0.5*height]
x1, y1 = geometry.intersection_of_line_and_rect( line, bbox, round_edges=0)
x2, y2 = geometry.intersection_of_line_and_rect( line, charge_bbox, round_edges=0)
x2, y2 = geometry.elongate_line( x1,y1,x2,y2, -self.space_around_atom)
x = x0 + x1 - x2
y = y0 + y1 - y2
# draw
self.context.set_source_rgb( *color)
self.context.move_to( round( x-xbearing-0.5*width), round( y+0.5*height))
self.context.show_text( charge)
def _draw_vertex(self, v):
pos = sum([(a.x < v.x) and -1 or 1 for a in v.neighbors
if abs(a.x - v.x) > 0.2])
if 'show_symbol' in v.properties_:
show_symbol = v.properties_['show_symbol']
else:
show_symbol = (v.symbol != "C" or v.degree == 0
or self.show_carbon_symbol)
if show_symbol:
x = v.x
y = v.y
text = v.symbol
hs = ""
if self.show_hydrogens_on_hetero or v.properties_.get(
'show_hydrogens', False):
if v.free_valency == 1:
hs = "H"
elif v.free_valency > 1:
hs = "H<sub>%d</sub>" % v.free_valency
if not hs:
pos = -1
if pos <= 0:
text += hs
else:
text = hs + text
# charge
charge = ""
if v.charge == 1:
charge = "<sup>+</sup>"
elif v.charge == -1:
charge = "<sup>−</sup>"
elif v.charge > 1:
charge = "<sup>%d+</sup>" % v.charge
elif v.charge < -1:
charge = "<sup>%d−</sup>" % abs(v.charge)
if charge:
if self._is_there_place(v, v.x + 3, v.y - 2) or v.charge < 0:
# we place negative charge regardless of available place
# otherwise minus might be mistaken for a bond
text += charge
charge = ""
# coloring
if self.color_atoms:
color = self.atom_colors.get(v.symbol, (0, 0, 0))
else:
color = (0, 0, 0)
center_letter = pos <= 0 and 'first' or 'last'
bbox = self._draw_text((x, y),
text,
center_letter=center_letter,
color=color)
self._vertex_to_bbox[v] = ((x, y),
geometry.expand_rectangle(
bbox, self.space_around_atom))
# sometimes charge is done here, if it wasn't done before
if charge:
assert v.charge > 0
# if charge was not dealt with we change its appearance from 2+ to ++
charge = v.charge * "+"
if self._is_there_place(v, v.x, v.y - 10):
angle = 1.5 * math.pi
elif self._is_there_place(v, v.x, v.y + 10):
angle = 0.5 * math.pi
else:
angle = self._find_place_around_atom(v)
self.context.set_font_size(self.subscript_size_ratio *
self.font_size)
xbearing, ybearing, width, height, x_advance, y_advance = self.context.text_extents(
charge)
x0 = v.x + 40 * math.cos(angle)
y0 = v.y + 40 * math.sin(angle)
line = (v.x, v.y, x0, y0)
charge_bbox = [
x0 - 0.5 * width, y0 - 0.5 * height, x0 + 0.5 * width,
y0 + 0.5 * height
]
x1, y1 = geometry.intersection_of_line_and_rect(line,
bbox,
round_edges=0)
x2, y2 = geometry.intersection_of_line_and_rect(line,
charge_bbox,
round_edges=0)
x2, y2 = geometry.elongate_line(x1, y1, x2, y2,
-self.space_around_atom)
x = x0 + x1 - x2
y = y0 + y1 - y2
# draw
self.context.set_source_rgb(*color)
self.context.move_to(round(x - xbearing - 0.5 * width),
round(y + 0.5 * height))
self.context.show_text(charge)
