def get_angle_at_side( v, d, d2, relation, attach_angle):
if attach_angle == 180:
# shortcut
return attach_angle
side = geometry.on_which_side_is_point( (d.x,d.y,v.x,v.y), (d2.x,d2.y))
an = angle + deg_to_rad( attach_angle)
x = v.x + self.bond_length*cos( an)
y = v.y + self.bond_length*sin( an)
if relation*side == geometry.on_which_side_is_point( (d.x,d.y,v.x,v.y), (x,y)):
return attach_angle
else:
return -attach_angle
def _draw_edge(self, e):
v1, v2 = e.vertices
start = self.transformer.transform_xy(v1.x, v1.y)
end = self.transformer.transform_xy(v2.x, v2.y)
parent = self._create_parent(e, self.top)
if e.order == 1:
self._draw_line(parent, start, end, line_width=self.line_width)
if e.order == 2:
side = 0
# find how to center the bonds
# rings have higher priority in setting the positioning
for ring in self.molecule.get_smallest_independent_cycles():
if v1 in ring and v2 in ring:
side += reduce(operator.add, [
geometry.on_which_side_is_point(
start + end,
(self.transformer.transform_xy(a.x, a.y)))
for a in ring if a != v1 and a != v2
])
# if rings did not decide, use the other neigbors
if not side:
for v in v1.neighbors + v2.neighbors:
if v != v1 and v != v2:
side += geometry.on_which_side_is_point(
start + end,
(self.transformer.transform_xy(v.x, v.y)))
if side:
self._draw_line(parent, start, end, line_width=self.line_width)
x1, y1, x2, y2 = geometry.find_parallel(
start[0], start[1], end[0], end[1],
self.bond_width * misc.signum(side))
self._draw_line(parent, (x1, y1), (x2, y2),
line_width=self.line_width)
else:
for i in (1, -1):
x1, y1, x2, y2 = geometry.find_parallel(
start[0], start[1], end[0], end[1],
i * self.bond_width * 0.5)
self._draw_line(parent, (x1, y1), (x2, y2),
line_width=self.line_width)
elif e.order == 3:
self._draw_line(parent, start, end, line_width=self.line_width)
for i in (1, -1):
x1, y1, x2, y2 = geometry.find_parallel(
start[0], start[1], end[0], end[1],
i * self.bond_width * 0.7)
self._draw_line(parent, (x1, y1), (x2, y2),
line_width=self.line_width)
def _process_multi_anelated_ring( self, ring, angle_shift=0):
out = []
to_go = [v for v in ring if v.x == None or v.y == None]
if not to_go:
# it was all already done
return []
back = [v for v in ring if v.x != None and v.y != None]
sorted_back = self.mol.sort_vertices_in_path( back)
if not sorted_back:
# the already set atoms are not in one path - we have to process it "per partes"
# it should not happen with the construction method we use
raise( "i am not able to handle this, it should normaly not happen. please send me the input.")
else:
v1 = sorted_back[0]
v2 = sorted_back[-1]
v3 = sorted_back[1]
to_go = self.mol.sort_vertices_in_path( to_go)
if v1 not in to_go[0].get_neighbors():
v1, v2 = v2, v1
blocked_angle = sum_of_ring_internal_angles( len( back))
overall_angle = sum_of_ring_internal_angles( len( ring))
da = optimal_ring_iternal_angle( len( ring)) # internal angle
# if there are 2 rings of same size inside each other, we need to use the angle_shift
if angle_shift:
da += 2*angle_shift/(len( to_go))
ca = deg_to_rad( 180-(overall_angle - blocked_angle - len( to_go) * da + angle_shift)/2) # connection angle
side = sum( [geometry.on_which_side_is_point( (v1.x,v1.y,v2.x,v2.y),(v.x,v.y)) for v in back if v != v1 and v != v2])
# we need to make sure that the ring is drawn on the right side
if side > 0:
ca = -ca
ca += geometry.clockwise_angle_from_east( v1.x-v2.x, v1.y-v2.y)
da = 180-da # for drawing we use external angle
# we must ensure that the ring will progress towards the second end
if geometry.on_which_side_is_point( (v1.x,v1.y,v3.x,v3.y),(v2.x,v2.y)) < 0:
da = -da
# dry run to see where we get
gcoords = gen_angle_stream( deg_to_rad( da), start_from= ca)
x, y = v1.x, v1.y
for i in range( len( to_go) +1):
a = gcoords.next()
x += self.bond_length*cos( a)
y += self.bond_length*sin( a)
# end of dry run, we can scale the bond_length now
length = geometry.line_length( (v1.x,v1.y,v2.x,v2.y))
real_length = geometry.line_length( (v1.x,v1.y,x,y))
bl = self.bond_length * length / real_length
gcoords = gen_angle_stream( deg_to_rad( da), start_from= ca)
# and here we go
self.apply_gen_to_atoms( gcoords, to_go, v1, bond_length=bl)
out += to_go
return out
def _process_simply_anelated_ring( self, ring, base):
out = []
inter = [v for v in ring if v.x != None and v.y != None]
if len( inter) == 1:
# rings are connected via one atom
v = inter.pop() # the atom of concatenation
ring = self.mol.sort_vertices_in_path( ring, start_from=v)
base_neighs = [a for a in v.get_neighbors() if a in base]
if len( base_neighs) < 2:
raise "this should not happen"
d1 = base_neighs[0]
d2 = base_neighs[1]
ca1 = geometry.clockwise_angle_from_east( v.x-d1.x, v.y-d1.y)
ca2 = geometry.clockwise_angle_from_east( v.x-d2.x, v.y-d2.y)
ca = (ca1+ca2)/2
if abs( ca1-ca2) < pi:
ca += -pi/2
else:
ca += pi/2
size = len( ring)
da = deg_to_rad(180 -180.0*(size-2)/size)
gcoords = gen_angle_stream( da, start_from=ca + da/2)
ring.remove( v)
# here we generate the coords
self.apply_gen_to_atoms( gcoords, ring, v)
ring.append( v)
out += ring
elif len( inter) == 2:
# there are two atoms common to the rings
v1, v2 = inter # the atoms of concatenation
ring = self.mol.sort_vertices_in_path( ring, start_from=v1)
ring.remove( v1)
ring.remove( v2)
if not v1 in ring[0].get_neighbors():
v1, v2 = v2, v1
side = sum( [geometry.on_which_side_is_point((v1.x,v1.y,v2.x,v2.y),(v.x,v.y)) for v in base])
if not side:
warnings.warn( "this should not happen")
ca = geometry.clockwise_angle_from_east( v1.x-v2.x, v1.y-v2.y)
size = len( ring)+2
da = deg_to_rad(180 -180.0*(size-2)/size)
if side > 0:
da = -da
gcoords = gen_angle_stream( da, start_from=ca+da)
self.apply_gen_to_atoms( gcoords, ring, v1)
ring.append( v1)
ring.append( v2)
out += ring
else:
# there are more than 2 atoms common
if len( ring) == len( base):
out += self._process_multi_anelated_ring( ring, angle_shift=15)
#raise( "i don't how to handle this yet")
else:
out += self._process_multi_anelated_ring( ring)
return out
def get_angle_gradient2( self, opt_angle, refv, v1, v2):
ang1 = geometry.clockwise_angle_from_east( v1.x-refv.x, v1.y-refv.y)
ang2 = geometry.clockwise_angle_from_east( v2.x-refv.x, v2.y-refv.y)
ang = ang1 - ang2
sign = -geometry.on_which_side_is_point( (refv.x, refv.y, v1.x, v1.y), (v2.x, v2.y))
while ang < 0:
ang += 2*pi
if ang > pi:
ang = 2*pi - ang
sign *= -1
dang = (ang - opt_angle) / 2
gx1 = (cos( ang1 - sign*dang) - cos( ang1)) * sqrt( (refv.x-v1.x)**2 + (refv.y-v1.y)**2) #self.bond_length #(v1.x-refv.x)
gy1 = (sin( ang1 - sign*dang) - sin( ang1)) * sqrt( (refv.x-v1.x)**2 + (refv.y-v1.y)**2) #self.bond_length #(v1.y-refv.y)
gx2 = (cos( ang2 + sign*dang) - cos( ang2)) * sqrt( (refv.x-v2.x)**2 + (refv.y-v2.y)**2) #self.bond_length #(v2.x-refv.x)
gy2 = (sin( ang2 + sign*dang) - sin( ang2)) * sqrt( (refv.x-v2.x)**2 + (refv.y-v2.y)**2) #self.bond_length #(v2.y-refv.y)
# control
ang1 = geometry.clockwise_angle_from_east( v1.x-refv.x+gx1, v1.y-refv.y+gy1)
ang2 = geometry.clockwise_angle_from_east( v2.x-refv.x+gx2, v2.y-refv.y+gy2)
ang = ang1 - ang2
sign = geometry.on_which_side_is_point( (refv.x, refv.y, v1.x, v1.y), (v2.x, v2.y))
while ang < 0:
ang += 2*pi
#sign *= -1
if ang > pi:
ang = 2*pi - ang
#sign *= -1
dang2 = (ang - opt_angle) / 2
if abs( dang2) > abs( dang):
print "f**k", rad_to_deg( ang1), rad_to_deg( ang2), rad_to_deg( dang)
else:
#rint "good", rad_to_deg( ang1), rad_to_deg( ang2), rad_to_deg( dang)
pass
return gx1, gy1, gx2, gy2
def _draw_edge( self, e):
v1, v2 = e.vertices
start = self.transformer.transform_xy( v1.x, v1.y)
end = self.transformer.transform_xy( v2.x, v2.y)
parent = self._create_parent( e, self.top)
if e.order == 1:
self._draw_line( parent, start, end, line_width=self.line_width)
if e.order == 2:
side = 0
# find how to center the bonds
# rings have higher priority in setting the positioning
for ring in self.molecule.get_smallest_independent_cycles():
if v1 in ring and v2 in ring:
side += reduce( operator.add, [geometry.on_which_side_is_point( start+end, (self.transformer.transform_xy( a.x,a.y))) for a in ring if a!=v1 and a!=v2])
# if rings did not decide, use the other neigbors
if not side:
for v in v1.neighbors + v2.neighbors:
if v != v1 and v!= v2:
side += geometry.on_which_side_is_point( start+end, (self.transformer.transform_xy( v.x, v.y)))
if side:
self._draw_line( parent, start, end, line_width=self.line_width)
x1, y1, x2, y2 = geometry.find_parallel( start[0], start[1], end[0], end[1], self.bond_width*misc.signum( side))
self._draw_line( parent, (x1, y1), (x2, y2), line_width=self.line_width)
else:
for i in (1,-1):
x1, y1, x2, y2 = geometry.find_parallel( start[0], start[1], end[0], end[1], i*self.bond_width*0.5)
self._draw_line( parent, (x1, y1), (x2, y2), line_width=self.line_width)
elif e.order == 3:
self._draw_line( parent, start, end, line_width=self.line_width)
for i in (1,-1):
x1, y1, x2, y2 = geometry.find_parallel( start[0], start[1], end[0], end[1], i*self.bond_width*0.7)
self._draw_line( parent, (x1, y1), (x2, y2), line_width=self.line_width)
def _draw_edge( self, e):
def draw_plain_or_colored_line( _start, _end, second=False):
"""second means if this is not the main line, drawing might be different"""
if not has_shown_vertex or not self.color_bonds:
if not second:
self._draw_line( _start, _end, line_width=self.line_width, capstyle=cairo.LINE_CAP_ROUND)
else:
self._draw_line( _start, _end, line_width=self.line_width, capstyle=cairo.LINE_CAP_BUTT)
else:
self._draw_colored_line( _start, _end, line_width=self.line_width, start_color=color1, end_color=color2)
def draw_plain_or_colored_wedge( _start, _end):
x1, y1 = _start
x2, y2 = _end
x, y, x0, y0 = geometry.find_parallel( x1, y1, x2, y2, self.wedge_width/2.0)
xa, ya, xb, yb = geometry.find_parallel( x1, y1, x2, y2, self.line_width/2.0)
# no coloring now
if not has_shown_vertex or not self.color_bonds:
self._create_cairo_path( [(xa, ya), (x0, y0), (2*x2-x0, 2*y2-y0), (2*x1-xa, 2*y1-ya)], closed=True)
self.context.set_source_rgb( 0,0,0)
self.context.fill()
else:
# ratio 0.4 looks better than 0.5 because the area difference
# is percieved more than length difference
ratio = 0.4
xm1 = ratio*xa + (1-ratio)*x0
ym1 = ratio*ya + (1-ratio)*y0
xm2 = (1-ratio)*(2*x2-x0) + ratio*(2*x1-xa)
ym2 = (1-ratio)*(2*y2-y0) + ratio*(2*y1-ya)
self.context.set_source_rgb( *color1)
self._create_cairo_path( [(xa,ya), (xm1,ym1), (xm2,ym2), (2*x1-xa, 2*y1-ya)], closed=True)
self.context.fill()
self.context.set_source_rgb( *color2)
self._create_cairo_path( [(xm1,ym1), (x0, y0), (2*x2-x0, 2*y2-y0), (xm2,ym2)], closed=True)
self.context.fill()
def draw_plain_or_colored_hatch( _start, _end):
x1, y1 = _start
x2, y2 = _end
# no coloring now
x, y, x0, y0 = geometry.find_parallel( x1, y1, x2, y2, self.wedge_width/2.0)
xa, ya, xb, yb = geometry.find_parallel( x1, y1, x2, y2, self.line_width/2.0)
d = math.sqrt( (x1-x2)**2 + (y1-y2)**2) # length of the bond
if d == 0:
return # to prevent division by zero
dx1 = (x0 - xa)/d
dy1 = (y0 - ya)/d
dx2 = (2*x2 -x0 -2*x1 +xa)/d
dy2 = (2*y2 -y0 -2*y1 +ya)/d
# we have to decide if the first line should be at the position of the first atom
draw_start = 1 # is index not boolean
if not v1 in self._vertex_to_bbox and v1.occupied_valency > 1:
draw_start = 1
draw_end = 1 # is added to index not boolean
if not v2 in self._vertex_to_bbox and v2.occupied_valency > 1:
draw_end = 0
# adjust the step length
step_size = 2*(self.line_width)
ns = round( d / step_size) or 1
step_size = d / ns
# now we finally draw
self.context.set_line_cap( cairo.LINE_CAP_BUTT)
self.context.set_source_rgb( *color1)
middle = 0.5 * (draw_start + int( round( d/ step_size)) + draw_end - 2)
for i in range( draw_start, int( round( d/ step_size)) +draw_end):
coords = [xa+dx1*i*step_size, ya+dy1*i*step_size, 2*x1-xa+dx2*i*step_size, 2*y1-ya+dy2*i*step_size]
if coords[0] == coords[2] and coords[1] == coords[3]:
if (dx1+dx2) > (dy1+dy2):
coords[0] += 1
else:
coords[1] += 1
self._create_cairo_path( [coords[:2],coords[2:]])
if i >= middle:
self.context.stroke()
self.context.set_source_rgb( *color2)
self.context.stroke()
# code itself
# at first detect the need to make 3D adjustments
self._transform = transform3d.transform3d()
self._invtransform = transform3d.transform3d()
transform = None
if e.order > 1:
atom1,atom2 = e.vertices
for n in atom1.neighbors + atom2.neighbors:
# e.atom1 and e.atom2 are in this list as well
if n.z != 0:
# engage 3d transform prior to detection of where to draw
transform = self._get_3dtransform_for_drawing( e)
#transform = None
break
if transform:
for n in atom1.neighbors + atom2.neighbors:
n.coords = transform.transform_xyz( *n.coords)
self._transform = transform
self._invtransform = transform.get_inverse()
# // end of 3D adjustments
# now the code itself
coords = self._where_to_draw_from_and_to( e)
if coords:
start = coords[:2]
end = coords[2:]
v1, v2 = e.vertices
if self.color_bonds:
color1 = self.atom_colors.get( v1.symbol, (0,0,0))
color2 = self.atom_colors.get( v2.symbol, (0,0,0))
else:
color1 = color2 = (0,0,0)
has_shown_vertex = bool( [1 for _v in e.vertices if _v in self._vertex_to_bbox])
if e.order == 1:
if e.type == 'w':
draw_plain_or_colored_wedge( start, end)
elif e.type == 'h':
draw_plain_or_colored_hatch( start, end)
else:
draw_plain_or_colored_line( start, end)
if e.order == 2:
side = 0
# find how to center the bonds
# rings have higher priority in setting the positioning
in_ring = False
for ring in self.molecule.get_smallest_independent_cycles_dangerous_and_cached():
double_bonds = len( [b for b in self.molecule.vertex_subgraph_to_edge_subgraph(ring) if b.order == 2])
if v1 in ring and v2 in ring:
in_ring = True
side += double_bonds * reduce( operator.add, [geometry.on_which_side_is_point( start+end, (a.x,a.y)) for a in ring if a!=v1 and a!=v2])
# if rings did not decide, use the other neigbors
if not side:
for v in v1.neighbors + v2.neighbors:
if v != v1 and v!= v2:
side += geometry.on_which_side_is_point( start+end, (v.x, v.y))
# if neighbors did not decide either
if not side and (in_ring or not has_shown_vertex):
if in_ring:
# we don't want centered bonds inside rings
side = 1 # select arbitrary value
else:
# bond between two unshown atoms - we want to center them only in some cases
if len( v1.neighbors) == 1 and len( v2.neighbors) == 1:
# both atoms have only one neighbor
side = 0
elif len( v1.neighbors) < 3 and len( v2.neighbors) < 3:
# try to figure out which side is more towards the center of the molecule
side = reduce( operator.add, [geometry.on_which_side_is_point( start+end, (a.x,a.y))
for a in self.molecule.vertices if a!=v1 and a!=v2], 0)
if not side:
side = 1 # we choose arbitrary value, we don't want centering
if side:
draw_plain_or_colored_line( start, end)
x1, y1, x2, y2 = geometry.find_parallel( start[0], start[1], end[0], end[1], self.bond_width*misc.signum( side))
# shorten the second line
length = geometry.point_distance( x1,y1,x2,y2)
if v2 not in self._vertex_to_bbox:
x2, y2 = geometry.elongate_line( x1, y1, x2, y2, -self.bond_second_line_shortening*length)
if v1 not in self._vertex_to_bbox:
x1, y1 = geometry.elongate_line( x2, y2, x1, y1, -self.bond_second_line_shortening*length)
draw_plain_or_colored_line( (x1, y1), (x2, y2), second=True)
else:
for i in (1,-1):
x1, y1, x2, y2 = geometry.find_parallel( start[0], start[1], end[0], end[1], i*self.bond_width*0.5)
draw_plain_or_colored_line( (x1, y1), (x2, y2))
elif e.order == 3:
self._draw_line( start, end, line_width=self.line_width)
for i in (1,-1):
x1, y1, x2, y2 = geometry.find_parallel( start[0], start[1], end[0], end[1], i*self.bond_width*0.7)
draw_plain_or_colored_line( (x1, y1), (x2, y2), second=True)
if transform:
# if transform was used, we need to transform back
for n in atom1.neighbors + atom2.neighbors:
n.coords = self._invtransform.transform_xyz( *n.coords)
def _draw_edge(self, e):
def draw_plain_or_colored_line(_start, _end, second=False):
"""second means if this is not the main line, drawing might be different"""
if not has_shown_vertex or not self.color_bonds:
if not second:
self._draw_line(_start,
_end,
line_width=self.line_width,
capstyle=cairo.LINE_CAP_ROUND)
else:
self._draw_line(_start,
_end,
line_width=self.line_width,
capstyle=cairo.LINE_CAP_BUTT)
else:
self._draw_colored_line(_start,
_end,
line_width=self.line_width,
start_color=color1,
end_color=color2)
def draw_plain_or_colored_wedge(_start, _end):
x1, y1 = _start
x2, y2 = _end
x, y, x0, y0 = geometry.find_parallel(x1, y1, x2, y2,
self.wedge_width / 2.0)
xa, ya, xb, yb = geometry.find_parallel(x1, y1, x2, y2,
self.line_width / 2.0)
# no coloring now
if not has_shown_vertex or not self.color_bonds:
self._create_cairo_path([(xa, ya), (x0, y0),
(2 * x2 - x0, 2 * y2 - y0),
(2 * x1 - xa, 2 * y1 - ya)],
closed=True)
self.context.set_source_rgb(0, 0, 0)
self.context.fill()
else:
# ratio 0.4 looks better than 0.5 because the area difference
# is percieved more than length difference
ratio = 0.4
xm1 = ratio * xa + (1 - ratio) * x0
ym1 = ratio * ya + (1 - ratio) * y0
xm2 = (1 - ratio) * (2 * x2 - x0) + ratio * (2 * x1 - xa)
ym2 = (1 - ratio) * (2 * y2 - y0) + ratio * (2 * y1 - ya)
self.context.set_source_rgb(*color1)
self._create_cairo_path([(xa, ya), (xm1, ym1), (xm2, ym2),
(2 * x1 - xa, 2 * y1 - ya)],
closed=True)
self.context.fill()
self.context.set_source_rgb(*color2)
self._create_cairo_path([(xm1, ym1), (x0, y0),
(2 * x2 - x0, 2 * y2 - y0),
(xm2, ym2)],
closed=True)
self.context.fill()
def draw_plain_or_colored_hatch(_start, _end):
x1, y1 = _start
x2, y2 = _end
# no coloring now
x, y, x0, y0 = geometry.find_parallel(x1, y1, x2, y2,
self.wedge_width / 2.0)
xa, ya, xb, yb = geometry.find_parallel(x1, y1, x2, y2,
self.line_width / 2.0)
d = math.sqrt((x1 - x2)**2 + (y1 - y2)**2) # length of the bond
if d == 0:
return # to prevent division by zero
dx1 = (x0 - xa) / d
dy1 = (y0 - ya) / d
dx2 = (2 * x2 - x0 - 2 * x1 + xa) / d
dy2 = (2 * y2 - y0 - 2 * y1 + ya) / d
# we have to decide if the first line should be at the position of the first atom
draw_start = 1 # is index not boolean
if not v1 in self._vertex_to_bbox and v1.occupied_valency > 1:
draw_start = 1
draw_end = 1 # is added to index not boolean
if not v2 in self._vertex_to_bbox and v2.occupied_valency > 1:
draw_end = 0
# adjust the step length
step_size = 2 * (self.line_width)
ns = round(d / step_size) or 1
step_size = d / ns
# now we finally draw
self.context.set_line_cap(cairo.LINE_CAP_BUTT)
self.context.set_source_rgb(*color1)
middle = 0.5 * (draw_start + int(round(d / step_size)) + draw_end -
2)
for i in range(draw_start, int(round(d / step_size)) + draw_end):
coords = [
xa + dx1 * i * step_size, ya + dy1 * i * step_size,
2 * x1 - xa + dx2 * i * step_size,
2 * y1 - ya + dy2 * i * step_size
]
if coords[0] == coords[2] and coords[1] == coords[3]:
if (dx1 + dx2) > (dy1 + dy2):
coords[0] += 1
else:
coords[1] += 1
self._create_cairo_path([coords[:2], coords[2:]])
if i >= middle:
self.context.stroke()
self.context.set_source_rgb(*color2)
self.context.stroke()
# code itself
# at first detect the need to make 3D adjustments
self._transform = transform3d.transform3d()
self._invtransform = transform3d.transform3d()
transform = None
if e.order > 1:
atom1, atom2 = e.vertices
for n in atom1.neighbors + atom2.neighbors:
# e.atom1 and e.atom2 are in this list as well
if n.z != 0:
# engage 3d transform prior to detection of where to draw
transform = self._get_3dtransform_for_drawing(e)
#transform = None
break
if transform:
for n in atom1.neighbors + atom2.neighbors:
n.coords = transform.transform_xyz(*n.coords)
self._transform = transform
self._invtransform = transform.get_inverse()
# // end of 3D adjustments
# now the code itself
coords = self._where_to_draw_from_and_to(e)
if coords:
start = coords[:2]
end = coords[2:]
v1, v2 = e.vertices
if self.color_bonds:
color1 = self.atom_colors.get(v1.symbol, (0, 0, 0))
color2 = self.atom_colors.get(v2.symbol, (0, 0, 0))
else:
color1 = color2 = (0, 0, 0)
has_shown_vertex = bool(
[1 for _v in e.vertices if _v in self._vertex_to_bbox])
if e.order == 1:
if e.type == 'w':
draw_plain_or_colored_wedge(start, end)
elif e.type == 'h':
draw_plain_or_colored_hatch(start, end)
else:
draw_plain_or_colored_line(start, end)
if e.order == 2:
side = 0
# find how to center the bonds
# rings have higher priority in setting the positioning
in_ring = False
for ring in self.molecule.get_smallest_independent_cycles_dangerous_and_cached(
):
double_bonds = len([
b for b in
self.molecule.vertex_subgraph_to_edge_subgraph(ring)
if b.order == 2
])
if v1 in ring and v2 in ring:
in_ring = True
side += double_bonds * reduce(operator.add, [
geometry.on_which_side_is_point(
start + end, (a.x, a.y))
for a in ring if a != v1 and a != v2
])
# if rings did not decide, use the other neigbors
if not side:
for v in v1.neighbors + v2.neighbors:
if v != v1 and v != v2:
side += geometry.on_which_side_is_point(
start + end, (v.x, v.y))
# if neighbors did not decide either
if not side and (in_ring or not has_shown_vertex):
if in_ring:
# we don't want centered bonds inside rings
side = 1 # select arbitrary value
else:
# bond between two unshown atoms - we want to center them only in some cases
if len(v1.neighbors) == 1 and len(v2.neighbors) == 1:
# both atoms have only one neighbor
side = 0
elif len(v1.neighbors) < 3 and len(v2.neighbors) < 3:
# try to figure out which side is more towards the center of the molecule
side = reduce(operator.add, [
geometry.on_which_side_is_point(
start + end, (a.x, a.y))
for a in self.molecule.vertices
if a != v1 and a != v2
], 0)
if not side:
side = 1 # we choose arbitrary value, we don't want centering
if side:
draw_plain_or_colored_line(start, end)
x1, y1, x2, y2 = geometry.find_parallel(
start[0], start[1], end[0], end[1],
self.bond_width * misc.signum(side))
# shorten the second line
length = geometry.point_distance(x1, y1, x2, y2)
if v2 not in self._vertex_to_bbox:
x2, y2 = geometry.elongate_line(
x1, y1, x2, y2,
-self.bond_second_line_shortening * length)
if v1 not in self._vertex_to_bbox:
x1, y1 = geometry.elongate_line(
x2, y2, x1, y1,
-self.bond_second_line_shortening * length)
draw_plain_or_colored_line((x1, y1), (x2, y2), second=True)
else:
for i in (1, -1):
x1, y1, x2, y2 = geometry.find_parallel(
start[0], start[1], end[0], end[1],
i * self.bond_width * 0.5)
draw_plain_or_colored_line((x1, y1), (x2, y2))
elif e.order == 3:
self._draw_line(start, end, line_width=self.line_width)
for i in (1, -1):
x1, y1, x2, y2 = geometry.find_parallel(
start[0], start[1], end[0], end[1],
i * self.bond_width * 0.7)
draw_plain_or_colored_line((x1, y1), (x2, y2), second=True)
if transform:
# if transform was used, we need to transform back
for n in atom1.neighbors + atom2.neighbors:
n.coords = self._invtransform.transform_xyz(*n.coords)
