def _draw_colored_line( self, start, end, line_width=1, capstyle=cairo.LINE_CAP_BUTT,
start_color=(0,0,0), end_color=(0,0,0)):
x1,y1 = start
x2,y2 = end
length = geometry.point_distance( x1,y1,x2,y2)
xn2,yn2 = geometry.elongate_line( x1,y1,x2,y2, -0.5*length)
line1 = [(x1,y1),(xn2,yn2)]
xn1,yn1 = geometry.elongate_line( x2,y2,x1,y1, -0.5*length)
line2 = [(xn1,yn1),(x2,y2)]
self.context.set_line_cap( cairo.LINE_CAP_BUTT) # this is forced here
self.context.set_line_width( line_width)
for line,color in zip( [line1,line2], [start_color,end_color]):
self.context.set_source_rgb( *color)
self._create_cairo_path( line, closed=False)
self.context.stroke()
def _draw_colored_line(self,
start,
end,
line_width=1,
capstyle=cairo.LINE_CAP_BUTT,
start_color=(0, 0, 0),
end_color=(0, 0, 0)):
x1, y1 = start
x2, y2 = end
length = geometry.point_distance(x1, y1, x2, y2)
xn2, yn2 = geometry.elongate_line(x1, y1, x2, y2, -0.5 * length)
line1 = [(x1, y1), (xn2, yn2)]
xn1, yn1 = geometry.elongate_line(x2, y2, x1, y1, -0.5 * length)
line2 = [(xn1, yn1), (x2, y2)]
self.context.set_line_cap(cairo.LINE_CAP_BUTT) # this is forced here
self.context.set_line_width(line_width)
for line, color in zip([line1, line2], [start_color, end_color]):
self.context.set_source_rgb(*color)
self._create_cairo_path(line, closed=False)
self.context.stroke()
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_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_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_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)
