def create_mark( self, mark='radical', angle='auto', draw=1, angle_resolution=1):
"""creates the mark, does not care about the chemical meaning of this"""
# decide where to put the mark
mark_name, mark_class = self._mark_to_name_and_class( mark)
if angle == 'auto':
x, y = self.find_place_for_mark( mark, resolution=angle_resolution)
else:
if not self.show:
dist = 5 + round( mark_class.standard_size / 2)
else:
bbox = self.bbox()
x2 = self.x + round( cos( angle) *1000)
y2 = self.y + round( sin( angle) *1000)
x1, y1 = geometry.intersection_of_line_and_rect( (self.x,self.y,x2,y2), bbox, round_edges=0)
dist = geometry.point_distance( self.x, self.y, x1, y1) + round( mark_class.standard_size / 2)
x = self.x + round( cos( angle) *dist)
y = self.y + round( sin( angle) *dist)
#ang = angle
m = mark_class( self, x, y, auto=(angle=='auto'))
if draw:
m.draw()
self.marks.add( m)
return m
def create_mark(self,
mark='radical',
angle='auto',
draw=1,
angle_resolution=1):
"""creates the mark, does not care about the chemical meaning of this"""
# decide where to put the mark
mark_name, mark_class = self._mark_to_name_and_class(mark)
if angle == 'auto':
x, y = self.find_place_for_mark(mark, resolution=angle_resolution)
else:
if not self.show:
dist = 5 + round(mark_class.standard_size / 2)
else:
bbox = self.bbox()
x2 = self.x + round(cos(angle) * 1000)
y2 = self.y + round(sin(angle) * 1000)
x1, y1 = geometry.intersection_of_line_and_rect(
(self.x, self.y, x2, y2), bbox, round_edges=0)
dist = geometry.point_distance(self.x, self.y, x1, y1) + round(
mark_class.standard_size / 2)
x = self.x + round(cos(angle) * dist)
y = self.y + round(sin(angle) * dist)
#ang = angle
m = mark_class(self, x, y, auto=(angle == 'auto'))
if draw:
m.draw()
self.marks.add(m)
return m
def _where_to_draw_from_and_to( self):
x1, y1 = self.atom1.get_xy()
x2, y2 = self.atom2.get_xy()
# at first check if the bboxes are not overlapping
bbox1 = list( misc.normalize_coords( self.atom1.bbox( substract_font_descent=True)))
bbox2 = list( misc.normalize_coords( self.atom2.bbox( substract_font_descent=True)))
if geometry.do_rectangles_intersect( bbox1, bbox2):
return None
# then we continue with computation
if self.atom1.show:
x1, y1 = geometry.intersection_of_line_and_rect( (x1,y1,x2,y2), bbox1, round_edges=0)
if self.atom2.show:
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):
x1, y1 = self.atom1.get_xy()
x2, y2 = self.atom2.get_xy()
# at first check if the bboxes are not overlapping
bbox1 = list( misc.normalize_coords( self.atom1.bbox( substract_font_descent=True)))
bbox2 = list( misc.normalize_coords( self.atom2.bbox( substract_font_descent=True)))
if geometry.do_rectangles_intersect( bbox1, bbox2):
return None
# then we continue with computation
if self.atom1.show:
x1, y1 = geometry.intersection_of_line_and_rect( (x1,y1,x2,y2), bbox1, round_edges=0)
if self.atom2.show:
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 find_place_for_mark( self, mark, resolution=30):
"""resolution says if the angles should be somehow 'rounded', it is given in degrees;
see geometry.point_on_circle for a similar thing"""
mark_name, mark_class = self._mark_to_name_and_class( mark)
# deal with marks centered
if mark_class.meta__mark_positioning == 'atom':
return self.x, self.y
# deal with statically positioned marks
if mark_class.meta__mark_positioning == 'righttop':
bbox = self.bbox()
return bbox[2]+2, bbox[1]
# deal with marks in linear_form
if self.is_part_of_linear_fragment():
if mark_name == "atom_number":
bbox = self.bbox()
return int( self.x-0.5*self.font_size), bbox[1]-2
if not self.show:
dist = 5 + round( mark_class.standard_size / 2)
else:
dist = 0.75*self.font_size + round( mark_class.standard_size / 2)
atms = self.get_neighbors()
x, y = self.get_xy()
# special cases
if not atms:
# single atom molecule
if self.show_hydrogens and self.pos == "center-first":
return x -dist, y-3
else:
return x +dist, y-3
# normal case
coords = [(a.x,a.y) for a in atms]
# we have to take marks into account
[coords.append( (m.x, m.y)) for m in self.marks]
# hydrogen positioning is also important
if self.show_hydrogens and self.show:
if self.pos == 'center-last':
coords.append( (x-10,y))
else:
coords.append( (x+10,y))
# now we can compare the angles
angles = [geometry.clockwise_angle_from_east( x1-x, y1-y) for x1,y1 in coords]
angles.append( 2*pi + min( angles))
angles.sort()
angles.reverse()
diffs = misc.list_difference( angles)
i = diffs.index( max( diffs))
angle = (angles[i] +angles[i+1]) / 2
# we calculate the distance here again as it is anisotropic (depends on direction)
bbox = list( misc.normalize_coords( self.bbox()))
x0, y0 = geometry.point_on_circle( x, y, 500, direction=(cos(angle), sin( angle)), resolution=resolution)
x1, y1 = geometry.intersection_of_line_and_rect( (x,y,x0,y0), bbox, round_edges=0)
dist = geometry.point_distance( x, y, x1, y1) + round( mark_class.standard_size / 2)
# //
retx, rety = geometry.point_on_circle( x, y, dist, direction=(cos(angle), sin( angle)), resolution=resolution)
# in visible text x,y are not on the center, therefore we compensate for it
# if self.show:
# y -= 0.166 * self.font_size
return retx, rety
def find_place_for_mark(self, mark, resolution=30):
"""resolution says if the angles should be somehow 'rounded', it is given in degrees;
see geometry.point_on_circle for a similar thing"""
mark_name, mark_class = self._mark_to_name_and_class(mark)
# deal with marks centered
if mark_class.meta__mark_positioning == 'atom':
return self.x, self.y
# deal with statically positioned marks
if mark_class.meta__mark_positioning == 'righttop':
bbox = self.bbox()
return bbox[2] + 2, bbox[1]
# deal with marks in linear_form
if self.is_part_of_linear_fragment():
if mark_name == "atom_number":
bbox = self.bbox()
return int(self.x - 0.5 * self.font_size), bbox[1] - 2
if not self.show:
dist = 5 + round(mark_class.standard_size / 2)
else:
dist = 0.75 * self.font_size + round(mark_class.standard_size / 2)
atms = self.get_neighbors()
x, y = self.get_xy()
# special cases
if not atms:
# single atom molecule
if self.show_hydrogens and self.pos == "center-first":
return x - dist, y - 3
else:
return x + dist, y - 3
# normal case
coords = [(a.x, a.y) for a in atms]
# we have to take marks into account
[coords.append((m.x, m.y)) for m in self.marks]
# hydrogen positioning is also important
if self.show_hydrogens and self.show:
if self.pos == 'center-last':
coords.append((x - 10, y))
else:
coords.append((x + 10, y))
# now we can compare the angles
angles = [
geometry.clockwise_angle_from_east(x1 - x, y1 - y)
for x1, y1 in coords
]
angles.append(2 * pi + min(angles))
angles.sort()
angles.reverse()
diffs = misc.list_difference(angles)
i = diffs.index(max(diffs))
angle = (angles[i] + angles[i + 1]) / 2
# we calculate the distance here again as it is anisotropic (depends on direction)
bbox = list(misc.normalize_coords(self.bbox()))
x0, y0 = geometry.point_on_circle(x,
y,
500,
direction=(cos(angle), sin(angle)),
resolution=resolution)
x1, y1 = geometry.intersection_of_line_and_rect((x, y, x0, y0),
bbox,
round_edges=0)
dist = geometry.point_distance(x, y, x1, y1) + round(
mark_class.standard_size / 2)
# //
retx, rety = geometry.point_on_circle(x,
y,
dist,
direction=(cos(angle),
sin(angle)),
resolution=resolution)
# in visible text x,y are not on the center, therefore we compensate for it
# if self.show:
# y -= 0.166 * self.font_size
return retx, rety