def normalize_bond_length(self, bond_length=30):
"""make the average bond-length be bond_length by scaling the structure up"""
if not self.edges or len(self.vertices) < 2:
return False
minx = None
maxx = None
miny = None
maxy = None
# atoms
for v in self.vertices:
if not maxx or v.x > maxx:
maxx = v.x
if not minx or v.x < minx:
minx = v.x
if not miny or v.y < miny:
miny = v.y
if not maxy or v.y > maxy:
maxy = v.y
scale = bond_length / self.get_mean_bond_length()
movex = (maxx + minx) / 2
movey = (maxy + miny) / 2
trans = transform3d.transform3d()
trans.set_move(-movex, -movey, 0)
trans.set_scaling(scale)
trans.set_move(movex, movey, 0)
for v in self.atoms:
v.x, v.y, v.z = trans.transform_xyz(v.x, v.y, v.z)
return True
def normalize_bond_length( self, bond_length=30):
"""make the average bond-length be bond_length by scaling the structure up"""
if not self.edges or len( self.vertices) < 2:
return False
minx = None
maxx = None
miny = None
maxy = None
# atoms
for v in self.vertices:
if not maxx or v.x > maxx:
maxx = v.x
if not minx or v.x < minx:
minx = v.x
if not miny or v.y < miny:
miny = v.y
if not maxy or v.y > maxy:
maxy = v.y
scale = bond_length / self.get_mean_bond_length()
movex = (maxx+minx)/2
movey = (maxy+miny)/2
trans = transform3d.transform3d()
trans.set_move( -movex, -movey, 0)
trans.set_scaling( scale)
trans.set_move( movex, movey, 0)
for v in self.atoms:
v.x, v.y, v.z = trans.transform_xyz( v.x, v.y, v.z)
return True
def create_transformation_to_rotate_around_particular_axis(
line_start, line_end, theta):
"""
taken from http://inside.mines.edu/~gmurray/ArbitraryAxisRotation/ArbitraryAxisRotation.html
"""
a, b, c = line_start
u, v, w = line_end
u -= a
v -= b
w -= c
u2 = u * u
v2 = v * v
w2 = w * w
cosT = cos(theta)
sinT = sin(theta)
l2 = u2 + v2 + w2
l = sqrt(l2)
if (l2 < 0.000000001):
raise ValueError("RotationMatrix: direction vector too short!")
m11 = (u2 + (v2 + w2) * cosT) / l2
m12 = (u * v * (1 - cosT) - w * l * sinT) / l2
m13 = (u * w * (1 - cosT) + v * l * sinT) / l2
m14 = (a * (v2 + w2) - u * (b * v + c * w) + (u * (b * v + c * w) - a *
(v2 + w2)) * cosT +
(b * w - c * v) * l * sinT) / l2
m21 = (u * v * (1 - cosT) + w * l * sinT) / l2
m22 = (v2 + (u2 + w2) * cosT) / l2
m23 = (v * w * (1 - cosT) - u * l * sinT) / l2
m24 = (b * (u2 + w2) - v * (a * u + c * w) + (v * (a * u + c * w) - b *
(u2 + w2)) * cosT +
(c * u - a * w) * l * sinT) / l2
m31 = (u * w * (1 - cosT) - v * l * sinT) / l2
m32 = (v * w * (1 - cosT) + u * l * sinT) / l2
m33 = (w2 + (u2 + v2) * cosT) / l2
m34 = (c * (u2 + v2) - w * (a * u + b * v) + (w * (a * u + b * v) - c *
(u2 + v2)) * cosT +
(a * v - b * u) * l * sinT) / l2
from transform3d import transform3d
t = transform3d([[m11, m12, m13, m14], [m21, m22, m23, m24],
[m31, m32, m33, m34], [0, 0, 0, 1]])
return t
def create_transformation_to_coincide_point_with_z_axis(mov, point):
"""takes 3d coordinates 'point' (vector mov->point) and returns 3d transform object
(transform3d.transform3d) that performs rotation to get 'point' onto z axis (x,y)=(0,0)
with positive 'z'.
NOTE: this is probably far from efficient, but it works
"""
from transform3d import transform3d
t = transform3d()
a, b, c = mov
t.set_move(-a, -b, -c)
x, y, z = t.transform_xyz(*point)
t.set_rotation_y(atan2(x, z))
x, y, z = t.transform_xyz(*point)
t.set_rotation_x(-atan2(y, sqrt(x**2 + z**2)))
x, y, z = t.transform_xyz(*point)
if z < 0:
t.set_rotation_x(pi)
#t.set_move( *mov)
return t
def create_transformation_to_coincide_point_with_z_axis( mov, point):
"""takes 3d coordinates 'point' (vector mov->point) and returns 3d transform object
(transform3d.transform3d) that performs rotation to get 'point' onto z axis (x,y)=(0,0)
with positive 'z'.
NOTE: this is probably far from efficient, but it works
"""
from transform3d import transform3d
t = transform3d()
a,b,c = mov
t.set_move( -a, -b, -c)
x,y,z = t.transform_xyz( *point)
t.set_rotation_y( atan2( x, z))
x,y,z = t.transform_xyz( *point)
t.set_rotation_x( -atan2( y, sqrt(x**2+z**2)))
x,y,z = t.transform_xyz( *point)
if z < 0:
t.set_rotation_x( pi)
#t.set_move( *mov)
return t
def create_transformation_to_rotate_around_particular_axis( line_start, line_end, theta):
"""
taken from http://inside.mines.edu/~gmurray/ArbitraryAxisRotation/ArbitraryAxisRotation.html
"""
a,b,c = line_start
u,v,w = line_end
u -= a
v -= b
w -= c
u2 = u*u;
v2 = v*v;
w2 = w*w;
cosT = cos(theta);
sinT = sin(theta);
l2 = u2 + v2 + w2;
l = sqrt(l2);
if (l2 < 0.000000001):
raise ValueError("RotationMatrix: direction vector too short!")
m11 = (u2 + (v2 + w2) * cosT)/l2;
m12 = (u*v * (1 - cosT) - w*l*sinT)/l2;
m13 = (u*w * (1 - cosT) + v*l*sinT)/l2;
m14 = (a*(v2 + w2) - u*(b*v + c*w)
+ (u*(b*v + c*w) - a*(v2 + w2))*cosT + (b*w - c*v)*l*sinT)/l2;
m21 = (u*v * (1 - cosT) + w*l*sinT)/l2;
m22 = (v2 + (u2 + w2) * cosT)/l2;
m23 = (v*w * (1 - cosT) - u*l*sinT)/l2;
m24 = (b*(u2 + w2) - v*(a*u + c*w)
+ (v*(a*u + c*w) - b*(u2 + w2))*cosT + (c*u - a*w)*l*sinT)/l2;
m31 = (u*w * (1 - cosT) - v*l*sinT)/l2;
m32 = (v*w * (1 - cosT) + u*l*sinT)/l2;
m33 = (w2 + (u2 + v2) * cosT)/l2;
m34 = (c*(u2 + v2) - w*(a*u + b*v)
+ (w*(a*u + b*v) - c*(u2 + v2))*cosT + (a*v - b*u)*l*sinT)/l2;
from transform3d import transform3d
t = transform3d( [[m11,m12,m13,m14],[m21,m22,m23,m24],[m31,m32,m33,m34],[0,0,0,1]])
return t
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)