def _is_there_place( self, atom, x, y):
x1, y1 = atom.x, atom.y
angle1 = geometry.clockwise_angle_from_east( x-x1, y-y1)
for n in atom.neighbors:
angle = geometry.clockwise_angle_from_east( n.x-x1, n.y-y1)
if abs( angle - angle1) < 0.3:
return False
return True
def _is_there_place(self, atom, x, y):
x1, y1 = atom.x, atom.y
angle1 = geometry.clockwise_angle_from_east(x - x1, y - y1)
for n in atom.neighbors:
angle = geometry.clockwise_angle_from_east(n.x - x1, n.y - y1)
if abs(angle - angle1) < 0.3:
return False
return True
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 _find_place_around_atom( self, atom): x, y = atom.x, atom.y coords = [(a.x,a.y) for a in atom.neighbors] # now we can compare the angles angles = [geometry.clockwise_angle_from_east( x1-x, y1-y) for x1,y1 in coords] angles.append( 2*math.pi + min( angles)) angles.sort() angles.reverse() diffs = misc.list_difference( angles) i = diffs.index( max( diffs)) angle = (angles[i] +angles[i+1]) / 2 return angle
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 _find_place_around_atom(self, atom):
x, y = atom.x, atom.y
coords = [(a.x, a.y) for a in atom.neighbors]
# now we can compare the angles
angles = [
geometry.clockwise_angle_from_east(x1 - x, y1 - y)
for x1, y1 in coords
]
angles.append(2 * math.pi + min(angles))
angles.sort()
angles.reverse()
diffs = misc.list_difference(angles)
i = diffs.index(max(diffs))
angle = (angles[i] + angles[i + 1]) / 2
return angle
def _continue_with_the_coords( self, mol, processed=[]):
"""processes the atoms in circles around the backbone (processed) until all is done"""
while processed:
new_processed = []
for v in processed:
if len( [o for o in self.mol.vertices if o.x == None]) == 0:
# its all done
return
# look if v is part of a ring
ring = None
for r in self.rings:
if v in r:
ring = r
break
if not ring:
# v is not in a ring - we can continue
new_processed += self.process_atom_neigbors( v)
else:
# v is in ring so we process the ring
if len( processed) > 1 and mol.defines_connected_subgraph_v( processed) and set( processed) <= ring:
new_processed += self.process_all_anelated_rings( processed)
else:
self.rings.remove( ring)
ring = mol.sort_vertices_in_path( ring, start_from=v)
ring.remove( v)
d = [a for a in v.get_neighbors() if a.x != None and a.y != None][0] # should always work
ca = geometry.clockwise_angle_from_east( v.x-d.x, v.y-d.y)
size = len( ring)+1
da = deg_to_rad( 180 -180*(size-2)/size)
gcoords = gen_angle_stream( da, start_from=ca-pi/2+da/2)
# here we generate the coords
self.apply_gen_to_atoms( gcoords, ring, v)
ring.append( v)
new_processed += ring
new_processed += self.process_all_anelated_rings( ring)
processed = new_processed
def process_atom_neigbors( self, v):
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
to_go = [a for a in v.get_neighbors() if a.x == None or a.y == None]
done = [a for a in v.get_neighbors() if a not in to_go]
if len( done) == 1 and (len( to_go) == 1 or len( to_go) == 2 and [1 for _t in to_go if _t in self.stereo]):
# only simple non-branched chain or branched with stereo
d = done[0]
if len( to_go) == 1:
t = to_go[0]
else:
t = [_t for _t in to_go if _t in self.stereo][0]
# decide angle
angle_to_add = 120
bond = v.get_edge_leading_to( t)
# triple bonds
if 3 in [_e.order for _e in v.get_neighbor_edges()]:
angle_to_add = 180
# cumulated double bonds
if bond.order == 2:
_b = v.get_edge_leading_to( d)
if _b.order == 2:
angle_to_add = 180
angle = geometry.clockwise_angle_from_east( d.x-v.x, d.y-v.y)
dns = d.get_neighbors()
placed = False
# stereochemistry (E/Z)
if t in self.stereo:
ss = [st for st in self.stereo[t] if not None in st.get_other_end( t).coords[:2]]
if ss:
st = ss[0] # we choose the first one if more are present
d2 = st.get_other_end( t)
# other is processed, we need to adapt
relation = st.value == st.OPPOSITE_SIDE and -1 or 1
angle_to_add = get_angle_at_side( v, d, d2, relation, angle_to_add)
placed = True
if not placed and len( dns) == 2:
# to support the all trans of simple chains without stereochemistry
d2 = (dns[0] == v) and dns[1] or dns[0]
if d2.x != None and d2.y != None:
angle_to_add = get_angle_at_side( v, d, d2, -1, angle_to_add)
an = angle + deg_to_rad( angle_to_add)
t.x = v.x + self.bond_length*cos( an)
t.y = v.y + self.bond_length*sin( an)
if len( to_go) > 1:
self.process_atom_neigbors( v)
else:
# branched chain
angles = [geometry.clockwise_angle_from_east( at.x-v.x, at.y-v.y) for at in done]
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]) / (len( to_go)+1)
gcoords = gen_coords_from_stream( gen_angle_stream( angle, start_from=angles[i+1]+angle),
length = self.bond_length)
for a in to_go:
dx, dy = gcoords.next()
a.x = v.x + dx
a.y = v.y + dy
return to_go