def add_atom_to( self, a1, bond_to_use=None, pos=None):
"""adds new atom bound to atom id with bond, the position of new atom can be specified in pos or is
decided calling find_place(), if x, y is specified and matches already existing atom it will be
used instead of creating new one """
if pos != None:
x, y = pos
else:
if bond_to_use:
x, y = self.find_place( a1, Screen.any_to_px( self.paper.standard.bond_length), added_order=bond_to_use.order)
else:
x, y = self.find_place( a1, Screen.any_to_px( self.paper.standard.bond_length))
a2 = None # the new atom
if pos:
# try if the coordinates are the same as of another atom
for at in self.atoms:
if abs( at.x - x) < 2 and abs( at.y - y) < 2 and not at == a1:
a2 = at
break
if not a2:
a2 = self.create_new_atom( x, y)
b = bond_to_use or bond( self.paper.standard, order=1, type='n')
self.add_edge( a1, a2, e=b)
b.molecule = self
b.draw()
return a2, b
def add_atom_to(self, a1, bond_to_use=None, pos=None):
"""adds new atom bound to atom id with bond, the position of new atom can be specified in pos or is
decided calling find_place(), if x, y is specified and matches already existing atom it will be
used instead of creating new one """
if pos != None:
x, y = pos
else:
if bond_to_use:
x, y = self.find_place(a1,
Screen.any_to_px(
self.paper.standard.bond_length),
added_order=bond_to_use.order)
else:
x, y = self.find_place(
a1, Screen.any_to_px(self.paper.standard.bond_length))
a2 = None # the new atom
if pos:
# try if the coordinates are the same as of another atom
for at in self.atoms:
if abs(at.x - x) < 2 and abs(at.y - y) < 2 and not at == a1:
a2 = at
break
if not a2:
a2 = self.create_new_atom(x, y)
b = bond_to_use or bond(self.paper.standard, order=1, type='n')
self.add_edge(a1, a2, e=b)
b.molecule = self
b.draw()
return a2, b
def switch_to_type( self, type):
if type in "wha" and self.type not in "wha":
# get the standard width only if the changes is not within the "wha" group
self.wedge_width = Screen.any_to_px( self.paper.standard.wedge_width)
elif type not in "wha" and self.type in "wha":
# when both are outside the 'wha' do the similar
self.bond_width = Screen.any_to_px( self.paper.standard.bond_width)
self.type = type
def switch_to_type( self, type):
if type in "wha" and self.type not in "wha":
# get the standard width only if the changes is not within the "wha" group
self.wedge_width = Screen.any_to_px( self.paper.standard.wedge_width)
elif type not in "wha" and self.type in "wha":
# when both are outside the 'wha' do the similar
self.bond_width = Screen.any_to_px( self.paper.standard.bond_width)
self.type = type
def read_standard_values( self, standard, old_standard=None):
meta_enabled.read_standard_values( self, standard, old_standard=old_standard)
# wedge width
if not old_standard or (standard.wedge_width != old_standard.wedge_width):
self.wedge_width = Screen.any_to_px( standard.wedge_width)
# line width
if not old_standard or (standard.line_width != old_standard.line_width):
self.line_width = Screen.any_to_px( standard.line_width)
# bond width
if not old_standard or (standard.bond_width != old_standard.bond_width):
if hasattr( self, 'bond_width'):
self.bond_width = misc.signum( self.bond_width) * Screen.any_to_px( standard.bond_width)
else:
self.bond_width = Screen.any_to_px( standard.bond_width)
def read_standard_values( self, standard, old_standard=None):
meta_enabled.read_standard_values( self, standard, old_standard=old_standard)
# wedge width
if not old_standard or (standard.wedge_width != old_standard.wedge_width):
self.wedge_width = Screen.any_to_px( standard.wedge_width)
# line width
if not old_standard or (standard.line_width != old_standard.line_width):
self.line_width = Screen.any_to_px( standard.line_width)
# bond width
if not old_standard or (standard.bond_width != old_standard.bond_width):
if hasattr( self, 'bond_width'):
self.bond_width = misc.signum( self.bond_width) * Screen.any_to_px( standard.bond_width)
else:
self.bond_width = Screen.any_to_px( standard.bond_width)
def read_standard_values(self, standard, old_standard=None):
meta_enabled.read_standard_values(self,
standard,
old_standard=old_standard)
if not old_standard or (standard.line_width !=
old_standard.line_width):
self.line_width = Screen.any_to_px(standard.line_width)
def get_transformed_template(self, n, coords, type="empty", paper=None):
"""type is type of connection - 'bond', 'atom1'(for single atom), 'atom2'(for atom with more than 1 bond), 'empty'"""
pap = paper or Store.app.paper
pap.onread_id_sandbox_activate() # must be here to mangle the ids
current = molecule(pap, package=self.templates[n])
pap.onread_id_sandbox_finish(apply_to=[current]) # id mangling
current.name = ""
self._scale_ratio = 1
trans = transform()
# type empty - just draws the template - no conection
if type == "empty":
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1 = coords
bond_length = Screen.any_to_px(Store.app.paper.standard.bond_length)
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
trans.set_move(-xt2, -yt2)
trans.set_scaling(bond_length / math.sqrt((xt1 - xt2) ** 2 + (yt1 - yt2) ** 2))
trans.set_move(x1, y1)
# type atom
elif type == "atom1" or type == "atom2":
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1, x2, y2 = coords
trans.set_move(-xt2, -yt2)
trans.set_scaling(
math.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2) / math.sqrt((xt1 - xt2) ** 2 + (yt1 - yt2) ** 2)
)
trans.set_rotation(math.atan2(xt1 - xt2, yt1 - yt2) - math.atan2(x1 - x2, y1 - y2))
trans.set_move(x2, y2)
# type bond
elif type == "bond":
if not (current.t_bond_first and current.t_bond_second):
warn("this template is not capable to be added to bond - sorry.")
return None
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
xt1, yt1 = current.t_bond_first.get_xy()
xt2, yt2 = current.t_bond_second.get_xy()
x1, y1, x2, y2 = coords
self._scale_ratio = math.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2) / math.sqrt(
(xt1 - xt2) ** 2 + (yt1 - yt2) ** 2
) # further needed for bond.bond_width transformation
trans.set_move(-xt1, -yt1)
trans.set_rotation(math.atan2(xt1 - xt2, yt1 - yt2) - math.atan2(x1 - x2, y1 - y2))
trans.set_scaling(self._scale_ratio)
trans.set_move(x1, y1)
self.transform_template(current, trans)
# remove obsolete info from template
if type == "atom1":
current.delete_items([current.t_atom], redraw=0, delete_single_atom=0)
elif type == "atom2":
current.t_atom.x = x1
current.t_atom.y = y1
current.t_atom = None
current.t_bond_first = None
current.t_bond_second = None
# return ready template
return current
def expand( self):
"""expands the group and returns list of atoms that new drawing afterwords"""
if self.group_type == "builtin":
names = Store.gm.get_template_names()
if self.symbol in names:
a2 = self.neighbors[0]
x1, y1 = a2.get_xy()
x2, y2 = self.get_xy()
self.group_graph = Store.gm.get_transformed_template( names.index( self.symbol), (x1,y1,x2,y2), type='atom1')
replacement = self.group_graph.next_to_t_atom
else:
print "unknown group %s" % a.symbol
return None
elif self.group_type == "chain":
self.group_graph = self.molecule.create_graph()
p = PT.formula_dict( self.symbol)
n = p['C']
last = None
for i in range( n):
v = self.group_graph.add_vertex()
v.x, v.y = None, None
if last:
self.group_graph.add_edge( last, v)
last = v
replacement = self.group_graph.vertices[0]
replacement.x = self.x
replacement.y = self.y
elif self.group_type == "implicit":
if not self.group_graph:
self.set_name( self.symbol, occupied_valency=self.occupied_valency)
for v in self.group_graph.vertices:
v.x, v.y = None, None
v.show = v.symbol != 'C'
assert self.connecting_atom != None
replacement = self.connecting_atom
replacement.x = self.x
replacement.y = self.y
self.molecule.eat_molecule( self.group_graph)
self.molecule.move_bonds_between_atoms( self, replacement)
self.molecule.delete_vertex( self)
if self.occupied_valency:
oasa.coords_generator.calculate_coords( self.molecule, bond_length=-1)
else:
# if the group is the only vertex of the molecule we must set the bond_length explicitly
# and the move the whole molecule
replacement.x = None
replacement.y = None
x, y = self.x, self.y
oasa.coords_generator.calculate_coords( self.molecule, bond_length=Screen.any_to_px( self.paper.standard.bond_length))
dx = x - replacement.x
dy = y - replacement.y
[a.move( dx, dy) for a in self.group_graph.vertices]
return self.group_graph.vertices
def oasa_mol_to_bkchem_mol(mol, paper):
m = molecule.molecule(paper)
if None in reduce(operator.add, [[a.x, a.y] for a in mol.atoms], []):
calc_position = 0
else:
calc_position = 1
minx = None
maxx = None
miny = None
maxy = None
# atoms
for a in mol.vertices:
a2 = oasa_atom_to_bkchem_atom(a, paper, m)
m.insert_atom(a2)
if calc_position:
# data for rescaling
if not maxx or a2.x > maxx:
maxx = a2.x
if not minx or a2.x < minx:
minx = a2.x
if not miny or a2.y < miny:
miny = a2.y
if not maxy or a2.y > maxy:
maxy = a2.y
# bonds
bond_lengths = []
for b in mol.edges:
b2 = oasa_bond_to_bkchem_bond(b, paper)
aa1, aa2 = b.vertices
atom1 = m.atoms[mol.vertices.index(aa1)]
atom2 = m.atoms[mol.vertices.index(aa2)]
m.add_edge(atom1, atom2, b2)
b2.molecule = m
if calc_position:
bond_lengths.append(
math.sqrt((b2.atom1.x - b2.atom2.x)**2 +
(b2.atom1.y - b2.atom2.y)**2))
# rescale
if calc_position:
bl = sum(bond_lengths) / len(bond_lengths)
scale = Screen.any_to_px(paper.standard.bond_length) / bl
movex = (maxx + minx) / 2
movey = (maxy + miny) / 2
trans = transform3d.transform3d()
trans.set_move(-movex, -movey, 0)
trans.set_scaling(scale)
trans.set_move(320, 240, 0)
for a in m.atoms:
a.x, a.y, a.z = trans.transform_xyz(a.x, a.y, a.z)
return m
def oasa_mol_to_bkchem_mol( mol, paper):
m = molecule.molecule( paper)
if None in reduce( operator.add, [[a.x, a.y] for a in mol.atoms], []):
calc_position = 0
else:
calc_position = 1
minx = None
maxx = None
miny = None
maxy = None
# atoms
for a in mol.vertices:
a2 = oasa_atom_to_bkchem_atom( a, paper, m)
m.insert_atom( a2)
if calc_position:
# data for rescaling
if not maxx or a2.x > maxx:
maxx = a2.x
if not minx or a2.x < minx:
minx = a2.x
if not miny or a2.y < miny:
miny = a2.y
if not maxy or a2.y > maxy:
maxy = a2.y
# bonds
bond_lengths = []
for b in mol.edges:
b2 = oasa_bond_to_bkchem_bond( b, paper)
aa1, aa2 = b.vertices
atom1 = m.atoms[ mol.vertices.index( aa1)]
atom2 = m.atoms[ mol.vertices.index( aa2)]
m.add_edge( atom1, atom2, b2)
b2.molecule = m
if calc_position:
bond_lengths.append( math.sqrt( (b2.atom1.x-b2.atom2.x)**2 + (b2.atom1.y-b2.atom2.y)**2))
# rescale
if calc_position:
bl = sum( bond_lengths) / len( bond_lengths)
scale = Screen.any_to_px( paper.standard.bond_length) / bl
movex = (maxx+minx)/2
movey = (maxy+miny)/2
trans = transform3d.transform3d()
trans.set_move( -movex, -movey, 0)
trans.set_scaling( scale)
trans.set_move( 320, 240, 0)
for a in m.atoms:
a.x, a.y, a.z = trans.transform_xyz( a.x, a.y, a.z)
return m
def _set_x(self, x):
self._x = Screen.any_to_px(x)
def done(self, button):
"""called on dialog exit"""
self.dialog.deactivate()
if button != _('OK'):
pass
else:
#print self.marks.get()
# apply changes
for o in self.items:
change = 0
# ATOM
if o.object_type == 'atom':
a = self.atom_show.index(Pmw.SELECT)
if a != 2:
o.show = a
change = 1
# positionning
a = self.atom_pos.index(Pmw.SELECT)
if a != 2:
o.pos = ('center-first', 'center-last')[a]
change = 1
if self.atom_charge.get():
a = int(self.atom_charge.get())
if hasattr(o, 'charge') and o.charge != a:
o.charge = a
change = 1
# hydrogens
a = int(self.atom_show_h.index(Pmw.SELECT))
if a != 2:
o.show_hydrogens = a
change = 1
# font is in common now
# BOND
elif o.object_type == 'bond':
# width is in common now
# bond_width
d = Screen.any_to_px(self.bond_dist.getvalue())
if d:
if d != abs(o.bond_width):
o.bond_width = d * misc.signum(o.bond_width)
change = 1
# wedge_width
d = Screen.any_to_px(self.wedge_width.getvalue())
if d:
if d != o.wedge_width:
o.wedge_width = d
change = 1
# ratio
ratio = self.double_length_ratio.getvalue()
if ratio:
ratio = float(self.double_length_ratio.getvalue())
if ratio != o.double_length_ratio:
o.double_length_ratio = ratio
change = 1
# ARROW - most is in common now
elif o.object_type == 'arrow':
if self.arrow_start_changed:
o.set_pins(start=self.arrow_start.get())
change = 1
if self.arrow_end_changed:
o.set_pins(end=self.arrow_end.get())
change = 1
if self.spline_changed:
o.spline = self.spline.get()
change = 1
# TEXT - all is in common now
# PLUS - all is in common now
# VECTOR - all is in common now
# COMMON PROPERTIES
# LINE COLOR
if hasattr(o, 'line_color') and self.line_color.color:
if self.line_color.color != o.line_color:
o.line_color = self.line_color.color
change = 1
# AREA COLOR
if hasattr(o, 'area_color') and self.area_color.color:
if self.area_color.color != o.area_color:
o.area_color = self.area_color.color
change = 1
# LINE WIDTH
if hasattr(o, 'line_width'):
w = Screen.any_to_px(self.line_width.getvalue())
if w:
if w != o.line_width:
o.line_width = w
change = 1
# FONT
if hasattr(o, 'font_family'):
if self.font_size.get():
a = int(self.font_size.get())
o.font_size = a
change = 1
if self.font_family.getcurselection(
) and self.font_family.getcurselection(
)[0] != self.used_family:
a = self.font_family.getcurselection()[0]
o.font_family = a
change = 1
# APPLY THE CHANGES
if change:
o.redraw()
self.changes_made = 1
self.cleanup()
def y(self, y): self._y = Screen.any_to_px( y)
def y(self, y):
self._y = Screen.any_to_px(y)
def get_transformed_template(self, n, coords, type='empty', paper=None):
"""type is type of connection - 'bond', 'atom1'(for single atom), 'atom2'(for atom with more than 1 bond), 'empty'"""
pap = paper or Store.app.paper
pap.onread_id_sandbox_activate() # must be here to mangle the ids
current = molecule(pap, package=self.templates[n])
pap.onread_id_sandbox_finish(apply_to=[current]) # id mangling
current.name = ''
self._scale_ratio = 1
trans = transform()
# type empty - just draws the template - no conection
if type == 'empty':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1 = coords
bond_length = Screen.any_to_px(
Store.app.paper.standard.bond_length)
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
trans.set_move(-xt2, -yt2)
trans.set_scaling(bond_length / math.sqrt((xt1 - xt2)**2 +
(yt1 - yt2)**2))
trans.set_move(x1, y1)
#type atom
elif type == 'atom1' or type == 'atom2':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1, x2, y2 = coords
trans.set_move(-xt2, -yt2)
trans.set_scaling(
math.sqrt((x1 - x2)**2 + (y1 - y2)**2) /
math.sqrt((xt1 - xt2)**2 + (yt1 - yt2)**2))
trans.set_rotation(
math.atan2(xt1 - xt2, yt1 - yt2) -
math.atan2(x1 - x2, y1 - y2))
trans.set_move(x2, y2)
#type bond
elif type == 'bond':
if not (current.t_bond_first and current.t_bond_second):
warn(
"this template is not capable to be added to bond - sorry."
)
return None
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
xt1, yt1 = current.t_bond_first.get_xy()
xt2, yt2 = current.t_bond_second.get_xy()
x1, y1, x2, y2 = coords
self._scale_ratio = math.sqrt(
(x1 - x2)**2 + (y1 - y2)**2) / math.sqrt(
(xt1 - xt2)**2 + (yt1 - yt2)**
2) # further needed for bond.bond_width transformation
trans.set_move(-xt1, -yt1)
trans.set_rotation(
math.atan2(xt1 - xt2, yt1 - yt2) -
math.atan2(x1 - x2, y1 - y2))
trans.set_scaling(self._scale_ratio)
trans.set_move(x1, y1)
self.transform_template(current, trans)
#remove obsolete info from template
if type == 'atom1':
current.delete_items([current.t_atom],
redraw=0,
delete_single_atom=0)
elif type == 'atom2':
current.t_atom.x = x1
current.t_atom.y = y1
current.t_atom = None
current.t_bond_first = None
current.t_bond_second = None
#return ready template
return current
def _set_x( self, x): self._x = Screen.any_to_px( x)
def _set_y(self, y):
self._y = Screen.any_to_px(y)
def done( self, button):
"""called on dialog exit"""
self.dialog.deactivate()
if button != _('OK'):
pass
else:
#print(self.marks.get())
# apply changes
for o in self.items:
change = 0
# ATOM
if o.object_type == 'atom':
a = self.atom_show.index( Pmw.SELECT)
if a != 2:
o.show = a
change = 1
# positionning
a = self.atom_pos.index( Pmw.SELECT)
if a != 2:
o.pos = ('center-first', 'center-last')[ a]
change = 1
if self.atom_charge.get():
a = int( self.atom_charge.get())
if hasattr( o, 'charge') and o.charge != a:
o.charge = a
change = 1
# hydrogens
a = int( self.atom_show_h.index( Pmw.SELECT))
if a != 2:
o.show_hydrogens = a
change = 1
# font is in common now
# BOND
elif o.object_type == 'bond':
# width is in common now
# bond_width
d = Screen.any_to_px( self.bond_dist.getvalue())
if d:
if d != abs( o.bond_width):
o.bond_width = d * misc.signum( o.bond_width)
change = 1
# wedge_width
d = Screen.any_to_px( self.wedge_width.getvalue())
if d:
if d != o.wedge_width:
o.wedge_width = d
change = 1
# ratio
ratio = self.double_length_ratio.getvalue()
if ratio:
ratio = float( self.double_length_ratio.getvalue())
if ratio != o.double_length_ratio:
o.double_length_ratio = ratio
change = 1
# ARROW - most is in common now
elif o.object_type == 'arrow':
if self.arrow_start_changed:
o.set_pins( start = self.arrow_start.get())
change = 1
if self.arrow_end_changed:
o.set_pins( end = self.arrow_end.get())
change = 1
if self.spline_changed:
o.spline = self.spline.get()
change = 1
# TEXT - all is in common now
# PLUS - all is in common now
# VECTOR - all is in common now
# COMMON PROPERTIES
# LINE COLOR
if hasattr( o, 'line_color') and self.line_color.color:
if self.line_color.color != o.line_color:
o.line_color = self.line_color.color
change = 1
# AREA COLOR
if hasattr( o, 'area_color') and self.area_color.color:
if self.area_color.color != o.area_color:
o.area_color = self.area_color.color
change = 1
# LINE WIDTH
if hasattr( o, 'line_width'):
w = Screen.any_to_px( self.line_width.getvalue())
if w:
if w != o.line_width:
o.line_width = w
change = 1
# FONT
if hasattr( o, 'font_family'):
if self.font_size.get():
a = int( self.font_size.get())
o.font_size = a
change = 1
if self.font_family.getcurselection() and self.font_family.getcurselection()[0] != self.used_family:
a = self.font_family.getcurselection()[0]
o.font_family = a
change = 1
# APPLY THE CHANGES
if change:
o.redraw()
self.changes_made = 1
self.cleanup()
def expand(self):
"""expands the group and returns list of atoms that new drawing afterwords"""
if self.group_type == "builtin":
names = Store.gm.get_template_names()
if self.symbol in names:
a2 = self.neighbors[0]
x1, y1 = a2.get_xy()
x2, y2 = self.get_xy()
self.group_graph = Store.gm.get_transformed_template(
names.index(self.symbol), (x1, y1, x2, y2), type='atom1')
replacement = self.group_graph.next_to_t_atom
else:
print("unknown group %s" % a.symbol)
return None
elif self.group_type == "chain":
self.group_graph = self.molecule.create_graph()
p = PT.formula_dict(self.symbol)
n = p['C']
last = None
for i in range(n):
v = self.group_graph.add_vertex()
v.x, v.y = None, None
if last:
self.group_graph.add_edge(last, v)
last = v
replacement = self.group_graph.vertices[0]
replacement.x = self.x
replacement.y = self.y
elif self.group_type == "implicit":
if not self.group_graph:
self.set_name(self.symbol,
occupied_valency=self.occupied_valency)
for v in self.group_graph.vertices:
v.x, v.y = None, None
v.show = v.symbol != 'C'
assert self.connecting_atom is not None
replacement = self.connecting_atom
replacement.x = self.x
replacement.y = self.y
self.molecule.eat_molecule(self.group_graph)
self.molecule.move_bonds_between_atoms(self, replacement)
self.molecule.delete_vertex(self)
if self.occupied_valency:
oasa.coords_generator.calculate_coords(self.molecule,
bond_length=-1)
else:
# if the group is the only vertex of the molecule we must set the bond_length explicitly
# and the move the whole molecule
replacement.x = None
replacement.y = None
x, y = self.x, self.y
oasa.coords_generator.calculate_coords(
self.molecule,
bond_length=Screen.any_to_px(self.paper.standard.bond_length))
dx = x - replacement.x
dy = y - replacement.y
[a.move(dx, dy) for a in self.group_graph.vertices]
return self.group_graph.vertices
def _set_y( self, y): self._y = Screen.any_to_px( y)
def x( self, x): self._x = Screen.any_to_px( x)
def read_standard_values( self, standard, old_standard=None):
meta_enabled.read_standard_values( self, standard, old_standard=old_standard)
if not old_standard or (standard.line_width != old_standard.line_width):
self.line_width = Screen.any_to_px( standard.line_width)
def x(self, x):
self._x = Screen.any_to_px(x)
