def delete_items(self, items, redraw=1, delete_single_atom=1):
"""deletes items and also makes cleaning of orphan bonds and atoms"""
if not items:
return items, [] # quick way to avoid costly evaluation
deleted = copy.copy(items)
for o in items:
if o.object_type == 'atom':
self.delete_atom(o)
else:
self.delete_bond(o)
if self.atoms:
# delete bonds that are not in connect anymore
bonds_in_connect = set()
for a in self.atoms:
for (e, v) in a.get_neighbor_edge_pairs():
if v in self.atoms:
bonds_in_connect.add(e)
deleted += [
self.delete_bond(o) for o in (self.bonds - bonds_in_connect)
]
# delete also orphan atoms
if delete_single_atom:
atms = [o for o in self.atoms if len(o.neighbors) == 0]
deleted += [self.delete_atom(o) for o in atms]
# recalculation of second line of double bond position, optimized to do it only when realy
# necessary, because its pretty expensive
# check_integrity should be called before redrawing, because it moves atoms and bonds
# to new molecules when the molecule is spit and avoids working on non-connected graph
offspring = self.check_integrity()
if redraw:
bonds_to_redraw = []
for b in deleted:
if b.object_type == 'bond':
for a in b.atoms:
if a in self.atoms:
bonds_to_redraw.extend(a.neighbor_edges)
[
o.redraw(recalc_side=1)
for o in misc.filter_unique(bonds_to_redraw)
if o.order == 2 and o.item
]
[o.decide_pos() for o in self.atoms if isinstance(o, atom)]
[o.redraw() for o in self.atoms]
else:
offspring = self.check_integrity()
deleted += map(self.delete_bond, copy.copy(self.bonds))
return deleted, offspring
def handle_overlap(self):
"deletes one of overlaping atoms and updates the bonds"
to_delete = []
bonds_to_check = set(
) # this can speedup the following for b in bonds_to_check by factor of 10 for big mols
for i in range(len(self.atoms)):
for j in range(i + 1, len(self.atoms)):
a = self.atoms[i]
b = self.atoms[j]
if (abs(a.x - b.x) < 4) and (abs(a.y - b.y) < 4):
if a not in to_delete:
for e, v in b.get_neighbor_edge_pairs():
e.change_atoms(b, a)
a.add_neighbor(v, e)
v.add_neighbor(a, e)
bonds_to_check.add(e)
to_delete.append(b)
deleted = misc.filter_unique(to_delete)
[self.delete_atom(o) for o in deleted]
# after all is done, find and delete orphan bonds and update the others
to_redraw = []
bonds = set(self.bonds)
for b in bonds_to_check:
if not b in self.bonds:
#print b, "not in self.bonds"
continue
recent_b = None
for recent_b in self.gen_bonds_between(b.atom1, b.atom2):
if recent_b != b:
break
if recent_b and recent_b != b:
self.delete_bond(b)
deleted.append(b)
to_redraw.append(recent_b) # we redraw the ones that remained
elif not recent_b:
b.atom1.add_neighbor(b.atom2, b)
b.atom2.add_neighbor(b.atom1, b)
to_redraw.append(b) # we redraw this also
for b in to_redraw:
b.redraw()
return deleted
def handle_overlap( self):
"deletes one of overlaping atoms and updates the bonds"
to_delete = []
bonds_to_check = set() # this can speedup the following for b in bonds_to_check by factor of 10 for big mols
for i in range( len( self.atoms)):
for j in range( i+1, len( self.atoms)):
a = self.atoms[i]
b = self.atoms[j]
if (abs( a.x-b.x) < 4) and (abs( a.y-b.y) <4):
if a not in to_delete:
for e,v in b.get_neighbor_edge_pairs():
e.change_atoms( b, a)
a.add_neighbor( v, e)
v.add_neighbor( a, e)
bonds_to_check.add( e)
to_delete.append( b)
deleted = misc.filter_unique( to_delete)
[self.delete_atom( o) for o in deleted]
# after all is done, find and delete orphan bonds and update the others
to_redraw = []
bonds = set( self.bonds)
for b in bonds_to_check:
if not b in self.bonds:
#print(b, "not in self.bonds")
continue
recent_b = None
for recent_b in self.gen_bonds_between( b.atom1, b.atom2):
if recent_b != b:
break
if recent_b and recent_b != b:
self.delete_bond( b)
deleted.append( b)
to_redraw.append( recent_b) # we redraw the ones that remained
elif not recent_b:
b.atom1.add_neighbor( b.atom2, b)
b.atom2.add_neighbor( b.atom1, b)
to_redraw.append( b) # we redraw this also
for b in to_redraw:
b.redraw()
return deleted
def delete_items( self, items, redraw=1, delete_single_atom=1):
"""deletes items and also makes cleaning of orphan bonds and atoms"""
if not items:
return items, [] # quick way to avoid costly evaluation
deleted = copy.copy( items)
for o in items:
if o.object_type == 'atom':
self.delete_atom( o)
else:
self.delete_bond( o)
if self.atoms:
# delete bonds that are not in connect anymore
bonds_in_connect = set()
for a in self.atoms:
for (e,v) in a.get_neighbor_edge_pairs():
if v in self.atoms:
bonds_in_connect.add( e)
deleted += [self.delete_bond( o) for o in (self.bonds - bonds_in_connect)]
# delete also orphan atoms
if delete_single_atom:
atms = [o for o in self.atoms if len(o.neighbors) == 0]
deleted += [self.delete_atom( o) for o in atms]
# recalculation of second line of double bond position, optimized to do it only when realy
# necessary, because its pretty expensive
# check_integrity should be called before redrawing, because it moves atoms and bonds
# to new molecules when the molecule is spit and avoids working on non-connected graph
offspring = self.check_integrity()
if redraw:
bonds_to_redraw = []
for b in deleted:
if b.object_type == 'bond':
for a in b.atoms:
if a in self.atoms:
bonds_to_redraw.extend( a.neighbor_edges)
[o.redraw( recalc_side=1) for o in misc.filter_unique( bonds_to_redraw) if o.order == 2 and o.item]
[o.decide_pos() for o in self.atoms if isinstance( o, atom)]
[o.redraw() for o in self.atoms]
else:
offspring = self.check_integrity()
deleted += map( self.delete_bond, copy.copy( self.bonds))
return deleted, offspring
def __init__(self, parent, items):
self.items = items
self.changes_made = 0
self.parent = parent
self.dialog = Pmw.Dialog(parent,
buttons=(_('OK'), _('Cancel')),
defaultbutton=_('OK'),
title=_('Configuration'),
command=self.done,
master='parent')
#parent.bind_all( "<Button-1>", self.raise_me, add='+')
self.pages = Pmw.NoteBook(self.dialog.interior())
self.pages.pack(anchor='w', pady=0, padx=0, fill='both', expand=1)
# create pages for different item types
self.atom_page = None
self.bond_page = None
self.arrow_page = None
self.text_page = None
self.plus_page = None
self.font_page = None
self.common_page = None
arrows = []
for o in items:
if o.object_type == 'point':
items.remove(o)
if o.arrow not in arrows:
arrows.append(o.arrow)
items += arrows
types = misc.filter_unique([o.object_type for o in items])
if 'atom' in types:
self.atom_page = self.pages.add(_('Atom'))
# charge
charges = misc.filter_unique(
[o.charge for o in items if hasattr(o, 'charge')])
if len(charges) == 1:
charge = charges[0]
else:
charge = ''
self.atom_charge = Pmw.Counter(self.atom_page,
labelpos='w',
label_text=_('Charge'),
entryfield_value=charge,
entryfield_validate={
'validator': 'integer',
'min': -4,
'max': 4
},
entry_width=3,
increment=1,
datatype='integer')
self.atom_charge.pack(anchor='nw', padx=10, pady=5)
# show?
shows = misc.filter_unique(
[o.show for o in items if hasattr(o, 'show')])
if len(shows) == 1:
show = int(shows[0])
else:
show = 2 # means the show should be preserved as is
self.atom_show = Pmw.OptionMenu(self.atom_page,
labelpos='nw',
label_text=_('Atom name'),
items=(_("don't show"), _("show"),
u""),
initialitem=show)
self.atom_show.pack(anchor='nw')
# positioning
poss = misc.filter_unique(
[o.pos for o in items if o.object_type == 'atom'])
if not poss:
pos = None
elif len(poss) == 1 and poss[0]:
pos = ['center-first', 'center-last'].index(poss[0])
else:
pos = 2 # means the centering should be preserved as is
if pos == None:
self.atom_pos = None
else:
self.atom_pos = Pmw.OptionMenu(
self.atom_page,
labelpos='nw',
label_text=_('Atom positioning'),
items=(_("center first letter"), _("center last letter"),
u""),
initialitem=pos)
self.atom_pos.pack(anchor='nw')
# show hydrogens
shows = misc.filter_unique(
[o.show_hydrogens for o in items if o.object_type == 'atom'])
if len(shows) == 1:
show = shows[0]
else:
show = 2 # means the show should be preserved as is
self.atom_show_h = Pmw.OptionMenu(self.atom_page,
labelpos='nw',
label_text=_('Hydrogens'),
items=(_("off"), _("on"), u""),
initialitem=show)
self.atom_show_h.pack(anchor='nw')
# marks
#self.marks = widgets.GraphicalAngleChooser( self.atom_page, 270)
#self.marks.pack()
# BOND
if 'bond' in types:
self.bond_page = self.pages.add(_('Bond'))
# bond_widths (former distances)
dists = misc.filter_unique(
map(abs,
[o.bond_width for o in items if o.object_type == 'bond']))
if len(dists) == 1:
dist = dists[0]
else:
dist = ''
if not misc.split_number_and_unit(dist)[1]:
dist = str(dist) + 'px'
self.bond_dist = widgets.WidthChooser(self.bond_page,
dist,
label=_('Bond width'))
self.bond_dist.pack(anchor='ne', padx=10, pady=5)
# wedge_widths
dists = misc.filter_unique(
map(abs,
[o.wedge_width for o in items if o.object_type == 'bond']))
if len(dists) == 1:
dist = dists[0]
else:
dist = ''
if not misc.split_number_and_unit(dist)[1]:
dist = str(dist) + 'px'
self.wedge_width = widgets.WidthChooser(
self.bond_page, dist, label=_('Wedge/Hatch width'))
self.wedge_width.pack(anchor='ne', padx=10, pady=5)
# double bond length ratio
ratios = misc.filter_unique([
o.double_length_ratio for o in items if o.object_type == 'bond'
])
if len(ratios) == 1:
ratio = ratios[0]
else:
ratio = ''
self.double_length_ratio = widgets.RatioCounter(
self.bond_page, ratio, label=_('Double-bond length ratio'))
self.double_length_ratio.pack(anchor='nw', padx=10, pady=5)
# ARROW
if 'arrow' in types:
self.arrow_page = self.pages.add(_('Arrow'))
self.arrow_end_changed = 0
self.arrow_start_changed = 0
arrow_items = [o for o in items if o.object_type == 'arrow']
# arrow start pins
arrow_starts = misc.filter_unique(
[o.get_pins()[0] for o in arrow_items])
self.arrow_start = Tkinter.IntVar()
if len(arrow_starts) == 1:
self.arrow_start.set(arrow_starts[0])
else:
self.arrow_start.set(0)
self.arrow_start_entry = Tkinter.Checkbutton(
self.arrow_page,
text=_('Arrow-head on start'),
variable=self.arrow_start,
command=self._arrow_start_changed)
self.arrow_start_entry.pack(anchor='w')
# arrow end pins
arrow_ends = misc.filter_unique(
[o.get_pins()[1] for o in arrow_items])
self.arrow_end = Tkinter.IntVar()
if len(arrow_ends) == 1:
self.arrow_end.set(arrow_ends[0])
else:
self.arrow_end.set(0)
self.arrow_end_entry = Tkinter.Checkbutton(
self.arrow_page,
text=_('Arrow-head on end'),
variable=self.arrow_end,
command=self._arrow_end_changed)
self.arrow_end_entry.pack(anchor='w')
# spline?
splines = misc.filter_unique([o.spline for o in arrow_items])
self.spline = Tkinter.IntVar()
if len(splines) == 1:
self.spline.set(splines[0])
else:
self.spline.set(0)
self.spline_entry = Tkinter.Checkbutton(
self.arrow_page,
text=_('Spline arrow'),
variable=self.spline,
command=self._spline_changed)
self.spline_changed = 0
self.spline_entry.pack(anchor='w')
# TEXTS
# PLUS
# FONT
font_items = filter(lambda x: hasattr(x, 'font_family'), items)
if font_items:
self.font_page = self.pages.add(_('Font'))
sizes = misc.filter_unique([o.font_size for o in font_items])
if len(sizes) == 1:
size = sizes[0]
else:
size = ''
self.font_size = widgets.FontSizeChooser(self.font_page, size)
self.font_size.pack(anchor='nw')
used_families = misc.filter_unique(
[o.font_family for o in font_items])
if len(used_families) == 1:
self.used_family = used_families[0]
else:
self.used_family = ''
self.font_family = widgets.FontFamilyChooser(
self.font_page, self.used_family)
self.font_family.pack(anchor="nw", side='bottom')
# COMMON
self.common_page = self.pages.add(_('Common'))
line_items = filter(lambda x: hasattr(x, 'line_width'), items)
if line_items:
widths = misc.filter_unique([o.line_width for o in line_items])
if len(widths) == 1:
width = widths[0]
else:
width = ''
if not misc.split_number_and_unit(width)[1]:
width = str(width) + 'px'
self.line_width = widgets.WidthChooser(self.common_page,
width,
label=_('Line width'))
self.line_width.pack(anchor='nw', padx=10, pady=5)
line_color_items = filter(lambda x: hasattr(x, 'line_color'), items)
if line_color_items:
lines = misc.filter_unique(
[o.line_color for o in line_color_items])
if len(lines) == 1:
line = lines[0]
else:
line = None
self.line_color = widgets.ColorButtonWithTransparencyChecker(
self.common_page, color=line, text=_("Line color"))
self.line_color.pack(anchor='nw', padx=10, pady=10)
area_color_items = filter(lambda x: hasattr(x, 'area_color'), items)
if area_color_items:
areas = misc.filter_unique(
[o.area_color for o in area_color_items])
if len(areas) == 1:
area = areas[0]
else:
area = None
self.area_color = widgets.ColorButtonWithTransparencyChecker(
self.common_page, color=area, text=_("Area color"))
self.area_color.pack(anchor='nw', padx=10, pady=5)
# RUN IT ALL
self.pages.setnaturalsize()
self.dialog.activate(globalMode=0)
def __init__( self, parent, items):
self.items = items
self.changes_made = 0
self.parent = parent
self.dialog = Pmw.Dialog( parent,
buttons=(_('OK'), _('Cancel')),
defaultbutton=_('OK'),
title=_('Configuration'),
command=self.done,
master='parent')
#parent.bind_all( "<Button-1>", self.raise_me, add='+')
self.pages = Pmw.NoteBook( self.dialog.interior())
self.pages.pack( anchor='w', pady=0, padx=0, fill='both', expand=1)
# create pages for different item types
self.atom_page = None
self.bond_page = None
self.arrow_page = None
self.text_page = None
self.plus_page = None
self.font_page = None
self.common_page = None
arrows = []
for o in items:
if o.object_type == 'point':
items.remove( o)
if o.arrow not in arrows:
arrows.append( o.arrow)
items += arrows
types = misc.filter_unique( [o.object_type for o in items])
if 'atom' in types:
self.atom_page = self.pages.add(_('Atom'))
# charge
charges = misc.filter_unique( [o.charge for o in items if hasattr( o, 'charge')])
if len( charges) == 1:
charge = charges[0]
else:
charge = ''
self.atom_charge = Pmw.Counter( self.atom_page,
labelpos = 'w',
label_text = _('Charge'),
entryfield_value = charge,
entryfield_validate={ 'validator':'integer', 'min':-4, 'max':4},
entry_width = 3,
increment = 1,
datatype = 'integer')
self.atom_charge.pack( anchor='nw', padx=10, pady=5)
# show?
shows = misc.filter_unique( [o.show for o in items if hasattr( o, 'show')])
if len( shows) == 1:
show = int( shows[0])
else:
show = 2 # means the show should be preserved as is
self.atom_show = Pmw.OptionMenu( self.atom_page,
labelpos = 'nw',
label_text = _('Atom name'),
items = (_("don't show"), _("show"), ""),
initialitem = show)
self.atom_show.pack( anchor = 'nw')
# positioning
poss = misc.filter_unique( [o.pos for o in items if o.object_type == 'atom'])
if not poss:
pos = None
elif len( poss) == 1 and poss[0]:
pos = ['center-first', 'center-last'].index( poss[0])
else:
pos = 2 # means the centering should be preserved as is
if pos == None:
self.atom_pos = None
else:
self.atom_pos = Pmw.OptionMenu( self.atom_page,
labelpos = 'nw',
label_text = _('Atom positioning'),
items = (_("center first letter"), _("center last letter"), ""),
initialitem = pos)
self.atom_pos.pack( anchor = 'nw')
# show hydrogens
shows = misc.filter_unique( [o.show_hydrogens for o in items if o.object_type == 'atom'])
if len( shows) == 1:
show = shows[0]
else:
show = 2 # means the show should be preserved as is
self.atom_show_h = Pmw.OptionMenu( self.atom_page,
labelpos = 'nw',
label_text = _('Hydrogens'),
items = (_("off"), _("on"), ""),
initialitem = show)
self.atom_show_h.pack( anchor = 'nw')
# marks
#self.marks = widgets.GraphicalAngleChooser( self.atom_page, 270)
#self.marks.pack()
# BOND
if 'bond' in types:
self.bond_page = self.pages.add(_('Bond'))
# bond_widths (former distances)
dists = misc.filter_unique( map( abs, [o.bond_width for o in items if o.object_type == 'bond']))
if len( dists) == 1:
dist = dists[0]
else:
dist = ''
if not misc.split_number_and_unit( dist)[1]:
dist = str( dist) + 'px'
self.bond_dist = widgets.WidthChooser( self.bond_page, dist, label=_('Bond width'))
self.bond_dist.pack( anchor='ne', padx=10, pady=5)
# wedge_widths
dists = misc.filter_unique( map( abs, [o.wedge_width for o in items if o.object_type == 'bond']))
if len( dists) == 1:
dist = dists[0]
else:
dist = ''
if not misc.split_number_and_unit( dist)[1]:
dist = str( dist) + 'px'
self.wedge_width = widgets.WidthChooser( self.bond_page, dist, label=_('Wedge/Hatch width'))
self.wedge_width.pack( anchor='ne', padx=10, pady=5)
# double bond length ratio
ratios = misc.filter_unique( [o.double_length_ratio for o in items if o.object_type == 'bond'])
if len( ratios) == 1:
ratio = ratios[0]
else:
ratio = ''
self.double_length_ratio = widgets.RatioCounter( self.bond_page,
ratio,
label=_('Double-bond length ratio'))
self.double_length_ratio.pack( anchor='nw', padx=10, pady=5)
# ARROW
if 'arrow' in types:
self.arrow_page = self.pages.add(_('Arrow'))
self.arrow_end_changed = 0
self.arrow_start_changed = 0
arrow_items = [o for o in items if o.object_type == 'arrow']
# arrow start pins
arrow_starts = misc.filter_unique( [o.get_pins()[0] for o in arrow_items])
self.arrow_start = Tkinter.IntVar()
if len( arrow_starts) == 1:
self.arrow_start.set( arrow_starts[0])
else:
self.arrow_start.set( 0)
self.arrow_start_entry = Tkinter.Checkbutton( self.arrow_page,
text=_('Arrow-head on start'),
variable = self.arrow_start,
command = self._arrow_start_changed)
self.arrow_start_entry.pack( anchor='w')
# arrow end pins
arrow_ends = misc.filter_unique( [o.get_pins()[1] for o in arrow_items])
self.arrow_end = Tkinter.IntVar()
if len( arrow_ends) == 1:
self.arrow_end.set( arrow_ends[0])
else:
self.arrow_end.set( 0)
self.arrow_end_entry = Tkinter.Checkbutton( self.arrow_page,
text=_('Arrow-head on end'),
variable = self.arrow_end,
command = self._arrow_end_changed)
self.arrow_end_entry.pack( anchor='w')
# spline?
splines = misc.filter_unique( [o.spline for o in arrow_items])
self.spline = Tkinter.IntVar()
if len( splines) == 1:
self.spline.set( splines[0])
else:
self.spline.set( 0)
self.spline_entry = Tkinter.Checkbutton( self.arrow_page,
text=_('Spline arrow'),
variable = self.spline,
command = self._spline_changed)
self.spline_changed = 0
self.spline_entry.pack( anchor='w')
# TEXTS
# PLUS
# FONT
font_items = filter( lambda x: hasattr( x, 'font_family'), items)
if font_items:
self.font_page = self.pages.add(_('Font'))
sizes = misc.filter_unique( [o.font_size for o in font_items])
if len( sizes) == 1:
size = sizes[0]
else:
size = ''
self.font_size = widgets.FontSizeChooser( self.font_page, size)
self.font_size.pack( anchor = 'nw')
used_families = misc.filter_unique( [o.font_family for o in font_items])
if len( used_families) == 1:
self.used_family = used_families[0]
else:
self.used_family = ''
self.font_family = widgets.FontFamilyChooser( self.font_page, self.used_family)
self.font_family.pack( anchor="nw", side = 'bottom')
# COMMON
self.common_page = self.pages.add(_('Common'))
line_items = filter( lambda x: hasattr( x, 'line_width'), items)
if line_items:
widths = misc.filter_unique( [o.line_width for o in line_items])
if len( widths) == 1:
width = widths[0]
else:
width = ''
if not misc.split_number_and_unit( width)[1]:
width = str( width) + 'px'
self.line_width = widgets.WidthChooser( self.common_page, width, label=_('Line width'))
self.line_width.pack( anchor='nw', padx=10, pady=5)
line_color_items = filter( lambda x: hasattr( x, 'line_color'), items)
if line_color_items:
lines = misc.filter_unique( [o.line_color for o in line_color_items])
if len( lines) == 1:
line = lines[0]
else:
line = None
self.line_color = widgets.ColorButtonWithTransparencyChecker( self.common_page, color=line, text=_("Line color"))
self.line_color.pack( anchor='nw', padx=10, pady=10)
area_color_items = filter( lambda x: hasattr( x, 'area_color'), items)
if area_color_items:
areas = misc.filter_unique( [o.area_color for o in area_color_items])
if len( areas) == 1:
area = areas[0]
else:
area = None
self.area_color = widgets.ColorButtonWithTransparencyChecker( self.common_page, color=area, text=_("Area color"))
self.area_color.pack( anchor='nw', padx=10, pady=5)
# RUN IT ALL
self.pages.setnaturalsize()
self.dialog.activate( globalMode=0)