def get_atoms(self):
# Get the text, whether it's a combobox item or not
val = self.combobox.widget.get()
if val == current_selection_string:
selection = self.gui.images.selected.copy()
if selection.any():
atoms = self.gui.atoms.copy()
return atoms[selection[:len(self.gui.atoms)]]
if val in atomic_numbers: # Note: This means val is a symbol!
return Atoms(val)
if val.isdigit() and int(val) < len(chemical_symbols):
return Atoms(numbers=[int(val)])
from ase.collections import g2
if val in g2.names:
return g2[val]
if os.path.exists(val):
return self.readfile(val) # May show UI error
ui.showerror(_('Cannot add atoms'),
_('{} is neither atom, molecule, nor file')
.format(val))
return None
def add(self):
newatoms = self.get_atoms()
if newatoms is None: # Error dialog was shown
return
newcenter = self.getcoords()
# Not newatoms.center() because we want the same centering method
# used for adding atoms relative to selections (mean).
previous_center = newatoms.positions.mean(0)
newatoms.positions += newcenter - previous_center
atoms = self.gui.atoms
if len(atoms) and self.picky.value:
from ase.geometry import get_distances
disps, dists = get_distances(atoms.positions, newatoms.positions)
mindist = dists.min()
if mindist < 0.5:
ui.showerror(
_('Bad positions'),
_('Atom would be less than 0.5 Å from '
'an existing atom. To override, '
'uncheck the check positions option.'))
return
self.gui.add_atoms_and_select(newatoms)
def save_dialog(gui, filename=None):
dialog = ui.SaveFileDialog(gui.window.win, _('Save ...'))
ui.Text(text).pack(dialog.top)
filename = filename or dialog.go()
if not filename:
return
filename, index = parse_filename(filename)
if index is None:
index = slice(gui.frame, gui.frame + 1)
elif isinstance(index, basestring):
index = string2index(index)
elif isinstance(index, slice):
pass
else:
if index < 0:
index += len(gui.images)
index = slice(index, index + 1)
format = filetype(filename, read=False)
io = get_ioformat(format)
extra = {}
remove_hidden = False
if format in ['png', 'eps', 'pov']:
bbox = np.empty(4)
size = gui.window.size / gui.scale
bbox[0:2] = np.dot(gui.center, gui.axes[:, :2]) - size / 2
bbox[2:] = bbox[:2] + size
extra['rotation'] = gui.axes
extra['show_unit_cell'] = gui.window['toggle-show-unit-cell']
extra['bbox'] = bbox
colors = gui.get_colors(rgb=True)
extra['colors'] = [
rgb for rgb, visible in zip(colors, gui.images.visible) if visible
]
remove_hidden = True
images = [
gui.images.get_atoms(i, remove_hidden=remove_hidden)
for i in range(*index.indices(len(gui.images)))
]
if len(images) > 1 and io.single:
# We want to write multiple images, but the file format does not
# support it. The solution is to write multiple files, inserting
# a number in the file name before the suffix.
j = filename.rfind('.')
filename = filename[:j] + '{0:05d}' + filename[j:]
for i, atoms in enumerate(images):
write(filename.format(i), atoms, **extra)
else:
try:
write(filename, images, **extra)
except Exception as err:
from ase.gui.ui import showerror
showerror(_('Error'), err)
raise
def get_atoms(self):
val = self.entry.value
if val in atomic_numbers: # Note: This means val is a symbol!
return Atoms(val)
if val.isdigit() and int(val) < len(chemical_symbols):
return Atoms(numbers=[int(val)])
from ase.collections import g2
if val in g2.names:
return g2[val]
if os.path.exists(val):
return self.readfile(val) # May show UI error
ui.showerror(_('Cannot add atoms'),
_('{} is neither atom, molecule, nor file').format(val))
return None
def add(self):
newatoms = self.get_atoms()
if newatoms is None: # Error dialog was shown
return
newcenter = self.getcoords()
# Not newatoms.center() because we want the same centering method
# used for adding atoms relative to selections (mean).
previous_center = newatoms.positions.mean(0)
newatoms.positions += newcenter - previous_center
atoms = self.gui.atoms
if len(atoms) and self.picky.value:
from ase.geometry import get_distances
disps, dists = get_distances(atoms.positions, newatoms.positions)
mindist = dists.min()
if mindist < 0.5:
ui.showerror(
_('Bad positions'),
_('Atom would be less than 0.5 Å from '
'an existing atom. To override, '
'uncheck the check positions option.'))
return
atoms += newatoms
if len(atoms) > self.gui.images.maxnatoms:
self.gui.images.initialize(list(self.gui.images),
self.gui.images.filenames)
self.gui.images.selected[:] = False
# 'selected' array may be longer than current atoms
self.gui.images.selected[len(atoms) - len(newatoms):len(atoms)] = True
self.gui.set_frame()
self.gui.draw()