/usr/share/pyshared/ase/gui/view.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Emacs: treat this as -*- python -*-
import os
import gtk
import tempfile
from math import cos, sin, sqrt, atan
from os.path import basename
import numpy as np
from ase.data.colors import jmol_colors
from ase.gui.repeat import Repeat
from ase.gui.rotate import Rotate
from ase.gui.render import Render
from ase.gui.colors import ColorWindow
from ase.utils import rotate
class View:
def __init__(self, vbox, rotations):
self.colormode = 'jmol' # The default colors
self.nselected = 0
self.light_green_markings = 0
self.axes = rotate(rotations)
# this is a hack, in order to be able to toggle menu actions off/on
# without getting into an infinte loop
self.menu_change = 0
self.atoms_to_rotate = None
self.drawing_area = gtk.DrawingArea()
self.drawing_area.set_size_request(450, 450)
self.drawing_area.connect('button_press_event', self.press)
self.drawing_area.connect('button_release_event', self.release)
self.drawing_area.connect('motion-notify-event', self.move)
# Signals used to handle backing pixmap:
self.drawing_area.connect('expose_event', self.expose_event)
self.drawing_area.connect('configure_event', self.configure_event)
self.drawing_area.set_events(gtk.gdk.BUTTON_PRESS_MASK |
gtk.gdk.BUTTON_RELEASE_MASK |
gtk.gdk.BUTTON_MOTION_MASK |
gtk.gdk.POINTER_MOTION_HINT_MASK)
vbox.pack_start(self.drawing_area)
self.drawing_area.show()
self.configured = False
self.frame = None
def set_coordinates(self, frame=None, focus=None):
if frame is None:
frame = self.frame
self.make_box()
self.bind(frame)
n = self.images.natoms
self.X = np.empty((n + len(self.B1) + len(self.bonds), 3))
#self.X[n:] = np.dot(self.B1, self.images.A[frame])
#self.B = np.dot(self.B2, self.images.A[frame])
self.set_frame(frame, focus=focus, init=True)
def set_frame(self, frame=None, focus=False, init=False):
if frame is None:
frame = self.frame
n = self.images.natoms
if self.frame > self.images.nimages:
self.frame = self.images.nimages - 1
if init or frame != self.frame:
A = self.images.A
nc = len(self.B1)
nb = len(self.bonds)
if init or (A[frame] != A[self.frame]).any():
self.X[n:n + nc] = np.dot(self.B1, A[frame])
self.B = np.empty((nc + nb, 3))
self.B[:nc] = np.dot(self.B2, A[frame])
if nb > 0:
P = self.images.P[frame]
Af = self.images.repeat[:, np.newaxis] * A[frame]
a = P[self.bonds[:, 0]]
b = P[self.bonds[:, 1]] + np.dot(self.bonds[:, 2:], Af) - a
d = (b**2).sum(1)**0.5
r = 0.65 * self.images.r
x0 = (r[self.bonds[:, 0]] / d).reshape((-1, 1))
x1 = (r[self.bonds[:, 1]] / d).reshape((-1, 1))
self.X[n + nc:] = a + b * x0
b *= 1.0 - x0 - x1
b[self.bonds[:, 2:].any(1)] *= 0.5
self.B[nc:] = self.X[n + nc:] + b
filenames = self.images.filenames
filename = filenames[frame]
if self.frame is None or filename != filenames[self.frame] or filename is None:
if filename is None:
filename = 'ase.gui'
filename = basename(filename)
self.window.set_title(filename)
self.frame = frame
self.X[:n] = self.images.P[frame]
self.R = self.X[:n]
if focus:
self.focus()
else:
self.draw()
def set_colors(self):
self.colormode = 'jmol'
self.set_jmol_colors()
def set_jmol_colors(self):
self.colors = [None] * (len(jmol_colors) + 1)
self.colordata = []
new = self.drawing_area.window.new_gc
alloc = self.colormap.alloc_color
for z in self.images.Z:
if self.colors[z] is None:
c, p, k = jmol_colors[z]
self.colors[z] = new(alloc(int(65535 * c),
int(65535 * p),
int(65535 * k)))
hasfound = {}
for z in self.images.Z:
if z not in hasfound:
hasfound[z] = True
self.colordata.append([z, jmol_colors[z]])
def plot_cell(self):
V = self.images.A[0]
R1 = []
R2 = []
for c in range(3):
v = V[c]
d = sqrt(np.dot(v, v))
n = max(2, int(d / 0.3))
h = v / (2 * n - 1)
R = np.arange(n)[:, None] * (2 * h)
for i, j in [(0, 0), (0, 1), (1, 0), (1, 1)]:
R1.append(R + i * V[(c + 1) % 3] + j * V[(c + 2) % 3])
R2.append(R1[-1] + h)
return np.concatenate(R1), np.concatenate(R2)
def make_box(self):
if not self.ui.get_widget('/MenuBar/ViewMenu/ShowUnitCell'
).get_active():
self.B1 = self.B2 = np.zeros((0, 3))
return
V = self.images.A[0]
nn = []
for c in range(3):
v = V[c]
d = sqrt(np.dot(v, v))
n = max(2, int(d / 0.3))
nn.append(n)
self.B1 = np.zeros((2, 2, sum(nn), 3))
self.B2 = np.zeros((2, 2, sum(nn), 3))
n1 = 0
for c, n in enumerate(nn):
n2 = n1 + n
h = 1.0 / (2 * n - 1)
R = np.arange(n) * (2 * h)
for i, j in [(0, 0), (0, 1), (1, 0), (1, 1)]:
self.B1[i, j, n1:n2, c] = R
self.B1[i, j, n1:n2, (c + 1) % 3] = i
self.B1[i, j, n1:n2, (c + 2) % 3] = j
self.B2[:, :, n1:n2] = self.B1[:, :, n1:n2]
self.B2[:, :, n1:n2, c] += h
n1 = n2
self.B1.shape = (-1, 3)
self.B2.shape = (-1, 3)
def bind(self, frame):
if not self.ui.get_widget('/MenuBar/ViewMenu/ShowBonds'
).get_active():
self.bonds = np.empty((0, 5), int)
return
from ase.atoms import Atoms
from ase.calculators.neighborlist import NeighborList
nl = NeighborList(self.images.r * 1.5, skin=0, self_interaction=False)
nl.update(Atoms(positions=self.images.P[frame],
cell=(self.images.repeat[:, np.newaxis] *
self.images.A[frame]),
pbc=self.images.pbc))
nb = nl.nneighbors + nl.npbcneighbors
self.bonds = np.empty((nb, 5), int)
if nb == 0:
return
n1 = 0
for a in range(self.images.natoms):
indices, offsets = nl.get_neighbors(a)
n2 = n1 + len(indices)
self.bonds[n1:n2, 0] = a
self.bonds[n1:n2, 1] = indices
self.bonds[n1:n2, 2:] = offsets
n1 = n2
i = self.bonds[:n2, 2:].any(1)
self.bonds[n2:, 0] = self.bonds[i, 1]
self.bonds[n2:, 1] = self.bonds[i, 0]
self.bonds[n2:, 2:] = -self.bonds[i, 2:]
def toggle_show_unit_cell(self, action):
self.set_coordinates()
def reset_tools_modes(self):
dummy = self.menu_change
self.menu_change = 1
self.atoms_to_rotate = None
for c_mode in ['Rotate', 'Orient', 'Move']:
self.ui.get_widget('/MenuBar/ToolsMenu/%sAtoms' % c_mode).set_active(False)
self.light_green_markings = 0
self.menu_change = 0
self.draw()
def toggle_mode(self, mode):
self.menu_change = 1
i_sum = 0
for c_mode in ['Rotate', 'Orient', 'Move']:
i_sum += self.ui.get_widget('/MenuBar/ToolsMenu/%sAtoms' % c_mode).get_active()
if i_sum == 0 or (i_sum == 1 and sum(self.images.selected) == 0):
self.reset_tools_modes()
return()
if i_sum == 2:
try:
self.images.selected = self.atoms_to_rotate_0.copy()
except:
self.atoms_to_rotate_0 = self.images.selected.copy()
if i_sum == 1:
self.atoms_to_rotate_0 = self.images.selected.copy()
for c_mode in ['Rotate', 'Orient', 'Move']:
if c_mode != mode:
self.ui.get_widget('/MenuBar/ToolsMenu/%sAtoms' % c_mode).set_active(False)
if self.ui.get_widget('/MenuBar/ToolsMenu/%sAtoms' % mode).get_active():
self.atoms_to_rotate_0 = self.images.selected.copy()
for i in range(len(self.images.selected)):
self.images.selected[i] = False
self.light_green_markings = 1
else:
try:
atr = self.atoms_to_rotate_0
for i in range(len(self.images.selected)):
self.images.selected[i] = atr[i]
except:
pass
self.menu_change = 0
self.draw()
def toggle_move_mode(self, action):
"""
Toggles the move mode, where the selected atoms can be moved with the arrow
keys and pg up/dn. If the shift key is pressed, the movement will be reduced.
The movement will be relative to the current rotation of the coordinate system.
The implementation of the move mode is found in the gui.scroll
"""
if not (self.menu_change):
self.toggle_mode('Move')
def toggle_rotate_mode(self, action):
"""
Toggles the rotate mode, where the selected atoms can be rotated with the arrow keys
and pg up/dn. If the shift key is pressed, the rotation angle will be reduced.
The atoms to be rotated will be marked with light green - and the COM of the selected
atoms will be used as the COM of the rotation. This can be changed while rotating the
selected atoms.
If only two atoms are seleceted, and the number of atoms to be rotated is different from
two, the selected atoms will define the axis of rotation.
The implementation of the rotate mode is found in the gui.scroll
"""
if not (self.menu_change):
self.toggle_mode('Rotate')
def toggle_orient_mode(self, action):
"""
Toggle the orientation mode - the orientation of the atoms will be changed
according to the arrow keys selected.
If nothing is selected, standard directions are x, y and z
if two atoms are selected, the standard directions are along their displacement vector
if three atoms are selected, the orientation is changed according to the normal of these
three vectors.
"""
if not (self.menu_change):
self.toggle_mode('Orient')
self.orient_normal = np.array([1.0, 0.0, 0.0])
sel_pos = []
for i, j in enumerate(self.atoms_to_rotate_0):
if j:
sel_pos.append(self.R[i])
if len(sel_pos) == 2:
self.orient_normal = sel_pos[0] - sel_pos[1]
if len(sel_pos) == 3:
v1 = sel_pos[1] - sel_pos[0]
v2 = sel_pos[1] - sel_pos[2]
self.orient_normal = np.cross(v1, v2)
self.orient_normal /= sum(self.orient_normal ** 2) ** 0.5
def toggle_show_axes(self, action):
self.draw()
def toggle_show_bonds(self, action):
self.set_coordinates()
def repeat_window(self, menuitem):
self.reset_tools_modes()
Repeat(self)
def rotate_window(self, menuitem):
Rotate(self)
def colors_window(self, menuitem):
ColorWindow(self)
def focus(self, x=None):
if (self.images.natoms == 0 and not
self.ui.get_widget('/MenuBar/ViewMenu/ShowUnitCell').get_active()):
self.scale = 1.0
self.center = np.zeros(3)
self.draw()
return
P = np.dot(self.X, self.axes)
n = self.images.natoms
P[:n] -= self.images.r[:, None]
P1 = P.min(0)
P[:n] += 2 * self.images.r[:, None]
P2 = P.max(0)
self.center = np.dot(self.axes, (P1 + P2) / 2)
S = 1.3 * (P2 - P1)
if S[0] * self.height < S[1] * self.width:
self.scale = self.height / S[1]
else:
self.scale = self.width / S[0]
self.draw()
def reset_view(self, menuitem):
self.axes = rotate('0.0x,0.0y,0.0z')
self.set_coordinates()
self.focus(self)
def get_colors(self, rgb = False):
Z = self.images.Z
if rgb:
# create a shape that is equivalent to self.colors,
# but contains rgb data instead gtk.gdk.GCX11 objects
colarray = [None] * max(len(jmol_colors)+1,len(self.colordata))
for z, c in self.colordata:
colarray[z] = c
else:
colarray = self.colors
if self.colormode == 'jmol' or self.colormode == 'atno':
colors = np.array(colarray)[Z]
elif self.colormode == 'tags':
colors = np.array(colarray)[self.images.T[self.frame]]
elif self.colormode == 'force':
F = self.images.F[self.frame]
F = np.sqrt(((F*self.images.dynamic[:,np.newaxis])**2).sum(axis=-1)) # The absolute force
nF = (F - self.colormode_force_data[0]) * self.colormode_force_data[1]
nF = np.clip(nF.astype(int), 0, len(self.colors)-1)
colors = np.array(colarray)[nF]
elif self.colormode == 'velocity':
V = self.images.V[self.frame]
V = np.sqrt((V*V).sum(axis=-1)) # The absolute velocity
nV = (V - self.colormode_velocity_data[0]) * self.colormode_velocity_data[1]
nV = np.clip(nV.astype(int), 0, len(self.colors)-1)
colors = np.array(colarray)[nV]
elif self.colormode == 'manual':
colors = colarray
elif self.colormode == 'same':
colors = [colarray[0]] * self.images.natoms
else:
raise RuntimeError('Unknown color mode: %s' % (self.colormode,))
return colors
def repeat_colors(self, repeat):
natoms = self.images.natoms
if self.colormode == 'manual':
a0 = 0
colors = self.colors
colordata = self.colordata
for i0 in range(repeat[0]):
for i1 in range(repeat[1]):
for i2 in range(repeat[2]):
a1 = a0 + natoms
colors[a0:a1] = self.colors[:natoms]
colordata[a0:a1] = self.colordata[:natoms]
a0 = a1
self.colors = colors
self.colordata = colordata
def my_arc(self, gc, fill, j, X, r, n, A):
if self.images.shapes is not None:
rx = (self.images.shapes[j, 0]).round().astype(int)
ry = (self.images.shapes[j, 1]).round().astype(int)
rz = (self.images.shapes[j, 2]).round().astype(int)
circle = rx == ry and ry == rz
else:
circle = True
if not circle:
Q = self.images.Q[j]
X2d = np.array([X[j][0], X[j][1]])
Ellipsoid = np.array([[1. / (rx*rx), 0, 0],
[0, 1. / (ry*ry), 0],
[0, 0, 1. / (rz*rz)]
])
# Ellipsoid rotatet by quaternion as Matrix X' = R X R_transpose
El_r = np.dot(Q.rotation_matrix(),
np.dot(Ellipsoid,
np.transpose(Q.rotation_matrix())))
# Ellipsoid rotated by quaternion and axes as
# Matrix X' = R_axes X' R_axes
El_v = np.dot(np.transpose(self.axes), np.dot(El_r, self.axes))
# Projection of rotatet ellipsoid on xy plane
El_p = Ell = np.array([
[El_v[0][0] - El_v[0][2] * El_v[0][2] / El_v[2][2],
El_v[0][1] - El_v[0][2] * El_v[1][2] / El_v[2][2]],
[El_v[0][1] - El_v[0][2] * El_v[1][2] / El_v[2][2],
El_v[1][1] - El_v[1][2] * El_v[1][2] / El_v[2][2]]
])
# diagonal matrix der Ellipse gibt halbachsen
El_p_diag = np.linalg.eig(El_p)
# Winkel mit dem Ellipse in xy gedreht ist aus
# eigenvektor der diagonal matrix
phi = atan(El_p_diag[1][0][1] / El_p_diag[1][0][0])
tupl = []
alpha = np.array(range(20)) *2* np.pi /20
El_xy = np.array([sqrt(1. / (El_p_diag[0][0])) *
np.cos(alpha)*np.cos(phi)
- sqrt(1./(El_p_diag[0][1])) *
np.sin(alpha) * np.sin(phi),
sqrt(1./(El_p_diag[0][0])) *
np.cos(alpha)*np.sin(phi)
+ sqrt(1./(El_p_diag[0][1])) *
np.sin(alpha) * np.cos(phi)])
tupl = (El_xy.transpose() * self.scale +
X[j][:2]).round().astype(int)
# XXX there must be a better way
tupl = [tuple(i) for i in tupl]
return self.pixmap.draw_polygon( gc, fill, tupl)
dx = dy = (2 * r).round().astype(int)
rj = dx[j]
return self.pixmap.draw_arc(gc, fill, A[j, 0], A[j, 1], rj, rj,
0, 23040)
def draw(self, status=True):
self.pixmap.draw_rectangle(self.white_gc, True, 0, 0,
self.width, self.height)
axes = self.scale * self.axes * (1, -1, 1)
offset = (np.dot(self.center, axes) -
(0.5 * self.width, 0.5 * self.height, 0))
X = np.dot(self.X, axes) - offset
n = self.images.natoms
self.indices = X[:, 2].argsort()
if self.ui.get_widget('/MenuBar/ViewMenu/ShowBonds').get_active():
r = self.images.r * (0.65 * self.scale)
else:
r = self.images.r * self.scale
P = self.P = X[:n, :2]
A = (P - r[:, None]).round().astype(int)
X1 = X[n:, :2].round().astype(int)
X2 = (np.dot(self.B, axes) - offset).round().astype(int)
d = (2 * r).round().astype(int)
selected_gc = self.selected_gc
colors = self.get_colors()
arc = self.pixmap.draw_arc
line = self.pixmap.draw_line
black_gc = self.black_gc
dynamic = self.images.dynamic
selected = self.images.selected
visible = self.images.visible
for a in self.indices:
if a < n:
ra = d[a]
if visible[a]:
self.my_arc(colors[a], True, a, X, r, n, A)
if self.light_green_markings and self.atoms_to_rotate_0[a]:
arc(self.green, False, A[a, 0] + 2, A[a, 1] + 2,
ra - 4, ra - 4, 0, 23040)
if not dynamic[a]:
R1 = int(0.14644 * ra)
R2 = int(0.85355 * ra)
line(black_gc,
A[a, 0] + R1, A[a, 1] + R1,
A[a, 0] + R2, A[a, 1] + R2)
line(black_gc,
A[a, 0] + R2, A[a, 1] + R1,
A[a, 0] + R1, A[a, 1] + R2)
if selected[a]:
self.my_arc(selected_gc, False, a, X, r, n, A)
elif visible[a]:
self.my_arc(black_gc, False, a, X, r, n, A)
else:
a -= n
line(black_gc, X1[a, 0], X1[a, 1], X2[a, 0], X2[a, 1])
if self.ui.get_widget('/MenuBar/ViewMenu/ShowAxes').get_active():
self.draw_axes()
if self.images.nimages > 1:
self.draw_frame_number()
self.drawing_area.window.draw_drawable(self.white_gc, self.pixmap,
0, 0, 0, 0,
self.width, self.height)
if status:
self.status()
def draw_axes(self):
from ase.quaternions import Quaternion
q = Quaternion().from_matrix(self.axes)
L = np.zeros((10, 2, 3))
L[:3, 1] = self.axes * 15
L[3:5] = self.axes[0] * 20
L[5:7] = self.axes[1] * 20
L[7:] = self.axes[2] * 20
L[3:, :, :2] += (((-4, -5), (4, 5)), ((-4, 5), ( 4, -5)),
((-4, 5), (0, 0)), ((-4, -5), ( 4, 5)),
((-4, 5), (4, 5)), (( 4, 5), (-4, -5)),
((-4, -5), (4, -5)))
L = L.round().astype(int)
L[:, :, 0] += 20
L[:, :, 1] = self.height - 20 - L[:, :, 1]
line = self.pixmap.draw_line
colors = ([self.black_gc] * 3 +
[self.red] * 2 + [self.green] * 2 + [self.blue] * 3)
for i in L[:, 1, 2].argsort():
(a, b), (c, d) = L[i, :, :2]
line(colors[i], a, b, c, d)
digits = np.array(((1, 1, 1, 1, 1, 1, 0),
(0, 1, 1, 0, 0, 0, 0),
(1, 0, 1, 1, 0, 1, 1),
(1, 1, 1, 1, 0, 0, 1),
(0, 1, 1, 0, 1, 0, 1),
(1, 1, 0, 1, 1, 0, 1),
(1, 1, 0, 1, 1, 1, 1),
(0, 1, 1, 1, 0, 0, 0),
(1, 1, 1, 1, 1, 1, 1),
(0, 1, 1, 1, 1, 0, 1)), bool)
bars = np.array(((0, 2, 1, 2),
(1, 2, 1, 1),
(1, 1, 1, 0),
(1, 0, 0, 0),
(0, 0, 0, 1),
(0, 1, 0, 2),
(0, 1, 1, 1))) * 5
def draw_frame_number(self):
n = str(self.frame)
x = self.width - 3 - 8 * len(n)
y = self.height - 27
color = self.black_gc
line = self.pixmap.draw_line
for c in n:
bars = View.bars[View.digits[int(c)]]
for a, b, c, d in bars:
line(color, a + x, b + y, c + x, d + y)
x += 8
def release(self, drawing_area, event):
if event.button != 1:
return
selected = self.images.selected
selected_ordered = self.images.selected_ordered
if event.time < self.t0 + 200: # 200 ms
d = self.P - self.xy
hit = np.less((d**2).sum(1), (self.scale * self.images.r)**2)
for a in self.indices[::-1]:
if a < self.images.natoms and hit[a]:
if event.state & gtk.gdk.CONTROL_MASK:
selected[a] = not selected[a]
if selected[a]:
selected_ordered += [a]
elif len(selected_ordered) > 0:
if selected_ordered[-1] == a:
selected_ordered = selected_ordered[:-1]
else:
selected_ordered = []
else:
selected[:] = False
selected[a] = True
selected_ordered = [a]
break
else:
selected[:] = False
selected_ordered = []
self.draw()
else:
A = (event.x, event.y)
C1 = np.minimum(A, self.xy)
C2 = np.maximum(A, self.xy)
hit = np.logical_and(self.P > C1, self.P < C2)
indices = np.compress(hit.prod(1), np.arange(len(hit)))
if not (event.state & gtk.gdk.CONTROL_MASK):
selected[:] = False
selected[indices] = True
if len(indices) == 1 and indices[0] not in self.images.selected_ordered:
selected_ordered += [indices[0]]
elif len(indices) > 1:
selected_ordered = []
self.draw()
indices = np.arange(self.images.natoms)[self.images.selected]
if len(indices) != len(selected_ordered):
selected_ordered = []
self.images.selected_ordered = selected_ordered
def press(self, drawing_area, event):
self.button = event.button
self.xy = (event.x, event.y)
self.t0 = event.time
self.axes0 = self.axes
self.center0 = self.center
def move(self, drawing_area, event):
x, y, state = event.window.get_pointer()
x0, y0 = self.xy
if self.button == 1:
window = self.drawing_area.window
window.draw_drawable(self.white_gc, self.pixmap,
0, 0, 0, 0,
self.width, self.height)
x0 = int(round(x0))
y0 = int(round(y0))
window.draw_rectangle(self.selected_gc, False,
min(x, x0), min(y, y0),
abs(x - x0), abs(y - y0))
return
if self.button == 2:
return
if state & gtk.gdk.SHIFT_MASK:
self.center = (self.center0 -
np.dot(self.axes, (x - x0, y0 - y, 0)) / self.scale)
else:
# Snap mode: the a-b angle and t should multipla of 15 degrees ???
a = x - x0
b = y0 - y
t = sqrt(a * a + b * b)
if t > 0:
a /= t
b /= t
else:
a = 1.0
b = 0.0
c = cos(0.01 * t)
s = -sin(0.01 * t)
rotation = np.array([(c * a * a + b * b, (c - 1) * b * a, s * a),
((c - 1) * a * b, c * b * b + a * a, s * b),
(-s * a, -s * b, c)])
self.axes = np.dot(self.axes0, rotation)
if self.images.natoms > 0:
com = self.X[:self.images.natoms].mean(0)
else:
com = self.images.A[self.frame].mean(0)
self.center = com - np.dot(com - self.center0,
np.dot(self.axes0, self.axes.T))
self.draw(status=False)
# Create a new backing pixmap of the appropriate size
def configure_event(self, drawing_area, event):
if self.configured:
w = self.width
h = self.height
else:
self.colormap = self.drawing_area.get_colormap()
self.black_gc = self.drawing_area.get_style().black_gc
self.white_gc = self.drawing_area.get_style().white_gc
self.red = self.drawing_area.window.new_gc(
self.colormap.alloc_color(62345, 0, 0), line_width=2)
self.green = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 54456, 0), line_width=2)
self.blue = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 0, 54456), line_width=2)
self.selected_gc = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 16456, 0),
line_width=3)
x, y, self.width, self.height = drawing_area.get_allocation()
self.pixmap = gtk.gdk.Pixmap(drawing_area.window,
self.width, self.height)
if self.configured:
self.scale *= sqrt(1.0 * self.width * self.height / (w * h))
self.draw()
self.configured = True
# Redraw the screen from the backing pixmap
def expose_event(self, drawing_area, event):
x , y, width, height = event.area
gc = self.white_gc
drawing_area.window.draw_drawable(gc, self.pixmap,
x, y, x, y, width, height)
def external_viewer(self, action):
name = action.get_name()
command = {'Avogadro' : 'avogadro',
'XMakeMol': 'xmakemol -f',
'RasMol':'rasmol -xyz',
'VMD': 'vmd'}[name]
fd, filename = tempfile.mkstemp('.xyz', 'ase.gui-')
os.close(fd)
self.images.write(filename)
os.system('(%s %s &); (sleep 60; rm %s) &' %
(command, filename, filename))
def render_window(self, action):
Render(self)
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