def __call__(self):
if self.name not in cmd.get_names('objects'):
import threading
threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
return
v = cmd.get_view()
if v == self.prev_v:
return
self.prev_v = v
t = v[12:15]
if self.corner:
vp = cmd.get_viewport()
R_mc = [v[0:3], v[3:6], v[6:9]]
off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
if self.corner in [2,3]:
off_c[0] *= -1
if self.corner in [3,4]:
off_c[1] *= -1
off_m = cpv.transform(R_mc, off_c)
t = cpv.add(t, off_m)
z = -v[11] / 30.0
m = [z, 0, 0, t[0] / z, 0, z, 0, t[1] / z, 0, 0, z, t[2] / z, 0, 0, 0, 1]
cmd.set_object_ttt(self.name, m, homogenous=1)
def __call__(self):
if self.name not in cmd.get_names('objects'):
import threading
threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
return
v = cmd.get_view()
if v == self.prev_v:
return
self.prev_v = v
t = v[12:15]
if self.corner:
vp = cmd.get_viewport()
R_mc = [v[0:3], v[3:6], v[6:9]]
off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
if self.corner in [2,3]:
off_c[0] *= -1
if self.corner in [3,4]:
off_c[1] *= -1
off_m = cpv.transform(R_mc, off_c)
t = cpv.add(t, off_m)
z = -v[11] / 30.0
m = [z, 0, 0, 0, 0, z, 0, 0, 0, 0, z, 0, t[0] / z, t[1] / z, t[2] / z, 1]
cmd.set_object_ttt(self.name, m)
def test_set_object_ttt(self):
M = [1.0, 0.0, 0.0, 0.0,
0.0, 0.0,-1.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.pseudoatom('m1')
cmd.set_object_ttt('m1', M)
self.assertArrayEqual(M, cmd.get_object_matrix('m1'), 1e-4)
def test_set_object_ttt(self):
M = [
1.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
0.0, 0.0, 1.0
]
cmd.pseudoatom('m1')
cmd.set_object_ttt('m1', M)
self.assertArrayEqual(M, cmd.get_object_matrix('m1'), 1e-4)
def matrix_to_ttt(names, reverse=0, state=-1, quiet=1):
'''
DESCRIPTION
Objects can have state matrices and view (frames) matrices. This function
takes the total matrix and stores it either as view matrix or as state
matrix (reverse=1). For movie frames, movie_auto_store must be set.
'''
from . import querying
reverse, state, quiet = int(reverse), int(state), int(quiet)
ostate = state
for object in cmd.get_object_list('(' + names + ')'):
if ostate < 1:
state = querying.get_object_state(object)
matrix = cmd.get_object_matrix(object, state)
cmd.matrix_reset(object)
if reverse:
cmd.reset(object)
cmd.transform_object(object, matrix, homogenous=1)
else:
cmd.set_object_ttt(object, matrix)
def matrix_to_ttt(names, reverse=0, state=-1, quiet=1):
'''
DESCRIPTION
Objects can have state matrices and view (frames) matrices. This function
takes the total matrix and stores it either as view matrix or as state
matrix (reverse=1). For movie frames, movie_auto_store must be set.
'''
from . import querying
reverse, state, quiet = int(reverse), int(state), int(quiet)
ostate = state
for object in cmd.get_object_list('(' + names + ')'):
if ostate < 1:
state = querying.get_object_state(object)
matrix = cmd.get_object_matrix(object, state)
for i in range(cmd.count_states(object)):
cmd.matrix_reset(object, i + 1)
if reverse:
cmd.reset(object)
cmd.transform_object(object, matrix, homogenous=1)
else:
cmd.set_object_ttt(object, matrix)
def testGetModel(self):
'''
Test coordinates and "reference" coordinates with various
transformations.
'''
# create two-state object
# displace state 1, will do tests on state 2
cmd.fragment('ala', 'm1')
cmd.create('m1', 'm1', 1, 2)
cmd.translate([1, 2, 3], 'm1', 1)
# prepare state 2
title = 'Alanin'
cmd.set_title('m1', 2, title)
cmd.reference(state=2)
# with original coordinates
m = cmd.get_model(state=2)
a = m.atom[0]
# title
self.assertEqual(title, m.molecule.title)
# bonds (covering count, indices and order)
self.assertEqual(
set(tuple(sorted(b.index)) + (b.order, ) for b in m.bond),
set([(0, 1, 1), (0, 5, 1), (1, 2, 1), (1, 4, 1), (1, 6, 1),
(2, 3, 2), (4, 7, 1), (4, 8, 1), (4, 9, 1)]))
# expect equal coord and ref_coord
coord = [-0.67689997, -1.23029995, -0.49050000]
self.assertArrayEqual(a.ref_coord, coord, delta=1e-4)
self.assertArrayEqual(a.coord, coord, delta=1e-4)
# modify ttt
cmd.set_object_ttt('m1', [
0,
1,
0,
0,
-1,
0,
0,
5,
0,
0,
1,
0,
0,
3,
0,
1,
]) # no state! API flaw, TTT object are not per state
m = cmd.get_model('m1', state=2)
a = m.atom[0]
# ttt should affect both equally
coord = [1.769700050354004, 5.6768999099731445, -0.49050000309944153]
self.assertArrayEqual(a.ref_coord, coord, delta=1e-4)
self.assertArrayEqual(a.coord, coord, delta=1e-4)
# modify coords
cmd.translate([10, 0, 0], state=2)
m = cmd.get_model('m1', state=2)
a = m.atom[0]
# no effect of ref_coord
ref = coord
coord = [11.769700050354004, 5.6768999099731445, -0.49050000309944153]
self.assertArrayEqual(a.ref_coord, ref, delta=1e-4)
self.assertArrayEqual(a.coord, coord, delta=1e-4)
# modify coords by alignment
cmd.fragment('ala', 'm2')
cmd.rotate('x', 90, 'm2')
cmd.align('m1', 'm2', mobile_state=2)
m = cmd.get_model('m1', state=2)
a = m.atom[0]
# no effect of ref_coord
coord = [3.490499973297119, 5.6768999099731445, -1.230299949645996]
self.assertArrayEqual(a.ref_coord, ref, delta=1e-4)
self.assertArrayEqual(a.coord, coord, delta=1e-4)
