def testLoadCoordset(self):
import numpy
cmd.fragment('gly', 'm1')
coords = cmd.get_coordset('m1')
cmd.load_coordset(coords, 'm1', state=2)
self.assertEqual(2, cmd.count_states('m1'))
# data manipulation with copy=0
cmd.get_coordset('m1', copy=0)[:] += 5.0
self.assertTrue(numpy.allclose(coords + 5.0, cmd.get_coords('m1')))
def testLoadCoordset(self):
import numpy
cmd.fragment('gly', 'm1')
coords = cmd.get_coordset('m1')
cmd.load_coordset(coords, 'm1', state=2)
self.assertEqual(2, cmd.count_states('m1'))
# data manipulation with copy=0
cmd.get_coordset('m1', copy=0)[:] += 5.0
self.assertTrue(numpy.allclose(coords + 5.0, cmd.get_coords('m1')))
def test2638(self):
cmd.set('retain_order')
cmd.fragment('ala', 'm1')
n = cmd.count_atoms()
##
## Make long identifiers
##
chain = [randhex()] * n
resn = [randhex()] * n
resv = [randint(10**4, 10**6 - 1)] * n
names = [randhex(4) + str(i) for i in range(n)]
identif_str = '(chain, resn, resv, name)'
identifiers = list(zip(chain, resn, resv, names))
afterload = []
cmd.alter('m1',
identif_str + ' = _next()',
space={'_next': next_decorator(identifiers)})
##
## Test if cif in/out preserves identifiers
##
with testing.mktemp('.cif') as filename:
cmd.save(filename, 'm1')
cmd.load(filename, 'm2')
cmd.iterate('m2',
'_afterload.append(' + identif_str + ')',
space={'_afterload': afterload})
self.assertEqual(identifiers, afterload)
##
## Test if various formats preserve coordinates
##
coords = cmd.get_coordset('m1')
for ext in ['.pdb', '.xyz', '.mol2', '.sdf']:
cmd.delete('m2')
with testing.mktemp(ext) as filename:
cmd.save(filename, 'm1')
cmd.load(filename, 'm2')
self.assertArrayEqual(coords,
cmd.get_coordset('m2'),
delta=1e-3,
msg='not preserving coordinates: ' + ext)
def test2638(self):
cmd.set('retain_order')
cmd.fragment('ala', 'm1')
n = cmd.count_atoms()
##
## Make long identifiers
##
chain = [randhex()] * n
resn = [randhex()] * n
resv = [randint(10**4, 10**6 - 1)] * n
names = [randhex(4) + str(i) for i in range(n)]
identif_str = '(chain, resn, resv, name)'
identifiers = list(zip(chain, resn, resv, names))
afterload = []
cmd.alter('m1', identif_str + ' = _next()',
space={'_next': next_decorator(identifiers)})
##
## Test if cif in/out preserves identifiers
##
with testing.mktemp('.cif') as filename:
cmd.save(filename, 'm1')
cmd.load(filename, 'm2')
cmd.iterate('m2', '_afterload.append(' + identif_str + ')',
space={'_afterload': afterload})
self.assertEqual(identifiers, afterload)
##
## Test if various formats preserve coordinates
##
coords = cmd.get_coordset('m1')
for ext in ['.pdb', '.xyz', '.mol2', '.sdf']:
cmd.delete('m2')
with testing.mktemp(ext) as filename:
cmd.save(filename, 'm1')
cmd.load(filename, 'm2')
self.assertArrayEqual(coords, cmd.get_coordset('m2'), delta=1e-3,
msg='not preserving coordinates: ' + ext)
def test_set_state_order(self):
import numpy
cmd.fragment('ala', 'm1')
for i in (2, 3):
cmd.create('m1', 'm1', i - 1, i);
cmd.rotate('x', 10.0, 'm1', i)
coords1 = cmd.get_coordset('m1', 1)
coords3 = cmd.get_coordset('m1', 3)
self.assertEqual(coords1.shape, (10, 3))
self.assertFalse(numpy.allclose(coords1, coords3))
cmd.set_state_order('m1', (3, 2, 1))
self.assertTrue(numpy.allclose(coords1, cmd.get_coordset('m1', 3)))
self.assertTrue(numpy.allclose(coords3, cmd.get_coordset('m1', 1)))
def test_set_state_order(self):
import numpy
cmd.fragment('ala', 'm1')
for i in (2, 3):
cmd.create('m1', 'm1', i - 1, i)
cmd.rotate('x', 10.0, 'm1', i)
coords1 = cmd.get_coordset('m1', 1)
coords3 = cmd.get_coordset('m1', 3)
self.assertEqual(coords1.shape, (10, 3))
self.assertFalse(numpy.allclose(coords1, coords3))
cmd.set_state_order('m1', (3, 2, 1))
self.assertTrue(numpy.allclose(coords1, cmd.get_coordset('m1', 3)))
self.assertTrue(numpy.allclose(coords3, cmd.get_coordset('m1', 1)))
def save_coords(object_name):
cmd.create("{}".format(object_name), object_name)
coordinate_set = cmd.get_coordset("{}".format(object_name), 1)
print("Got ", object_name, "'s coordinates: ", coordinate_set)
print(type(coordinate_set))
filename_string = '{name}_coordinates.npy'.format(name=object_name)
np.save(filename_string, coordinate_set, allow_pickle=True)
move_to_coords(filename_string)
print("Coordinates saved successfully under ./Coordinates/{}".format(
filename_string))
def testDistanceMode4(self):
# create two 2-state objects
cmd.fragment('gly', 'm1', origin=0)
cmd.create('m1', 'm1', 1, 2)
cmd.create('m2', 'm1', 1, 1)
cmd.create('m2', 'm1', 1, 2)
# shift one state by 5 and the other by 9 angstrom
cs = cmd.get_coordset('m1', state=1, copy=0)
cs += [5., 0., 0.]
cs = cmd.get_coordset('m2', state=2, copy=0)
cs += [9., 0., 0.]
# creates one distance measure per state
d = cmd.distance('d1', '?m1', '?m2', mode=4)
# expecting 7 = (5 + 9) / 2
self.assertAlmostEqual(d, 7.0, delta=1e-4)
# one distance measurement has 2 * 3 coordinates
d1states = cmd.get_session('d1', 1, 1, 0, 0)['names'][0][5][2]
self.assertEqual(len(d1states[0][1]), 6)
self.assertEqual(len(d1states[1][1]), 6)
def testDistanceMode4(self):
# create two 2-state objects
cmd.fragment('gly', 'm1', origin=0)
cmd.create('m1', 'm1', 1, 2)
cmd.create('m2', 'm1', 1, 1)
cmd.create('m2', 'm1', 1, 2)
# shift one state by 5 and the other by 9 angstrom
cs = cmd.get_coordset('m1', state=1, copy=0)
cs += [5., 0., 0.]
cs = cmd.get_coordset('m2', state=2, copy=0)
cs += [9., 0., 0.]
# creates one distance measure per state
d = cmd.distance('d1', '?m1', '?m2', mode=4)
# expecting 7 = (5 + 9) / 2
self.assertAlmostEqual(d, 7.0, delta=1e-4)
# one distance measurement has 2 * 3 coordinates
d1states = cmd.get_session('d1', 1, 1, 0, 0)['names'][0][5][2]
self.assertEqual(len(d1states[0][1]), 6)
self.assertEqual(len(d1states[1][1]), 6)
def test(self):
cmd.load(self.datafile('PYMOL-2985.sdf'), 'm1')
cset_before = cmd.get_coordset('m1')
cmd.clean('m1')
cset_after = cmd.get_coordset('m1')
self.assertArrayNotEqual(cset_before, cset_after)
def test(self):
cmd.load(self.datafile('PYMOL-2985.sdf'), 'm1')
cset_before = cmd.get_coordset('m1')
cmd.clean('m1')
cset_after = cmd.get_coordset('m1')
self.assertArrayNotEqual(cset_before, cset_after)
from pymol import cmd
import os
import sys
#cmd.h_add(selection='(all)')
#preset.ball_and_stick(selection='all', mode=1)
lis = cmd.get_object_list(selection='(all)')
for i in lis:
xyz = cmd.get_coordset(i, 1)
print xyz