def testAlignConcat(self):
command = self.command + ' --align ca --pdb {1:s} {0:s} {0:s}'.format(
self.dcdpath, self.pdbpath)
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
select = self.ag.ca
coords = self.dcd[:]
concat = parseDCD(self.output)
assert_equal(concat.numAtoms(), coords.numAtoms())
coords.setCoords(self.ag.getCoords())
coords.setAtoms(select)
coords.superpose()
coords.setAtoms(None)
coords = coords._getCoordsets()
concat = concat._getCoordsets()
assert_equal(coords, concat[:3])
assert_equal(coords, concat[3:])
def testAlignConcat(self):
command = self.command + ' --align ca --pdb {1:s} {0:s} {0:s}'.format(
self.dcdpath, self.pdbpath)
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
select = self.ag.ca
coords = self.dcd[:]
concat = parseDCD(self.output)
assert_equal(concat.numAtoms(), coords.numAtoms())
coords.setCoords(self.ag.getCoords())
coords.setAtoms(select)
coords.superpose()
coords.setAtoms(None)
coords = coords._getCoordsets()
concat = concat._getCoordsets()
assert_equal(coords, concat[:3])
assert_equal(coords, concat[3:])
def testWrite(self):
dcd = DCDFile(self.dcd, 'w')
dcd.write(ENSEMBLE.getCoordsets())
dcd.close()
e = parseDCD(self.dcd)
assert_allclose(e._getCoordsets(), ENSEMBLE._getCoordsets(),
rtol=RTOL, atol=ATOL,
err_msg='failed to parse DCD file correctly')
def testWrite(self):
dcd = DCDFile(self.dcd, 'w')
dcd.write(ENSEMBLE.getCoordsets())
dcd.close()
e = parseDCD(self.dcd)
assert_allclose(e._getCoordsets(), ENSEMBLE._getCoordsets(),
rtol=RTOL, atol=ATOL,
err_msg='failed to parse DCD file correctly')
def testSimpleConcat(self):
command = self.command + ' {0:s} {0:s} {0:s}'.format(self.dcdpath)
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
coords = self.dcd[:]._getCoordsets()
concat = parseDCD(self.output)._getCoordsets()
assert_equal(coords, concat[:3])
assert_equal(coords, concat[3:6])
assert_equal(coords, concat[6:])
def testSimpleConcat(self):
command = self.command + ' {0:s} {0:s} {0:s}'.format(self.dcdpath)
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
coords = self.dcd[:]._getCoordsets()
concat = parseDCD(self.output)._getCoordsets()
assert_equal(coords, concat[:3])
assert_equal(coords, concat[3:6])
assert_equal(coords, concat[6:])
def testWriteModeAppend(self):
dcd = DCDFile(writeDCD(self.dcd, ENSEMBLE), 'a')
dcd.write(ENSEMBLE.getCoordsets())
dcd.close()
e = parseDCD(self.dcd)
n_csets = len(ENSEMBLE)
coordsets = e._getCoordsets()
assert_equal(coordsets, coordsets,
'failed to parse DCD file correctly')
assert_allclose(coordsets[:n_csets], ENSEMBLE._getCoordsets(),
rtol=RTOL, atol=ATOL,
err_msg='failed to parse DCD file correctly')
def testWriteModeAppend(self):
dcd = DCDFile(writeDCD(self.dcd, ENSEMBLE), 'a')
dcd.write(ENSEMBLE.getCoordsets())
dcd.close()
e = parseDCD(self.dcd)
n_csets = len(ENSEMBLE)
coordsets = e._getCoordsets()
assert_equal(coordsets, coordsets,
'failed to parse DCD file correctly')
assert_allclose(coordsets[:n_csets], ENSEMBLE._getCoordsets(),
rtol=RTOL, atol=ATOL,
err_msg='failed to parse DCD file correctly')
def testSelectConcat(self):
command = self.command + ' -s ca --pdb {1:s} {0:s} {0:s}'.format(
self.dcdpath, self.pdbpath)
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
select = self.ag.ca
assert_equal(select.numAtoms(), 10)
coords = self.dcd[:]
coords.setAtoms(select)
coords = coords._getCoordsets()
concat = parseDCD(self.output)
assert_equal(concat.numAtoms(), select.numAtoms())
concat = concat._getCoordsets()
assert_equal(select.numAtoms(), coords.shape[1])
assert_equal(select.numAtoms(), concat.shape[1])
assert_equal(coords, concat[:3])
assert_equal(coords, concat[3:])
def testSelectConcat(self):
command = self.command + ' -s ca --pdb {1:s} {0:s} {0:s}'.format(
self.dcdpath, self.pdbpath)
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
select = self.ag.ca
assert_equal(select.numAtoms(), 10)
coords = self.dcd[:]
coords.setAtoms(select)
coords = coords._getCoordsets()
concat = parseDCD(self.output)
assert_equal(concat.numAtoms(), select.numAtoms())
concat = concat._getCoordsets()
assert_equal(select.numAtoms(), coords.shape[1])
assert_equal(select.numAtoms(), concat.shape[1])
assert_equal(coords, concat[:3])
assert_equal(coords, concat[3:])
def testParseDCD(self):
e = parseDCD(writeDCD(self.dcd, ALLATOMS))
assert_equal(e._getCoordsets(),
DCD._getCoordsets(),
err_msg='failed to parse DCD file correctly')
def testParseDCD(self):
e = parseDCD(writeDCD(self.dcd, ALLATOMS))
assert_equal(e._getCoordsets(), DCD._getCoordsets(),
err_msg='failed to parse DCD file correctly')
