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 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 setUp(self):
self.output = join(TEMPDIR, 'test_prody_catdcd.dcd')
self.dcdpath = pathDatafile('dcd')
self.pdbpath = pathDatafile('multi_model_truncated')
self.dcd = DCDFile(self.dcdpath)
self.ag = parsePDB(self.pdbpath, model=1)
self.command = 'catdcd -o ' + self.output
self.tearDown()
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 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')