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 testGNMCommand(self):
pdb = pathDatafile('multi_model_truncated')
command = self.command + pdb
prefix = splitext(split(pdb)[1])[0]
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
self.assertTrue(isfile(fn), msg=fn + ' not found')
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 testGNMCommand(self):
pdb = pathDatafile('multi_model_truncated')
command = self.command + pdb
prefix = splitext(split(pdb)[1])[0]
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
self.assertTrue(isfile(fn), msg=fn+' not found')
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 testPCACommandDCD(self):
dcd = pathDatafile('dcd')
command = self.command + dcd
prefix = splitext(split(dcd)[1])[0]
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
self.assertTrue(isfile(fn), msg=fn + ' not found')
def testPCACommandDCD(self):
dcd = pathDatafile('dcd')
command = self.command + dcd
prefix = splitext(split(dcd)[1])[0]
namespace = prody_parser.parse_args(shlex.split(command))
namespace.func(namespace)
for suffix in self.suffixes:
fn = join(TEMPDIR, prefix + suffix)
self.assertTrue(isfile(fn), msg=fn+' not found')
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 testSelectException2(self):
command = self.command + ' -s None {0:s} {0:s}'.format(self.dcdpath)
namespace = prody_parser.parse_args(shlex.split(command))
self.assertRaises(ValueError, namespace.func, namespace)
def testIOException(self):
command = self.command + ' {0:s} {0:s}'.format('deneme.dcd')
namespace = prody_parser.parse_args(shlex.split(command))
self.assertRaises(IOError, namespace.func, namespace)
def testAlignException(self):
command = self.command + ' --align ca {0:s} {0:s}'.format(self.dcdpath)
namespace = prody_parser.parse_args(shlex.split(command))
self.assertRaises(ValueError, namespace.func, namespace)
def testSelectException2(self):
command = self.command + ' -s None {0:s} {0:s}'.format(self.dcdpath)
namespace = prody_parser.parse_args(shlex.split(command))
self.assertRaises(ValueError, namespace.func, namespace)
def testIOException(self):
command = self.command + ' {0:s} {0:s}'.format('deneme.dcd')
namespace = prody_parser.parse_args(shlex.split(command))
self.assertRaises(IOError, namespace.func, namespace)
def testAlignException(self):
command = self.command + ' --align ca {0:s} {0:s}'.format(
self.dcdpath)
namespace = prody_parser.parse_args(shlex.split(command))
self.assertRaises(ValueError, namespace.func, namespace)
