def test_applyQuaternion04(self):
"""applyQuaternion04 -- random pts 360 about random-axis"""
state = StateToCoords(self.random_points, tolist=1)
q = RandomArray.uniform(self.min, self.max, (4, ))
q[3] = 360.0
result = state.applyQuaternion(q)
self.assertArrayEqual(self.random_points, result)
def test_applyQuaternion05(self):
"""applyQuaternion05 -- random pts 3*120 about x-axis"""
state = StateToCoords(self.random_points, tolist=1)
q = (0.0, 0.0, 1.0, 120.0)
for n in range(3):
result = state.applyQuaternion(q)
self.assertArrayEqual(self.random_points, result, 0)
def test_applyTranslation03(self):
"""applyTranslation03 -- random pts x (random there and back)"""
state = StateToCoords(self.random_points, tolist=1)
trn = RandomArray.uniform(self.min, self.max, (3,))
state.applyTranslation(trn)
trn = -1*trn
self.assertArrayEqual(self.random_points, state.applyTranslation(trn))
def test_applyTranslation03(self):
"""applyTranslation03 -- random pts x (random there and back)"""
state = StateToCoords(self.random_points, tolist=1)
trn = RandomArray.uniform(self.min, self.max, (3, ))
state.applyTranslation(trn)
trn = -1 * trn
self.assertArrayEqual(self.random_points, state.applyTranslation(trn))
def test_applyQuaternion05(self):
"""applyQuaternion05 -- random pts 3*120 about x-axis"""
state = StateToCoords(self.random_points, tolist=1)
q = (0.0, 0.0, 1.0, 120.0)
for n in xrange(3):
result = state.applyQuaternion(q)
self.assertArrayEqual(self.random_points, result,0)
def test_applyQuaternion04(self):
"""applyQuaternion04 -- random pts 360 about random-axis"""
state = StateToCoords(self.random_points, tolist=1)
q = RandomArray.uniform(self.min, self.max, (4,))
q[3] = 360.0
result = state.applyQuaternion(q)
self.assertArrayEqual(self.random_points, result)
def test_applyQuaternion03(self):
"""applyQuaternion02 -- known pts 90 about z-axis"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyQuaternion((0.0, 0.0, 1.0, 90.0))
expected = [[0., 1., 2.], [0., 1., 1.], [-1., 1., 1.], [0., 0., 1.],
[0., 0., 0.], [-1., 0., 0.], [-1., 0., -1.],
[-1., 1., -1.], [-2., 1., -1.], [-1., 1., -2.]]
self.assertArrayEqual(expected, result)
def test_applyQuaternion06(self):
"""applyQuaternion06 -- random pts 2*180 about random-axis"""
state = StateToCoords(self.random_points, tolist=1)
q = RandomArray.uniform(self.min, self.max, (4, ))
q[3] = 180.0
for n in range(2):
result = state.applyQuaternion(q)
self.assertArrayEqual(self.random_points, result)
def test_applyQuaternion06(self):
"""applyQuaternion06 -- random pts 2*180 about random-axis"""
state = StateToCoords(self.random_points, tolist=1)
q = RandomArray.uniform(self.min, self.max, (4,))
q[3] = 180.0
for n in xrange(2):
result = state.applyQuaternion(q)
self.assertArrayEqual(self.random_points, result)
def test_applyQuaternion021(self):
"""applyQuaternion021 -- known pts 90 about x-axis; origin(1., 0., 1.)"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyQuaternion((1.0, 0.0, 0.0, 90.0), (1., 0., 1.))
expected = [[1., -1., 1.], [1., 0., 1.], [1., 0., 2.], [0., 0., 1.],
[0., 1., 1.], [0., 1., 2.], [0., 2., 2.], [1., 2., 2.],
[1., 2., 3.], [1., 3., 2.]]
self.assertArrayEqual(expected, result)
def test_applyOrientation01(self):
"""applyOrientation01 -- Q, T, O combined"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyOrientation(quat=(1.0, 0.0, 0.0, 90.0),
trans=(10., 10., 10.),
origin=(1., 0., 1.))
expected = [[11., 9., 11.], [11., 10., 11.], [11., 10., 12.],
[10., 10., 11.], [10., 11., 11.], [10., 11., 12.],
[10., 12., 12.], [11., 12., 12.], [11., 12., 13.],
[11., 13., 12.]]
self.assertArrayEqual(expected, result)
def test_applyState(self):
"""applyState -- computed values untested"""
value = TestState(q=(1.0, 0.0, 0.0, 90.0),
t=(10., 10., 10.),
o=(1., 0., 1.),
tList=[0., 0., 270.])
state = StateToCoords(self.known_points, self.torTree, tolist=1)
result = state.applyState(value)
expected = [[11., 9., 11.], [11., 10., 11.], [11., 10., 12.],
[10., 10., 11.], [10., 11., 11.], [10., 11., 12.],
[10., 12., 12.], [11., 12., 12.], [11., 13., 12.],
[11., 12., 11.]]
self.assertArrayEqual(expected, result)
def test_applyQuaternion03(self):
"""applyQuaternion02 -- known pts 90 about z-axis"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyQuaternion((0.0, 0.0, 1.0, 90.0))
expected = [[ 0., 1., 2.],
[ 0., 1., 1.],
[-1., 1., 1.],
[ 0., 0., 1.],
[ 0., 0., 0.],
[-1., 0., 0.],
[-1., 0., -1.],
[-1., 1., -1.],
[-2., 1., -1.],
[-1., 1., -2.]]
self.assertArrayEqual(expected, result)
def test_applyQuaternion021(self):
"""applyQuaternion021 -- known pts 90 about x-axis; origin(1., 0., 1.)"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyQuaternion((1.0, 0.0, 0.0, 90.0), (1., 0., 1.))
expected = [[1., -1., 1.],
[1., 0., 1.],
[1., 0., 2.],
[0., 0., 1.],
[0., 1., 1.],
[0., 1., 2.],
[0., 2., 2.],
[1., 2., 2.],
[1., 2., 3.],
[1., 3., 2.]]
self.assertArrayEqual(expected, result)
def test_applyOrientation01(self):
"""applyOrientation01 -- Q, T, O combined"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyOrientation( quat=(1.0, 0.0, 0.0, 90.0),
trans= (10., 10., 10.),
origin=(1., 0., 1.))
expected = [[11., 9., 11.],
[11., 10., 11.],
[11., 10., 12.],
[10., 10., 11.],
[10., 11., 11.],
[10., 11., 12.],
[10., 12., 12.],
[11., 12., 12.],
[11., 12., 13.],
[11., 13., 12.]]
self.assertArrayEqual(expected, result)
def test_applyState(self):
"""applyState -- computed values untested"""
value = TestState(q=(1.0, 0.0, 0.0, 90.0),
t=(10., 10., 10.),
o=(1., 0., 1.),
tList=[0., 0., 270.])
state = StateToCoords(self.known_points, self.torTree, tolist=1)
result = state.applyState(value)
expected = [[11., 9., 11.],
[11., 10., 11.],
[11., 10., 12.],
[10., 10., 11.],
[10., 11., 11.],
[10., 11., 12.],
[10., 12., 12.],
[11., 12., 12.],
[11., 13., 12.],
[11., 12., 11.]]
self.assertArrayEqual(expected, result)
def __init__(self, mol, origin):
"""
"""
self.mol = mol
self.origin = origin
self.conformations = []
#conformations are 1-based to fit with autodock 1-based rank
self.current_conf = None
mol.allAtoms.addConformation(mol.allAtoms.coords)
self.confIndex = len(mol.allAtoms[0]._coords) - 1
if hasattr(mol, 'torTree'):
mol.stoc = self.stoc = StateToCoords(mol, origin, self.confIndex)
def test_applyQuaternion01(self):
"""applyQuaternion01 -- known pts 360 about x-axis"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyQuaternion((1.0, 0.0, 0.0, 360.0))
self.assertArrayEqual(self.known_points, result)
def test_applyOrientation00(self):
"""applyOrientation00 -- random pts with defaults"""
state = StateToCoords(self.random_points, tolist=1)
self.assertEqual(self.random_points, state.applyOrientation())
def test_applyQuaternion01(self):
"""applyQuaternion01 -- known pts 360 about x-axis"""
state = StateToCoords(self.known_points, tolist=1)
result = state.applyQuaternion((1.0, 0.0, 0.0, 360.0))
self.assertArrayEqual(self.known_points, result)
def test_applyTranslation00(self):
"""applyTranslation00 -- random pts x (0., 0., 0.)"""
state = StateToCoords(self.random_points, tolist=1)
zzz = Numeric.zeros((3,), 'f')
self.assertEqual(self.random_points, state.applyTranslation(zzz))
def test_applyTranslation02(self):
"""applyTranslation02 -- known pts x (1., 1., 1.)"""
state = StateToCoords(self.known_points, tolist=1)
ones = numpy.ones((3, ), 'f')
expected = (numpy.array(self.known_points) + ones).tolist()
self.assertEqual(expected, state.applyTranslation(ones))
def test_applyTranslation01(self):
"""applyTranslation01 -- random pts x (random translation)"""
state = StateToCoords(self.random_points, tolist=0)
trn = RandomArray.uniform(self.min, self.max, (3, ))
expected = (numpy.array(self.random_points) + trn)
self.assertArrayEqual(expected, state.applyTranslation(trn))
def test_applyTranslation00(self):
"""applyTranslation00 -- random pts x (0., 0., 0.)"""
state = StateToCoords(self.random_points, tolist=1)
zzz = numpy.zeros((3, ), 'f')
self.assertEqual(self.random_points, state.applyTranslation(zzz))
def test_applyTranslation01(self):
"""applyTranslation01 -- random pts x (random translation)"""
state = StateToCoords(self.random_points, tolist=0)
trn = RandomArray.uniform(self.min, self.max, (3,))
expected = (Numeric.array(self.random_points) + trn)
self.assertArrayEqual(expected, state.applyTranslation(trn))
def test_applyTranslation02(self):
"""applyTranslation02 -- known pts x (1., 1., 1.)"""
state = StateToCoords(self.known_points, tolist=1)
ones = Numeric.ones((3,), 'f')
expected = (Numeric.array(self.known_points) + ones).tolist()
self.assertEqual(expected, state.applyTranslation(ones))
def test_applyOrientation00(self):
"""applyOrientation00 -- random pts with defaults"""
state = StateToCoords(self.random_points, tolist=1)
self.assertEqual(self.random_points, state.applyOrientation())
sys.exit()
m = Read(filename)[0]
if verbose: print('read ', filename)
#validate specified ligand file
assert hasattr(m, 'torTree'), "specified ligand does not have a torsion tree"
ndihe = m.parser.keys.count('BRANCH')
if verbose: print(m.name, ' has ', ndihe, ' torsions')
#1. prepare molecule
m.buildBondsByDistance()
orig_coords = m.allAtoms.coords[:]
m.allAtoms.addConformation(m.allAtoms.coords)
coord_index = 1
origin = m.getCenter()
m.stoc = StateToCoords(m, origin, 1)
#build reference dictionary of original bonds
orig = len(m.allAtoms.bonds[0])
orig_d = {}
for a in m.allAtoms: orig_d[a]=set(a.bonds.getAtoms())
#try a new random state up to ntries times
# convert trans to space centered on m
for new_try in range(ntries):
#reset coords in working slot to original coords for new try
m.allAtoms.updateCoords(orig_coords, ind=coord_index)
TRANS = []
for ind in range(3):
#do not subtract origin here, i don't understand why not
#TRANS.append((random.uniform(-1,1)*tscale)-origin[i])
TRANS.append(random.uniform(-1,1)*tscale)
lig.buildBondsByDistance()
# add extra slot to ._coords for changing coordinates
lig.allAtoms.addConformation(lig.allAtoms.coords)
#?is this necessary
lig.allAtoms.setConformation(1)
ntors = lig.ndihe
length_of_state = 7 + lig.ndihe
# @@ handle to the input ligLines
ligLines = lig.parser.allLines
#setup StateToCoords object
origin = lig.getCenter()
if use_zero_origin or interim_state:
origin = [0., 0., 0.]
#note: index of _coords to use is always 1
lig.stoc = StateToCoords(lig, origin, 1)
outptr = sys.stdout
if outputfile:
outptr = open(outputfile, 'w')
#if SINGLESTATE:
# eg:
#"State: 29.303 14.415 23.603 0.5609 0.4518 0.2662 -0.6406 -20.89 -0.65 81.86 -17.36 28.83 -10.80 -23.98 114.21"
#states = state.split()
#['State:', '29.303', '14.415', '23.603', '0.5609', '0.4518', '0.2662', '-0.6406', '-20.89', '-0.65', '81.86', '-17.36', '28.83', '-10.80', '-23.98', '114.21']
if statefile:
sptr = open(statefile)
states = sptr.readlines()
sptr.close()
if not len(states):
