def __init__(self, mol, origin, confIndex):
Kinematics.__init__(self, mol.allAtoms.coords, mol.torTree, tolist=1)
# this stoc object will leave always deposite it's coords
# in the given confIndex slot.
self.confIndex = confIndex
mol.allAtoms.setConformation(confIndex)
def __prepareNode(node, allAtoms, o):
"""Supply each node with atomSet, coords, and atomRange,
Pre-compute and save the torsionUnitVector,
Transform the coords to their local space by subtracting
the origin
"""
atomSet = []
coords = []
for i in node.atomList:
atom = allAtoms[i]
atomSet.append(atom)
# start with the original coordinates
c = atom.coords
# subract the origin
coords.append((c[0]-o[0], c[1]-o[1], c[2]-o[2], 1.0))
node.atomSet = atomSet
node.coords = coords
node.atomRange = range(len(atomSet))
if node.bond[0] != None: # skip the root node
node.a = allAtoms[node.bond[0]]
node.b = allAtoms[node.bond[1]]
# add atomSets to each node
root = mol.torTree.rootNode
root.pre_traverse(__prepareNode, root, mol.allAtoms, origin)
def __init__(self, mol, origin, confIndex):
Kinematics.__init__(self, mol.allAtoms.coords, mol.torTree, tolist=1)
# this stoc object will leave always deposite it's coords
# in the given confIndex slot.
self.confIndex = confIndex
mol.allAtoms.setConformation(confIndex)
def __prepareNode(node, allAtoms, o):
"""Supply each node with atomSet, coords, and atomRange,
Pre-compute and save the torsionUnitVector,
Transform the coords to their local space by subtracting
the origin
"""
atomSet = []
coords = []
for i in node.atomList:
atom = allAtoms[i]
atomSet.append(atom)
# start with the original coordinates
c = atom.coords
# subract the origin
coords.append((c[0] - o[0], c[1] - o[1], c[2] - o[2], 1.0))
node.atomSet = atomSet
node.coords = coords
node.atomRange = list(range(len(atomSet)))
if node.bond[0] != None: # skip the root node
node.a = allAtoms[node.bond[0]]
node.b = allAtoms[node.bond[1]]
# add atomSets to each node
root = mol.torTree.rootNode
root.pre_traverse(__prepareNode, root, mol.allAtoms, origin)
def test_applyAngList022(self):
"""applyAngList -- return correct coords ( 0,-90, 0)"""
ko = Kinematics(self.known_points, self.torTree, tolist=0)
result = ko.applyAngList([0., -90., 0.], self.idmtx)[:, :3]
self.known_points[0] = [1., 1., 1.]
self.known_points[2] = [1., 0., 0.]
self.assertArrayEqual(self.known_points, result)
def test_applyAngList022(self):
"""applyAngList -- return correct coords ( 0,-90, 0)"""
ko = Kinematics(self.known_points, self.torTree, tolist=0)
result = ko.applyAngList([0.,-90.,0.], self.idmtx)[:,:3]
self.known_points[0] = [1., 1., 1.]
self.known_points[2] = [1., 0., 0.]
self.assertArrayEqual(self.known_points, result)
def test_applyTorsion02(self):
"""applyTorsion -- return correct coords torsion=1, angle=90."""
ko = Kinematics(self.known_points, self.torTree, tolist=0)
result = ko.applyTorsion(ko.torsions[1], 90.)[:, :3]
self.known_points[0] = [1., -1., 1.]
self.known_points[2] = [1., 0., 2.]
self.assertArrayEqual(self.known_points, result)
def test_applyTorsion02(self):
"""applyTorsion -- return correct coords torsion=1, angle=90."""
ko = Kinematics(self.known_points, self.torTree, tolist=0)
result = ko.applyTorsion(ko.torsions[1], 90.)[:,:3]
self.known_points[0] = [1., -1., 1.]
self.known_points[2] = [1., 0., 2.]
self.assertArrayEqual(self.known_points, result)
def test_applyAngList021(self):
"""applyAngList -- return correct coords (90, 0, 0)"""
ko = Kinematics(self.known_points, self.torTree, tolist=0)
result = ko.applyAngList([90.0, 0.0, 0.0], self.idmtx)[:, :3]
self.known_points[0] = [0.0, 1.0, 2.0]
self.known_points[1] = [0.0, 1.0, 1.0]
self.known_points[2] = [-1.0, 1.0, 1.0]
self.assertArrayEqual(self.known_points, result)
def test_applyTorsion02(self):
"""applyTorsion -- apply torsions in any order"""
ko1 = Kinematics(self.known_points, self.torTree, tolist=0)
ko1.applyTorsion(ko1.torsions[0], 90.)
result1 = ko1.applyTorsion(ko1.torsions[1], -90.)
ko2 = Kinematics(self.known_points, self.torTree, tolist=0)
ko2.applyTorsion(ko2.torsions[1], -90.)
result2 = ko2.applyTorsion(ko2.torsions[0], 90.)
self.assertArrayEqual(result1, result2)
def test_applyTorsion02(self):
"""applyTorsion -- apply torsions in any order"""
ko1 = Kinematics(self.known_points, self.torTree, tolist=0)
ko1.applyTorsion(ko1.torsions[0], 90.)
result1 = ko1.applyTorsion(ko1.torsions[1], -90.)
ko2 = Kinematics(self.known_points, self.torTree, tolist=0)
ko2.applyTorsion(ko2.torsions[1], -90.)
result2 = ko2.applyTorsion(ko2.torsions[0], 90.)
self.assertArrayEqual(result1, result2)
def test_applyAngList04(self):
"""applyAngList -- one-at-time equals all-at-once"""
ko1 = Kinematics(self.known_points, self.torTree, tolist=0)
ko2 = Kinematics(self.known_points, self.torTree, tolist=0)
result1 = ko1.applyAngList([90., -90., 0.], self.idmtx)[:, :3]
# do the rotations separately
ko2.applyAngList([90., 0., 0.])
result2 = ko2.applyAngList([0., -90., 0.], self.idmtx)[:, :3]
self.assertArrayEqual(result1, result2)
def test_applyAngList04(self):
"""applyAngList -- one-at-time equals all-at-once"""
ko1 = Kinematics(self.known_points, self.torTree, tolist=0)
ko2 = Kinematics(self.known_points, self.torTree, tolist=0)
result1 = ko1.applyAngList([90.,-90.,0.], self.idmtx)[:,:3]
# do the rotations separately
ko2.applyAngList([90.,0.,0.])
result2 = ko2.applyAngList([0.,-90.,0.], self.idmtx)[:,:3]
self.assertArrayEqual(result1, result2)
def test_applyAngList01(self):
"""applyAngList -- return correct coords (360., 360., 360.)"""
ko = Kinematics(self.known_points, self.torTree, tolist=0)
result = ko.applyAngList([360.,360.,360.], self.idmtx)[:,:3]
self.assertArrayEqual(self.known_points, result)
def test_applyTorsion01(self):
"""applyTorsion -- return correct coords torsion=0, angle=0."""
ko = Kinematics(self.known_points, self.torTree, tolist=1)
self.assertEqual(self.known_points,
ko.applyTorsion(ko.torsions[0], 0.))
def test_applyAngList05(self):
"""applyAngList -- ValueError if len(angList) != len(torsions)"""
ko = Kinematics(self.known_points, self.torTree, tolist=1)
self.assertRaises(ValueError, ko.applyAngList, ([0, 0], self.idmtx))
def test_applyAngList01(self):
"""applyAngList -- return correct coords (360., 360., 360.)"""
ko = Kinematics(self.known_points, self.torTree, tolist=0)
result = ko.applyAngList([360., 360., 360.], self.idmtx)[:, :3]
self.assertArrayEqual(self.known_points, result)
def test_applyAngList00(self):
"""applyAngList -- return correct coords (0., 0., 0.)"""
ko = Kinematics(self.known_points, self.torTree, tolist=1)
self.assertEqual(self.known_points,
ko.applyAngList([0, 0, 0], self.idmtx))
def test_applyAngList00(self):
"""applyAngList -- return correct coords (0., 0., 0.)"""
ko = Kinematics(self.known_points, self.torTree, tolist=1)
self.assertEqual(self.known_points, ko.applyAngList([0,0,0], self.idmtx))
def test_applyTorsion01(self):
"""applyTorsion -- return correct coords torsion=0, angle=0."""
ko = Kinematics(self.known_points, self.torTree, tolist=1)
self.assertEqual(self.known_points, ko.applyTorsion( ko.torsions[0], 0.) )
