class DockingResult(object):
"""Represents a LightDock docking result line"""
def __init__(self,
id_swarm=0,
id_glowworm=0,
receptor_id=0,
ligand_id=0,
luciferin=0.0,
num_neighbors=0,
vision_range=0.0,
pose=None,
rmsd=-1.0,
pdb_file='',
contacts=0,
scoring=0.0):
self.id_swarm = id_swarm
self.id_glowworm = id_glowworm
self.receptor_id = receptor_id
self.ligand_id = ligand_id
self.luciferin = luciferin
self.num_neighbors = num_neighbors
self.vision_range = vision_range
self.pose = pose
self.translation = np.array(pose[:3])
self.rotation = Quaternion(pose[3], pose[4], pose[5],
pose[6]).normalize()
self.coord = DockingResult.pose_repr(pose)
self.rmsd = rmsd
self.pdb_file = pdb_file
self.contacts = contacts
self.scoring = scoring
def __str__(self):
return "%5d %6d %60s %6d %6d %11.5f %5d %7.3f %8.3f %16s %6d %8.3f" % (
self.id_swarm, self.id_glowworm, self.coord, self.receptor_id,
self.ligand_id, self.luciferin, self.num_neighbors,
self.vision_range, self.rmsd, self.pdb_file, self.contacts,
self.scoring)
def distance_trans(self, other):
return np.linalg.norm(self.translation - other.translation)
def distance_rot(self, other):
return self.rotation.distance(other.rotation)
@staticmethod
def pose_repr(coord):
fields = [("%5.3f" % c) for c in coord]
return "(%s)" % (', '.join(fields))
class DockingResult(object):
"""Represents a LightDock docking result line"""
def __init__(self, id_cluster=0, id_glowworm=0, receptor_id=0, ligand_id=0, luciferin=0.0,
num_neighbors=0, vision_range=0.0, pose=None, rmsd=-1.0,
pdb_file='', contacts=0, scoring=0.0):
self.id_cluster = id_cluster
self.id_glowworm = id_glowworm
self.receptor_id = receptor_id
self.ligand_id = ligand_id
self.luciferin = luciferin
self.num_neighbors = num_neighbors
self.vision_range = vision_range
self.pose = pose
self.translation = np.array(pose[:3])
self.rotation = Quaternion(pose[3], pose[4], pose[5], pose[6]).normalize()
self.coord = DockingResult.pose_repr(pose)
self.rmsd = rmsd
self.pdb_file = pdb_file
self.contacts = contacts
self.scoring = scoring
def __str__(self):
return "%5d %6d %60s %6d %6d %11.5f %5d %7.3f %8.3f %16s %6d %8.3f" % (self.id_cluster,
self.id_glowworm,
self.coord,
self.receptor_id,
self.ligand_id,
self.luciferin,
self.num_neighbors,
self.vision_range,
self.rmsd,
self.pdb_file,
self.contacts,
self.scoring)
def distance_trans(self, other):
return np.linalg.norm(self.translation - other.translation)
def distance_rot(self, other):
return self.rotation.distance(other.rotation)
@staticmethod
def pose_repr(coord):
fields = [("%5.3f" % c) for c in coord]
return "(%s)" % (', '.join(fields))
def test_distance_composite_rotation(self):
q1 = Quaternion(1.0, 0, 0, 0)
q2 = Quaternion(0.5, 0.5, 0.5, 0.5)
assert_almost_equals(0.75, q1.distance(q2))
def test_distance_is_half(self):
q1 = Quaternion(0.707106781, 0.0, 0.707106781, 0.0)
q2 = Quaternion(0, 0, 1.0, 0)
assert_almost_equals(0.5, q1.distance(q2))
def test_distance_is_one(self):
q1 = Quaternion(0.707106781, 0.0, 0.707106781, 0.0)
q2 = Quaternion(0.707106781, 0.0, -0.707106781, 0.0)
assert_almost_equals(1.0, q1.distance(q2))
def test_distance_is_zero(self):
q = Quaternion(0.707106781, 0.0, 0.707106781, 0.0)
assert_almost_equals(0.0, q.distance(q))
def test_distance_composite_rotation(self):
q1 = Quaternion(1.0, 0, 0, 0)
q2 = Quaternion(0.5, 0.5, 0.5, 0.5)
assert_almost_equals(0.75, q1.distance(q2))
def test_distance_is_half(self):
q1 = Quaternion(0.707106781, 0.0, 0.707106781, 0.0)
q2 = Quaternion(0, 0, 1.0, 0)
assert_almost_equals(0.5, q1.distance(q2))
def test_distance_is_one(self):
q1 = Quaternion(0.707106781, 0.0, 0.707106781, 0.0)
q2 = Quaternion(0.707106781, 0.0, -0.707106781, 0.0)
assert_almost_equals(1.0, q1.distance(q2))
def test_distance_is_zero(self):
q = Quaternion(0.707106781, 0.0, 0.707106781, 0.0)
assert_almost_equals(0.0, q.distance(q))
