def dist_pairs(input_file, model_number, pairs_of_atoms):
"""
:param model_number:
:param pairs_of_atoms: list of eqvivalent atoms
:return: results - a list of tuples[(atom_name, model_number, point1, point2, distance)()]
"""
atom2point = lambda a: point_3d(a.x, a.y, a.z)
short_file_name = os.path.basename(input_file)
results = []
for pair in pairs_of_atoms:
point1, point2 = atom2point(pair[0]), atom2point(pair[1])
# print (point1)
# print (point2)
dist = distance.between_points(point1, point2)
# print (dist)
curr_result = (
short_file_name,
pair[0].atom_name,
model_number,
pair[0].resname,
pair[0].resseq,
point1,
point2,
dist
)
results.append(curr_result)
return results
def sym_axis(input_file, axis, verbose):
"""
\b
calculates the distance of each amino acid from the symmetry axis.
homomer symmetric axis distance
"""
_caller = "atoms_pairs command"
cliutils = cu(click, is_verbose=verbose)
_axis = validate_trimer_options(cliutils, input_file, axis, verbose)
mypdb = pdb.from_file(input_file)
atoms_names = ["CA", "CB"]
results = []
vector3d = point_3d(*_axis)
for atom_name in atoms_names:
siever = atom_names_siever(atom_name)
for model in mypdb:
for chain in model:
msg = "atom:{:<3} model number:{} ,chain_id: {}"
cliutils.verbose(msg.format(atom_name, model.model_number,
chain.chain_id),
caller=_caller)
is_match = lambda atom: siever.is_match(atom, atom_name)
current_results = symetric_axis_distance.dist_from_vector(
input_file=input_file,
model_number=model.model_number,
chain_id=chain.chain_id,
atoms=filter(is_match, chain),
vector3d=vector3d)
results.extend(current_results)
symetric_axis_distance.print_results(results)
def dist_from_vector(input_file, model_number, chain_id, atoms, vector3d):
short_file_name = os.path.basename(input_file)
results = []
for atom in atoms:
point = point_3d(atom.x, atom.y, atom.z)
dist = distance.between_point_and_vector(point, vector3d)
curr_result = (short_file_name, atom.atom_name, model_number, chain_id,
atom.resname, atom.resseq, point, dist)
results.append(curr_result)
return results
def test_distance_between_point_and_vector(self):
point_a = point_3d(*self.coordinates[1])
vector = point_3d(*self.coordinates[3])
distance_a_b = distance.between_point_and_vector(point_a, vector)
self.assertTrue(distance_a_b - 1 < 0.00000000001)
def test_distance_between_points(self):
point_a = point_3d(*self.coordinates[0])
point_b = point_3d(*self.coordinates[1])
distance_a_b = distance.between_points(point_a, point_b)
self.assertEqual(distance_a_b, math.sqrt(3))
def test_vector(self):
vector = point_3d(*self.coordinates[3])
self.assertEqual(vector.is_vector(), True)
vector = point_3d(*self.coordinates[4])
self.assertEqual(vector.is_vector(), True)
def test_point(self):
point = point_3d(*self.coordinates[0])
self.assertEqual(point.y, 0)
self.assertEqual(str(point), str((0.0, 0.0, 0.0)))
self.assertEqual(point.is_vector(), False)