def COM(object): com_n = Vector(0,0,0) com_d = 0.0 for atom in object.get_atoms(): position = atom.get_vector() com_n += Vector(position._ar*np.array(atom.mass)) com_d += atom.mass com = com_n.__div__(com_d) return com
def analyse(input_file_name,
refer_file_name,
moved_chain_id,
fixed_chain_id,
r_moved_chain_id,
r_fixed_chain_id,
output_file1,
output_file2,
r_model_number=0):
structure = PDBParser(PERMISSIVE=1).get_structure('to_analyse',
input_file_name)
reference = PDBParser(PERMISSIVE=1).get_structure('reference',
refer_file_name)
r_chain_moved = reference[r_model_number][r_moved_chain_id]
r_chain_fixed = reference[r_model_number][r_fixed_chain_id]
theta = []
phi = []
theta_x = []
theta_y = []
theta_z = []
d = []
coords_x = []
coords_y = []
coords_z = []
matrix_entries = [_[:] for _ in [[]] * 9]
for model_number, model in enumerate(structure):
chain_moved = structure[model_number][moved_chain_id]
chain_fixed = structure[model_number][fixed_chain_id]
com_denominator = 0.0
com_numerator = Vector(0, 0, 0)
for atom in chain_moved.get_atoms():
position = atom.get_vector()
com_numerator += Vector(position._ar * np.array(atom.mass))
com_denominator += atom.mass
moved_centre = com_numerator.__div__(com_denominator)
com_denominator = 0.0
com_numerator = Vector(0, 0, 0)
for atom in chain_fixed.get_atoms():
position = atom.get_vector()
com_numerator += Vector(position._ar * np.array(atom.mass))
com_denominator += atom.mass
fixed_centre = com_numerator.__div__(com_denominator)
com_denominator = 0.0
com_numerator = Vector(0, 0, 0)
reference_set = np.asarray([
coord for coord in
[atom.get_coord() for atom in r_chain_fixed.get_atoms()]
])
coordinate_set = np.asarray([
coord for coord in
[atom.get_coord() for atom in chain_fixed.get_atoms()]
])
sup = SVDSuperimposer()
sup.set(reference_set, coordinate_set)
sup.run()
R, V = sup.get_rotran()
for atom in model.get_atoms():
atom.transform(R, V)
for atom in chain_moved.get_atoms():
com_numerator += Vector(
(atom.get_vector())._ar * np.array(atom.mass))
com_denominator += atom.mass
moved_centre = com_numerator.__div__(com_denominator)
com_denominator = 0.0
com_numerator = Vector(0, 0, 0)
for atom in chain_fixed.get_atoms():
com_numerator += Vector(
(atom.get_vector())._ar * np.array(atom.mass))
com_denominator += atom.mass
fixed_centre = com_numerator.__div__(com_denominator)
if fixed_centre.norm() > 0.5:
print("Fixed chain norm is " + str(fixed_centre.norm()) +
" in model " + str(model_number) +
". Should have been at the origin. Check code...")
com_denominator = 0.0
com_numerator = Vector(0, 0, 0)
x = moved_centre._ar[0]
y = moved_centre._ar[1]
z = moved_centre._ar[2]
coords_x.append(x)
coords_y.append(y)
coords_z.append(z)
d.append((moved_centre - fixed_centre).norm())
if moved_centre.norm() > 1e-6:
theta.append(moved_centre.angle(Vector(0, 0, 1)))
norm = np.sqrt(x * x + y * y)
if norm > 1e-6:
phi.append(np.arctan2(y, x))
else:
theta.append(0.0)
reference_set = np.asarray([
coord for coord in
[atom.get_coord() for atom in r_chain_moved.get_atoms()]
])
coordinate_set = np.asarray([
coord for coord in
[atom.get_coord() for atom in chain_moved.get_atoms()]
])
sup = SVDSuperimposer()
sup.set(reference_set, coordinate_set)
sup.run()
R, V = sup.get_rotran()
theta_x.append(np.arctan2(R[2][1], R[2][2]))
theta_y.append(
np.arctan2(-R[2][0],
np.sqrt(R[2][1] * R[2][1] + R[2][2] * R[2][2])))
theta_z.append(np.arctan2(R[1][0], R[0][0]))
for _ in range(3):
matrix_entries[_].append(R[0][_])
matrix_entries[_ + 3].append(R[1][_])
matrix_entries[_ + 6].append(R[2][_])
f_results1 = open(output_file1, "w+")
for frame in range(0, len(structure)):
f_results1.write(
str(frame) + '\t' + str(d[frame]) + '\t' + str(theta[frame]) +
'\t' + str(phi[frame]) + '\t' + str(theta_x[frame]) + '\t' +
str(theta_y[frame]) + '\t' + str(theta_z[frame]) + '\n')
f_results1.close()
f_results2 = open(output_file2, "w+")
for frame in range(0, len(structure)):
f_results2.write(
str(frame) + '\t' + str(coords_x[frame]) + '\t' +
str(coords_y[frame]) + '\t' + str(coords_z[frame]) + '\t')
for _ in range(3):
f_results2.write(str(matrix_entries[_][frame]) + '\t')
f_results2.write(str(matrix_entries[_ + 3][frame]) + '\t')
f_results2.write(str(matrix_entries[_ + 6][frame]) + '\t')
f_results2.write('\n')
f_results2.close()
def create_random_pdb(separation_distance, move_chain_id, fix_chain_id, input_file_name, output_pdb_name, model_number = 0):
results = {}
structure = PDBParser(PERMISSIVE=1).get_structure('whatever', input_file_name)
chain_moved = structure[model_number][move_chain_id]
chain_fixed = structure[model_number][fix_chain_id]
old_fixed_centre = COM(chain_fixed)
old_moved_centre = COM(chain_moved)
com_denominator=0.0
com_numerator = Vector(0,0,0)
for atom in chain_moved.get_atoms():
position = atom.get_vector()
atom.set_coord(position - old_fixed_centre)
#first step is to move origin to the com of fixed_chain.
#So far the atoms in the moved_chain have been relocated.
for atom in chain_fixed.get_atoms():
position = atom.get_vector()
atom.set_coord(position - old_fixed_centre)
#now fixed_chain has been relocated. All coordinates are now wrt com of fixed_chain
moved_centre = old_moved_centre - old_fixed_centre
fixed_centre = Vector(0,0,0)
d = (old_fixed_centre - old_moved_centre).norm()
results["1_Input_Separation"] = d
results["1_Old_fixed_chain_com"]=old_fixed_centre
results["1_Old_moved_chain_com"]= old_moved_centre
results["0_Intended_Output_Separation"] = separation_distance
R1 = generate_3d()
R2 = generate_3d()
max_distance = 0.0
com_numerator = Vector(0,0,0)
com_denominator=0.0
#Now we scale the separation distance and also rotate the chain_moved
for atom in chain_moved.get_atoms():
position = atom.get_vector()
a = moved_centre.normalized()._ar * np.array(separation_distance)
atom.set_coord((position - moved_centre).left_multiply(R2) + Vector(a))
max_distance = max(max_distance, (atom.get_vector().norm()))
position = atom.get_vector()
com_numerator += Vector(position._ar*np.array(atom.mass))
com_denominator +=atom.mass
final_moved_centre = com_numerator.__div__(com_denominator)
com_denominator=0.0
com_numerator = Vector(0,0,0)
#Now we rotate the chain_fixed
for atom in chain_fixed.get_atoms():
position = atom.get_vector()
atom.set_coord(position.left_multiply(R1))
max_distance = max(max_distance, (atom.get_vector().norm()))
position = atom.get_vector()
com_numerator += Vector(position._ar*np.array(atom.mass))
com_denominator +=atom.mass
final_fixed_centre = com_numerator.__div__(com_denominator)
d = (final_fixed_centre - final_moved_centre).norm()
w = PDBIO()
w.set_structure(structure)
w.save(output_pdb_name)
results["2_Output_Separation"]=d
results["2_fixed_chain_com"]=final_fixed_centre
results["2_moved_chain_com"]=final_moved_centre
results["Max_distance"]=max_distance
return results