def get_rmsd_to(self, other_rnamodel, output='', dont_move=False):
"""Calc rmsd P-atom based rmsd to other rna model"""
sup = Bio.PDB.Superimposer()
if dont_move:
# fix http://biopython.org/DIST/docs/api/Bio.PDB.Vector%27.Vector-class.html
coords = array([a.get_vector().get_array() for a in self.atoms])
other_coords = array([a.get_vector().get_array() for a in other_rnamodel.atoms])
s = SVDSuperimposer()
s.set(coords,other_coords)
return s.get_init_rms()
try:
sup.set_atoms(self.atoms, other_rnamodel.atoms)
except:
print(self.fn, len(self.atoms), other_rnamodel.fn, len(other_rnamodel.atoms))
for a,b in zip(self.atoms, other_rnamodel.atoms):
print(a.parent, b.parent)#a.get_full_id(), b.get_full_id())
rms = round(sup.rms, 3)
if output:
io = Bio.PDB.PDBIO()
sup.apply(self.struc.get_atoms())
io.set_structure( self.struc )
io.save("aligned.pdb")
io = Bio.PDB.PDBIO()
sup.apply(other_rnamodel.struc.get_atoms())
io.set_structure( other_rnamodel.struc )
io.save("aligned2.pdb")
return rms
def create_DM(pdb_atoms_list, alignement_type):
"""
This function is used to clusterize all structures.
"""
svd = SVDSuperimposer()
size = len(pdb_atoms_list)
FullDM = DistanceMatrix(size)
pbar = pg.ProgressBar(widgets=WIDGETS,
maxval=(size * (size - 1) / 2)).start()
counter = 0
for i, frame1 in enumerate(pdb_atoms_list):
for j, frame2 in enumerate(pdb_atoms_list[i + 1:]):
svd.set(frame1, frame2)
svd.run()
rms = svd.get_rms() #RMS with local alignement
rms_raw = svd.get_init_rms(
) #RMS with the GLOBAL alignement made before
if alignement_type == "l":
FullDM.set(i, i + j + 1, rms)
else:
FullDM.set(i, i + j + 1, rms_raw)
pbar.update(counter)
counter += 1
pbar.finish()
return FullDM
def get_rmsd_to(self, other_rnamodel, output='', dont_move=False):
"""Calc rmsd P-atom based rmsd to other rna model"""
sup = Bio.PDB.Superimposer()
if dont_move:
# fix http://biopython.org/DIST/docs/api/Bio.PDB.Vector%27.Vector-class.html
coords = array([a.get_vector().get_array() for a in self.atoms])
other_coords = array([a.get_vector().get_array() for a in other_rnamodel.atoms])
s = SVDSuperimposer()
s.set(coords,other_coords)
return s.get_init_rms()
try:
sup.set_atoms(self.atoms, other_rnamodel.atoms)
except:
print(self.fn, len(self.atoms), other_rnamodel.fn, len(other_rnamodel.atoms))
for a,b in zip(self.atoms, other_rnamodel.atoms):
print(a.parent, b.parent)#a.get_full_id(), b.get_full_id())
rms = round(sup.rms, 3)
if output:
io = Bio.PDB.PDBIO()
sup.apply(self.struc.get_atoms())
io.set_structure( self.struc )
io.save("aligned.pdb")
io = Bio.PDB.PDBIO()
sup.apply(other_rnamodel.struc.get_atoms())
io.set_structure( other_rnamodel.struc )
io.save("aligned2.pdb")
return rms
class SVDSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = array([[51.65, -1.90, 50.07], [50.40, -1.23, 50.65],
[50.68, -0.04, 51.54], [50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54], [51.09, -1.88, 47.58],
[52.36, -1.20, 48.03], [52.71, -1.18, 49.38]])
self.sup = SVDSuperimposer()
self.sup.set(self.x, self.y)
def test_get_init_rms(self):
x = array([[1.19, 1.28, 1.37], [1.46, 1.55, 1.64], [1.73, 1.82, 1.91]])
y = array([[1.91, 1.82, 1.73], [1.64, 1.55, 1.46], [1.37, 1.28, 1.19]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
init_rms = 0.8049844719
self.assertTrue(float("%.3f" % self.sup.get_init_rms()),
float("%.3f" % init_rms))
def test_oldTest(self):
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(self.y, decimals=3)))
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
self.sup.run()
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(self.y, decimals=3)))
rot = array([[0.68304983, 0.53664371, 0.49543563],
[-0.52277295, 0.83293229, -0.18147242],
[-0.51005037, -0.13504564, 0.84947707]])
tran = array([38.78608157, -20.65451334, -15.42227366])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3),
around(rot, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3),
around(tran, decimals=3)))
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
rms = 0.00304266526014
self.assertEqual(float("%.3f" % self.sup.get_rms()),
float("%.3f" % rms))
rot_get, tran_get = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot_get, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(tran_get, decimals=3), around(tran,
decimals=3)))
y_on_x1 = dot(self.y, rot) + tran
y_x_solution = array(
[[5.16518846e+01, -1.90018270e+00, 5.00708397e+01],
[5.03977138e+01, -1.22877050e+00, 5.06488200e+01],
[5.06801788e+01, -4.16095666e-02, 5.15368866e+01],
[5.02202228e+01, -1.94372374e-02, 5.28534537e+01]])
self.assertTrue(
array_equal(around(y_on_x1, decimals=3),
around(y_x_solution, decimals=3)))
y_on_x2 = self.sup.get_transformed()
self.assertTrue(
array_equal(around(y_on_x2, decimals=3),
around(y_x_solution, decimals=3)))
def run_system(dir):
pdb = os.path.basename(dir).split('_')[0]
org_dir = os.getcwd()
os.chdir(dir)
f_coord = "coord.h5"
f_RMSD = "RMSD.txt"
f_OC = os.path.join("..","..","cmap_coordinates",pdb+'.txt')
if not os.path.exists(f_OC):
print "Missing coordinates for cmap", dir
os.chdir(org_dir)
return dir
if not os.path.exists(f_coord):
print "Missing coordinates, extract_coordinates.py first", dir
os.chdir(org_dir)
return dir
if os.path.exists(f_RMSD) and not _FORCE:
print "RMSD file exists, skipping", dir
os.chdir(org_dir)
return dir
h5 = h5py.File(f_coord,'r')
C = h5["coord"][:]
h5.close()
OC = np.loadtxt(f_OC)
# Move the coordinates to something sensible
#C -= C.mean(axis=0)
#OC -= OC.mean(axis=0)
median_OC = np.median([np.linalg.norm(a-b)
for a,b in zip(OC,OC[1:])])
median_C = np.median([np.linalg.norm(a-b)
for a,b in zip(C[-1],C[-1][1:])])
assert(C[0].shape == OC.shape)
RMSD = []
org_RMSD = []
sup = SVDSuperimposer()
RG = []
OC -= OC.mean(axis=0)
OC_RG = ((np.linalg.norm(OC,axis=1)**2).sum()/len(OC)) ** 0.5
for cx in C:
cx -= cx.mean(axis=0)
rg_cx = ((np.linalg.norm(cx,axis=1)**2).sum()/len(cx)) ** 0.5
RG.append(rg_cx)
sup.set(OC,cx)
sup.run()
RMSD.append(sup.get_rms())
org_RMSD.append(sup.get_init_rms())
rot, tran = sup.get_rotran()
cx = np.dot(cx, rot) + tran
RMSD = np.array(RMSD)
org_RMSD = np.array(org_RMSD)
RG = np.array(RG)
#print dir, RMSD[-20:].mean(), org_RMSD[-20:].mean(),RG[-20:].mean()
print "{} {: 0.4f} {: 0.4f}".format(dir, RMSD[-200:].mean(),
RG[-200:].mean() / OC_RG)
'''
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(OC[:,0],OC[:,1],OC[:,2],'b')
#ax.plot(OC[:,0],OC[:,1],OC[:,2],'k',alpha=0.5)
ax.scatter(cx[:,0],cx[:,1],cx[:,2],color='r')
#ax.plot(cx[:,0],cx[:,1],cx[:,2],'k',alpha=0.5)
plt.show()
exit()
print OC
#exit()
'''
np.savetxt(f_RMSD,RMSD)
os.chdir(org_dir)
return dir
class SVDSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = array([[51.65, -1.90, 50.07],
[50.40, -1.23, 50.65],
[50.68, -0.04, 51.54],
[50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]])
self.sup = SVDSuperimposer()
self.sup.set(self.x, self.y)
def test_get_init_rms(self):
x = array([[1.19, 1.28, 1.37],
[1.46, 1.55, 1.64],
[1.73, 1.82, 1.91]])
y = array([[1.91, 1.82, 1.73],
[1.64, 1.55, 1.46],
[1.37, 1.28, 1.19]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
init_rms = 0.8049844719
self.assertTrue(
float('%.3f' % self.sup.get_init_rms()), float('%.3f' % init_rms))
def test_oldTest(self):
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3)))
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
self.sup.run()
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3)))
rot = array([[0.68304983, 0.53664371, 0.49543563],
[-0.52277295, 0.83293229, -0.18147242],
[-0.51005037, -0.13504564, 0.84947707]])
tran = array([38.78608157, -20.65451334, -15.42227366])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3), around(tran, decimals=3)))
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
rms = 0.00304266526014
self.assertEqual(
float('%.3f' % self.sup.get_rms()), float('%.3f' % rms))
rot_get, tran_get = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot_get, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(tran_get, decimals=3), around(tran, decimals=3)))
y_on_x1 = dot(self.y, rot) + tran
y_x_solution = array(
[[5.16518846e+01, -1.90018270e+00, 5.00708397e+01],
[5.03977138e+01, -1.22877050e+00, 5.06488200e+01],
[5.06801788e+01, -4.16095666e-02, 5.15368866e+01],
[5.02202228e+01, -1.94372374e-02, 5.28534537e+01]])
self.assertTrue(
array_equal(around(y_on_x1, decimals=3), around(y_x_solution, decimals=3)))
y_on_x2 = self.sup.get_transformed()
self.assertTrue(
array_equal(around(y_on_x2, decimals=3), around(y_x_solution, decimals=3)))
