def dfunc(p, centers):
#cpos = 372; natoms = 124
indr = np.arange(9, 122 * 3)
natoms_r = 119
xi = p[indr].reshape((natoms_r, 3))
xi -= np.mean(xi, axis=0)
xi = xi.T.astype(np.float64)
d = np.empty((centers.shape[0], ))
for ci, ck in enumerate(centers):
cen = ck[indr].reshape((natoms_r, 3))
d[ci] = qcp.CalcRMSDRotationalMatrix(xi,
cen.T.astype(np.float64),
natoms_r,
None,
None,
center_ref=0,
center_conf=1,
copy=0)
return d.astype(pcoord_dtype)
def interpolate_conformations(confA, confB, N):
assert confA.shape == confB.shape
natoms = confA.shape[0]
x0 = confA.copy()
xN = confB.copy()
# Align confA and confB
x0 -= np.mean(x0, axis=0)
xN -= np.mean(xN, axis=0)
R = np.zeros((9, ), dtype=np.float64)
rmsd = qcp.CalcRMSDRotationalMatrix(x0.T.astype(np.float64),
xN.T.astype(np.float64), natoms, R,
None)
print('RMSD: {}'.format(rmsd))
R = np.matrix(R.reshape(3, 3))
xN = xN * R
# Interpolate coordinates form x0 to xN
confs = np.zeros((N, natoms * 3))
x0 = np.ravel(x0)
xN = np.ravel(xN)
for k in xrange(natoms * 3):
confs[:, k] = np.linspace(x0[k], xN[k], N)
return confs
def average_position(self, n_iter):
"""Get average position of replicas in each bin as of n_iter for the
the user selected update interval
"""
nbins = self.system.bin_mapper.nbins
ndim = self.system.pcoord_ndim
natoms = ndim // 6
cpos = natoms * 3
avg_pos = np.zeros((nbins, ndim), dtype=self.system.pcoord_dtype)
sum_bin_weight = np.zeros((nbins, ), dtype=self.system.pcoord_dtype)
start_iter = max(n_iter - min(self.windowsize, n_iter), 1)
stop_iter = n_iter + 1
for n in xrange(start_iter, stop_iter):
with self.data_manager.lock:
iter_group = self.data_manager.get_iter_group(n)
seg_index = iter_group['seg_index'][...]
pcoords = iter_group['pcoord'][:, -1, :] # Only read final point
bin_indices = self.system.bin_mapper.assign(pcoords)
weights = seg_index['weight']
uniq_indices = np.unique(bin_indices)
for indx in uniq_indices:
ii = np.where(bin_indices == indx)[0]
bpc = pcoords[ii, :cpos]
nmemb = bpc.shape[0]
# (1) Align all structures to confA
xref = self.strings.centers[0, :cpos].reshape((natoms, 3))
xref -= np.mean(xref, axis=0)
xref = xref.T.astype(np.float64)
for k in xrange(nmemb):
xi = bpc[k, :].reshape((natoms, 3))
R = np.zeros((9, ), dtype=np.float64)
qcp.CalcRMSDRotationalMatrix(xref,
xi.T.astype(np.float64),
natoms,
R,
None,
center_ref=0,
center_conf=1,
copy=0)
R = np.matrix(R.reshape(3, 3))
xi[:] = xi * R
avg_pos[indx, :cpos] += xi.ravel() * weights[ii[k]]
sum_bin_weight += np.bincount(bin_indices.astype(np.int),
weights=weights,
minlength=nbins)
# Some bins might have zero samples so exclude to avoid divide by zero
occ_ind = np.nonzero(sum_bin_weight)
avg_pos[occ_ind] /= sum_bin_weight[occ_ind][:, np.newaxis]
return avg_pos, sum_bin_weight
def _h_rmsd(self, coord1, coord2):
return pyqcprot.CalcRMSDRotationalMatrix(coord1, coord2, None, None)
frag_b[1][6] = -10.001
frag_b[2][6] = 17.996
# Allocate rotation array
rot = numpy.zeros((9,),dtype=numpy.float64)
# Calculate center of geometry
comA = numpy.sum(frag_a,axis=1)/N
comB = numpy.sum(frag_b,axis=1)/N
# Center each fragment
frag_a = frag_a - comA.reshape(3,1)
frag_b = frag_b - comB.reshape(3,1)
# Calculate rmsd and rotation matrix
rmsd = qcp.CalcRMSDRotationalMatrix(frag_a,frag_b,N,rot,None)
print 'qcp rmsd = ',rmsd
print 'rotation matrix:'
print rot.reshape((3,3))
# Calculate rmsd after applying rotation
def rmsd(a,b):
"""Returns RMSD between two coordinate sets a and b."""
return numpy.sqrt(numpy.sum(numpy.power(a-b,2))/a.shape[1])
# rotate frag_b to obtain optimal alignment
frag_br = frag_b.T*numpy.matrix(rot.reshape((3,3)))
rmsd = rmsd(frag_br.T,frag_a)
print 'rmsd after applying rotation: ',rmsd
# reference centre of mass system
ref_com = ref_atoms.centerOfMass()
ref_coordinates = ref_atoms.coordinates() - ref_com
# allocate the array for selection atom coords
traj_coordinates = traj_atoms.coordinates().copy()
# R: rotation matrix that aligns r-r_com, x~-x~com
# (x~: selected coordinates, x: all coordinates)
# Final transformed traj coordinates: x' = (x-x~_com)*R + ref_com
for k, ts in enumerate(frames):
# shift coordinates for rotation fitting
# selection is updated with the time frame
x_com = traj_atoms.centerOfMass()
traj_coordinates[:] = traj_atoms.coordinates() - x_com
R = numpy.zeros((9, ), dtype=numpy.float64)
# Need to transpose coordinates such that the coordinate array is
# 3xN instead of Nx3. Also qcp requires that the dtype be float64
a = ref_coordinates.T.astype('float64')
b = traj_coordinates.T.astype('float64')
rmsd[k] = qcp.CalcRMSDRotationalMatrix(a, b, natoms, R, None)
R = numpy.matrix(R.reshape(3, 3))
# Transform each atom in the trajectory (use inplace ops to avoid copying arrays)
ts._pos -= x_com
ts._pos[:] = ts._pos * R # R acts to the left & is broadcasted N times.
ts._pos += ref_com
writer.write(traj.atoms) # write whole input trajectory system
numpy.savetxt('rmsd.out', rmsd)