def run(infile, prefix, covariance):
# read in pdb file (parmed)
pdb = read_PDB(infile)
if covariance:
A = set_A(pdb, covariance=covariance)
# set B
B = set_B(pdb, covariance=covariance)
else:
# set A
A = set_A(pdb, covariance=covariance)
# set B
B = set_B(pdb, covariance=covariance)
import code; code.interact(local=dict(globals(), **locals()))
# solve Ax=B
x = solve_SVD(A,B)
# calc new ADP and residual and print residual
UTLS, TLS_residual = calc_ADP_from_TLS(x,A,B)
print "The ADP TLS residual is %6.4f." %TLS_residual
# write tls file
write_TLS(x, prefix)
# write out pdb file(parmed) plug in UTLS
out_pdb = pdb
# for i,atom in enumerate(atomlist):
# for Uij in range(6):
# atom.UIJ[Uij] = UTLS[i*6+Uij]
# calculate iso Bfactor from Uij (matlab)
write_PDB(out_pdb, "%s.pdb" %prefix)
def run(infile, prefix, covariance_file):
# read in pdb file (parmed)
pdb = read_PDB(infile)
assert pdb.box is not None, "ERROR: CRYST1 record required in PDB file!"
# get centroid
com = center_of_mass(pdb)
if not covariance_file:
# set A
A = set_A(pdb, com)
# set B
B = set_B(pdb)
# solve Ax=B
x = solve_SVD(A,B)
# calc new ADP and residual and print residual
UTLS, SSE, MSE, r2 = calc_ADP_from_TLS(x,A,B)
else:
# expanded A with 6*n(n-1)/2-3n equations
A_cov = set_A_cov(pdb, com)
# 6*n(n-1)/2-3n covariances
B_cov, uu = set_B_cov(pdb, covariance_file)
# 21 TLS parameters
x = solve_SVD(A_cov, B_cov)
# calc new ADP and residual and print residual
UTLS, SSE, MSE, r2 = calc_ADP_from_TLS_cov(pdb, com, uu, x)
#print statistics
print " *** ADP FIT STATISTICS ***"
print "The ADP Sum of Squared Errors is %6.4f." %SSE
print "The ADP Mean Squared Error is %6.4f." %MSE
print "The ADP R-square statistic is %6.4f." %r2
# populate TLS matrices
T,L,S = set_TLS(x)
# shift TLS to center of reaction
T,L,S,cor = center_of_reaction_shift(T,L,S, com)
# write TLS to file
write_TLS(T,L,S,cor,pdb, prefix)
# import code; code.interact(local=dict(globals(), **locals()))
# import sys; sys.exit()
# write out pdb file with new ADP/Bfactors
for i,atom in enumerate(pdb.atoms):
atom.anisou = UTLS[i*6:i*6+6]
Bfac, Ueq = Adp2B(np.array(pdb.box),atom.anisou, method=2)
atom.bfactor = Bfac
write_PDB(pdb, "%s.pdb" %prefix, write_anisou=True)
return 0
