ball_data = bbtmio.read_ball_file(ball_fn) ################################################ # recenter pdb balls file print( '\tPreparing recentered and aligned pdb balls file' ) ball_pdb_fn = pdbfn[:-4]+'_pdb.balls' if os.path.isfile(ball_pdb_fn) and not args['overwrite']: print( '\tFile '+pdbcode+'_pdb.balls exists. Nothing changed.\n' ) else: ball_coord_mat = bbtmio.get_ball_coords( ball_data ) pdbball_data = bbtmio.read_ball_file(ball_ori_fn) # recenter pdbball_coord_mat = bbtmio.recenter_coord_mat( bbtmio.get_pdb_coords(structure,bbin_data), bbin_data ) pdbball_data = bbtmio.set_ball_coords(pdbball_data, pdbball_coord_mat) # align rotation_matrix, pdbball_coord_mat = bbtmio.align_coordmat(pdbball_coord_mat, ball_coord_mat) pdbball_data = bbtmio.set_ball_coords(pdbball_data, pdbball_coord_mat) bbtmio.write_ball_file(pdbball_data, ball_pdb_fn) print( '\tFile '+pdbcode+'_pdb.balls written.\n' ) ball_pdb_data = bbtmio.read_ball_file(ball_pdb_fn) ################################################ # calculate displacement from ideal barrel print( '\tCalculate displacement from ideal to real' ) dfn = pdbfn[:-4]+'.displacement' if os.path.isfile(dfn) and not args['overwrite']: print( '\tFile '+pdbcode+'.displacement exists. Nothing changed.\n' ) else: #ball_data = bbtmio.read_ball_file(ball_fn) #ball82_data = bbtmio.read_ball_file(ball_fn+'82')
ks3 = np.array( [ 1.31824322, 0.88899824, 0.9253788 , 0.72740754, 2.81697644, 0.66983903, 0.36771102] )
ks = np.mean(np.vstack((ks1,ks2,ks3)), axis=0)
@classmethod
def get_k(cls, btype, a1type, a2type):
return 100 if btype=='SP' else 100000000 * np.dot( cls.kta.get_assign_vec(a1type, a2type, btype), cls.ks )
for coden in testset:
ses = bbtmdsm.StiffnessEquSys('../../../data/testdata/'+coden+'.balls.ideallarge.ext', '../../../data/testdata/'+coden+'.sticks.ideallarge.ext', testkassigner )
ses.solve()
u = ses.u.reshape(ses.u.shape[0]/3, 3)
ideallargecoords = bbtmio.get_ball_coords( bbtmio.read_ball_file('../../../data/testdata/'+coden+'.balls.ideallarge') )
pdbcoords = bbtmio.get_ball_coords( bbtmio.read_ball_file('../../../data/'+coden+'_pdb.balls') )
afteru = ideallargecoords + u
newafteru = bbtmio.recenter_coord_mat(afteru, bbtmio.read_bbin_file('../../../data/'+coden+'.bbin'))
bbtmio.write_ball_file( bbtmio.set_ball_coords( bbtmio.read_ball_file('../../../data/testdata/'+coden+'.balls.ideallarge'), newafteru ), coden+'.balls.au')
dummy,newpdbcoords = bbtmio.align_coordmat(pdbcoords, newafteru)
disp = newafteru - newpdbcoords
rmsd = np.mean(np.square(np.linalg.norm(disp, axis=1))) ** 0.5
print coden, disp.shape[0], rmsd
#sys.exit(0)