import numpy as np import sys import os sys.path.append(os.path.abspath(os.path.dirname(__file__))+'/../../../pyscripts/') import bbtmio import bbtmequs import typeutils from typeutils import * import equtils import bbtmml codes = [ '1BXW', '1FEP', '1I78', '1K24', '1KMO', '1NQE', '1P4T' ] for code in codes: deformedcoords = bbtmio.get_ball_coords( bbtmio.read_ball_file(code+'.balls.deformed') ) reconstructedcoords = bbtmio.get_ball_coords( bbtmio.read_ball_file(code+'.balls.reconstruct') ) disp = deformedcoords - reconstructedcoords rmsd = np.mean(np.square(np.linalg.norm(disp, axis=1))) ** 0.5 print code, rmsd
print( '\tFile '+pdbcode+'_origin.balls and .sticks exist. Nothing changed.\n' )
else:
os.system('exec/barrel.out '+pdbfn[:-4]+'.bbin')
print( '\tFile '+pdbcode+'_origin.balls and .sticks written.\n' )
ball_data = bbtmio.read_ball_file(ball_ori_fn)
# temporary file, register for cleaning
files_to_clean.append(ball_ori_fn)
################################################
# recenter balls
print( '\tRecentering the coordinate matrix in balls file' )
ball_fn = pdbfn[:-4]+'.balls'
if os.path.isfile(ball_fn) and not args['overwrite']:
print( '\tFile '+pdbcode+'.balls exists. Nothing changed.\n' )
else:
ball_coord_mat = bbtmio.recenter_coord_mat( bbtmio.get_ball_coords(ball_data), bbin_data)
ball_data = bbtmio.set_ball_coords(ball_data, ball_coord_mat)
bbtmio.write_ball_file(ball_data, ball_fn)
print( '\tFile '+pdbcode+'.balls written.\n' )
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
ks2 = np.array( [ 2.49441195, 0.65856546, 0.86605534, 0.79412971, 2.91011336, 1.71480196, 0.68283227] )
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)
codes = [ '1K24' ] # generated deformed balls file for code in codes: extballfn = datapath+'testdata/'+code+'.balls.ideallarge.ext' extstickfn = datapath+code+'.sticks.ext' pdbfn = datapath+code+'.pdb' #memsec = equtils.wimley_section_divide(equtils.opm_mempos(pdbfn, extballfn)) memsec = equtils.uni_section_divide(equtils.opm_mempos(pdbfn, extballfn)) f = equtils.ForceGen.get_force_vector( extballfn,memsec ) equsys = bbtmequs.StiffnessEquSys(extballfn, extstickfn, f, TestKAssigner ) equsys.solve() disp = equsys.result['u'].reshape(equsys.result['u'].shape[0]/3, 3) ballfn = datapath+'testdata/'+code+'.balls.ideallarge' balldat = bbtmio.read_ball_file(ballfn) ballcoords = bbtmio.get_ball_coords(balldat) # rec means after reconstruction recballcoords = ballcoords + disp recballdat = bbtmio.set_ball_coords(balldat, recballcoords) recballfn = code+'.balls.reconstruct' bbtmio.write_ball_file(recballdat, recballfn) dispfn = code+'.displacement.reconstruct' bbtmio.write_displacement_file(ballcoords, recballcoords, dispfn)
import numpy as np import sys import os sys.path.append(os.path.abspath(os.path.dirname(__file__))+'/../../../pyscripts/') import bbtmio import bbtmequs import typeutils from typeutils import * import equtils import bbtmml datapath = '../../../data/' codes = [ '1BXW', '1FEP', '1I78', '1K24'] #codes = [ '1BXW', '1FEP', '1I78', '1K24', '1KMO', '1NQE', '1P4T' ] for code in codes: deformedcoords = bbtmio.get_ball_coords( bbtmio.read_ball_file(datapath+code+'_pdb.balls') ) reconstructedcoords = bbtmio.get_ball_coords( bbtmio.read_ball_file(code+'.balls.reconstruct') ) disp = deformedcoords - reconstructedcoords rmsd = np.mean(np.square(np.linalg.norm(disp, axis=1))) ** 0.5 print code, rmsd