def solvestiffness(pdbpathlist, ballpathlist, stickpathlist, disppathlist, ktypeassinger, notrelative=False): equsysset = [] for i in range(len(pdbpathlist)): pdbfn = pdbpathlist[i] ballfn = ballpathlist[i] stickfn = stickpathlist[i] dispfn = disppathlist[i] f = equtils.ForceGen.get_force_vector( ballfn, equtils.wimley_section_divide(equtils.opm_mempos(pdbfn, ballfn)) ) equsys = bbtmequs.DisplacementEquSys(ballfn, stickfn, dispfn, f, ktypeassinger) #seciddict = equtils.section_divide(ballfn, equtils.wimley_section_divide(equtils.opm_mempos(pdbfn, ballfn)) ) seciddict = equtils.section_divide(ballfn, equtils.uni_section_divide(equtils.opm_mempos(pdbfn, ballfn)) ) equsys.divide_system(seciddict) equsysset.append( equsys ) totequsys = equsysset[0] for i in range(1,len(equsysset)): totequsys = totequsys + equsysset[i] totequsys.solve(notrelative) return totequsys.result
k = np.dot(cls.ktypeassigner.get_assign_vec(btype, a1type, a2type), cls.kvec) return k datapath = '../../../data/' #codes = [ '1BXW', '1FEP', '1I78', '1K24', '1KMO', '1NQE', '1P4T' ] 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)
