""" Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.6 omm_readinputs.py This module is for reading inputs in OpenMM. Correspondance: j712l362@ku.edu or wonpil@ku.edu Last update: July 22, 2015 """ from simtk.unit import * from simtk.openmm import * from simtk.openmm.app import * class _OpenMMReadInputs(): def __init__(self): self.toppar_path = None self.input_psf = None self.input_box = None self.input_crd = None self.input_rst = None self.input_chk = None self.output_dcd = None self.output_rst = None self.output_chk = None self.mini_nstep = 0 # Number of steps for minimization self.mini_Tol = 1.0 # Minimization energy tolerance self.gen_vel = 'no' # Generate initial velocities self.gen_temp = 300.0 # Temperature for generating initial velocities (K) self.gen_seed = None # Seed for generating initial velocities self.nstep = 0 # Number of steps to run self.dt = 0.002 # Time-step (ps) self.nstout = 100 # Writing output frequency (steps) self.nstdcd = 0 # Wrtiing coordinates trajectory frequency (steps) self.coulomb = PME # Electrostatic cut-off method self.ewald_Tol = 0.0005 # Ewald error tolerance self.vdw = 'Force-switch' # vdW cut-off method self.r_on = 1.0 # Switch-on distance (nm) self.r_off = 1.2 # Switch-off distance (nm) self.temp = 300.0 # Temperature (K) self.fric_coeff = 1 # Friction coefficient for Langevin dynamics self.pcouple = 'no' # Turn on/off pressure coupling self.p_ref = 1.0 # Pressure (Pref or Pxx, Pyy, Pzz; bar) self.p_type = 'membrane' # MonteCarloBarotat type self.p_scale = True, True, True # For MonteCarloAnisotropicBarostat self.p_XYMode = MonteCarloMembraneBarostat.XYIsotropic # For MonteCarloMembraneBarostat self.p_ZMode = MonteCarloMembraneBarostat.ZFree # For MonteCarloMembraneBarostat self.p_tens = 0.0 # Sulface tension for MonteCarloMembraneBarostat (dyne/cm) self.p_freq = 15 # Pressure coupling frequency (steps) self.cons = HBonds # Constraints method self.rest = 'no' # Turn on/off restraints self.fc_bb = 0.0 # Positional restraint force constant for protein backbone (kJ/mol/nm^2) self.fc_sc = 0.0 # Positional restraint force constant for protein side-chain (kJ/mol/nm^2) self.fc_lpos = 0.0 # Positional restraint force constant for lipids (kJ/mol/nm^2) self.fc_ldih = 0.0 # Dihedral restraint force constant for lipids (kJ/mol/rad^2) self.fc_cdih = 0.0 # Dihedral restraint force constant for carbohydrates (kJ/mol/rad^2) def read(self, inputFile): for line in open(inputFile, 'r'): if line.find('#') >= 0: line = line.split('#')[0] line = line.strip() if len(line) > 0: segments = line.split('=') input_param = segments[0].upper().strip() try: input_value = segments[1].strip() except: input_value = None if input_value: if input_param == 'TOPPAR_PATH': self.toppar_path = input_value if input_param == 'INPUT_PSF': self.input_psf = input_value if input_param == 'INPUT_BOX': self.input_box = input_value if input_param == 'INPUT_CRD': self.input_crd = input_value if input_param == 'INPUT_RST': self.input_rst = input_value if input_param == 'INPUT_CHK': self.input_chk = input_value if input_param == 'OUTPUT_DCD': self.output_dcd = input_value if input_param == 'OUTPUT_RST': self.output_rst = input_value if input_param == 'OUTPUT_CHK': self.output_chk = input_value if input_param == 'MINI_NSTEP': self.mini_nstep = int(input_value) if input_param == 'MINI_TOL': self.mini_Tol = float(input_value) if input_param == 'GEN_VEL': if input_value.upper() == 'YES': self.gen_vel = 'yes' if input_value.upper() == 'NO': self.gen_vel = 'no' if input_param == 'GEN_TEMP': self.gen_temp = float(input_value) if input_param == 'GEN_SEED': self.gen_seed = int(input_value) if input_param == 'NSTEP': self.nstep = int(input_value) if input_param == 'DT': self.dt = float(input_value) if input_param == 'NSTOUT': self.nstout = int(input_value) if input_param == 'NSTDCD': self.nstdcd = int(input_value) if input_param == 'COULOMB': if input_value.upper() == 'NOCUTOFF': self.coulomb = NoCutoff if input_value.upper() == 'CUTOFFNONPERIODIC': self.coulomb = CutoffNonPeriodic if input_value.upper() == 'CUTOFFPERIODIC': self.coulomb = CutoffPeriodic if input_value.upper() == 'EWALD': self.coulomb = Ewald if input_value.upper() == 'PME': self.coulomb = PME if input_param == 'EWALD_TOL': self.ewald_Tol = float(input_value) if input_param == 'VDW': if input_value.upper() == 'FORCE-SWITCH': self.vdw = 'Force-switch' if input_param == 'R_ON': self.r_on = float(input_value) if input_param == 'R_OFF': self.r_off = float(input_value) if input_param == 'TEMP': self.temp = float(input_value) if input_param == 'FRIC_COEFF': self.fric_coeff = float(input_value) if input_param == 'PCOUPLE': if input_value.upper() == 'YES': self.pcouple = 'yes' if input_value.upper() == 'NO': self.pcouple = 'no' if input_param == 'P_REF': if input_value.find(',') < 0: self.p_ref = float(input_value) else: Pxx = float(input_value.split(',')[0]) Pyy = float(input_value.split(',')[1]) Pzz = float(input_value.split(',')[2]) self.p_ref = Pxx, Pyy, Pzz if input_param == 'P_TYPE': if input_value.upper() == 'ISOTROPIC': self.p_type = 'isotropic' if input_value.upper() == 'MEMBRANE': self.p_type = 'membrane' if input_value.upper() == 'ANISOTROPIC': self.p_type = 'anisotropic' if input_param == 'P_SCALE': scaleX = True scaleY = True scaleZ = True if input_value.upper().find('X') < 0: scaleX = False if input_value.upper().find('Y') < 0: scaleY = False if input_value.upper().find('Z') < 0: scaleZ = False self.p_scale = scaleX, scaleY, scaleZ if input_param == 'P_XYMODE': if input_value.upper() == 'XYISOTROPIC': self.p_XYMode = MonteCarloMembraneBarostat.XYIsotropic if input_value.upper() == 'XYANISOTROPIC': self.p_XYMode = MonteCarloMembraneBarostat.XYAnisotropic if input_param == 'P_ZMODE': if input_value.upper() == 'ZFREE': self.p_ZMode = MonteCarloMembraneBarostat.ZFree if input_value.upper() == 'ZFIXED': self.p_ZMode = MonteCarloMembraneBarostat.ZFixed if input_value.upper() == 'CONSTANTVOLUME': self.p_ZMode = MonteCarloMembraneBarostat.ConstantVolume if input_param == 'P_TENS': self.p_tens = float(input_value) if input_param == 'P_FREQ': self.p_freq = int(input_value) if input_param == 'CONS': if input_value.upper() == 'NONE': self.cons = None if input_value.upper() == 'HBONDS': self.cons = HBonds if input_value.upper() == 'ALLBONDS': self.cons = AllBonds if input_value.upper() == 'HANGLES': self.cons = HAngles if input_param == 'REST': if input_value.upper() == 'YES': self.rest = 'yes' if input_value.upper() == 'NO': self.rest = 'no' if input_param == 'FC_BB': self.fc_bb = float(input_value) if input_param == 'FC_SC': self.fc_sc = float(input_value) if input_param == 'FC_LPOS': self.fc_lpos = float(input_value) if input_param == 'FC_LDIH': self.fc_ldih = float(input_value) if input_param == 'FC_CDIH': self.fc_cdih = float(input_value) return self def read_inputs(inputFile): return _OpenMMReadInputs().read(inputFile)