def _checkInput(self): async_re._checkInput(self) #make sure BEDAM + TEMPERATURE is wanted if self.keywords.get('RE_TYPE') != 'BEDAMTEMPT': self._exit("RE_TYPE is not BEDAMTEMPT") #BEDAM runs with IMPACT if self.keywords.get('ENGINE') != 'IMPACT': self._exit("ENGINE is not IMPACT") #input files self.extfiles = self.keywords.get('ENGINE_INPUT_EXTFILES') if not (self.extfiles is None): if self.extfiles != '': self.extfiles = self.extfiles.split(',') #list of lambdas if self.keywords.get('LAMBDAS') is None: self._exit("LAMBDAS needs to be specified") lambdas = self.keywords.get('LAMBDAS').split(',') #list of temperatures if self.keywords.get('TEMPERATURES') is None: self._exit("TEMPERATURES needs to be specified") temperatures = self.keywords.get('TEMPERATURES').split(',') #build parameters for the lambda/temperatures combined states self.nreplicas = self._buildBEDAMStates(lambdas,temperatures) #executive file's directory if self.keywords.get('JOB_TRANSPORT') is 'SSH': if self.keywords.get('EXEC_DIRECTORY') is None: self._exit("EXEC DIRECTORY needs to be specified")
def _checkInput(self): async_re._checkInput(self) #make sure BEDAM + TEMPERATURE is wanted if self.keywords.get('RE_TYPE') != 'BEDAMTEMPT': self._exit("RE_TYPE is not BEDAMTEMPT") #BEDAM runs with IMPACT if self.keywords.get('ENGINE') != 'IMPACT': self._exit("ENGINE is not IMPACT") #input files self.extfiles = self.keywords.get('ENGINE_INPUT_EXTFILES') if not (self.extfiles is None): if self.extfiles != '': self.extfiles = self.extfiles.split(',') #list of lambdas if self.keywords.get('LAMBDAS') is None: self._exit("LAMBDAS needs to be specified") lambdas = self.keywords.get('LAMBDAS').split(',') #list of temperatures if self.keywords.get('TEMPERATURES') is None: self._exit("TEMPERATURES needs to be specified") temperatures = self.keywords.get('TEMPERATURES').split(',') #build parameters for the lambda/temperatures combined states self.nreplicas = self._buildBEDAMStates(lambdas, temperatures) #executive file's directory if self.keywords.get('JOB_TRANSPORT') is 'SSH': if self.keywords.get('EXEC_DIRECTORY') is None: self._exit("EXEC DIRECTORY needs to be specified")
def _checkInput(self): async_re._checkInput(self) #make sure BEDAM + TEMPERATURE is wanted if self.keywords.get('RE_TYPE') != 'BEDAMTEMPT': self._exit("RE_TYPE is not BEDAMTEMPT") #BEDAM runs with openmm //edit on 10.15 if self.keywords.get('ENGINE') != 'OPENMM': self._exit("ENGINE is not OPENMM") #input files self.extfiles = self.keywords.get('ENGINE_INPUT_EXTFILES') if not (self.extfiles is None): if self.extfiles != '': self.extfiles = self.extfiles.split(',') #list of lambdas if self.keywords.get('LAMBDAS') is None: self._exit("LAMBDAS needs to be specified") lambdas = self.keywords.get('LAMBDAS').split(',') #list of temperatures if self.keywords.get('TEMPERATURES') is None: self._exit("TEMPERATURES needs to be specified") temperatures = self.keywords.get('TEMPERATURES').split(',') #build parameters for the lambda/temperatures combined states self.nreplicas = self._buildBEDAMStates(lambdas,temperatures) #executive file's directory if self.keywords.get('JOB_TRANSPORT') is 'SSH': if self.keywords.get('EXEC_DIRECTORY') is None: self._exit("EXEC DIRECTORY needs to be specified") #added on 10.19.15 self.implicitsolvent = self.keywords.get('IMPLICITSOLVENT') self.totalsteps = self.keywords.get('TOTALSTEPS') self.jobname = self.keywords.get('ENGINE_INPUT_BASENAME') self.stepgap = self.keywords.get('STEPGAP')
def _checkInput(self): async_re._checkInput(self) #make sure DATE is wanted if self.keywords.get('RE_TYPE') != 'DATE': self._exit("RE_TYPE is not DATE") #number of replicas if self.keywords.get('NREPLICAS') is None: self._exit("NREPLICAS needs to be specified") self.nreplicas = int(self.keywords.get('NREPLICAS'))
def _checkInput(self): async_re._checkInput(self) #make sure BEDAM + TEMPERATURE is wanted if self.keywords.get('RE_TYPE') != 'BEDAMTEMPT': self._exit("RE_TYPE is not BEDAMTEMPT") #BEDAM runs with IMPACT if self.keywords.get('ENGINE') != 'IMPACT': self._exit("ENGINE is not IMPACT") #input files self.extfiles = self.keywords.get('ENGINE_INPUT_EXTFILES') if not (self.extfiles is None): if self.extfiles != '': self.extfiles = self.extfiles.split(',') #list of temperatures if self.keywords.get('TEMPERATURES') is None: self._exit("TEMPERATURES needs to be specified") temperatures = self.keywords.get('TEMPERATURES').split(',') #list of STARTING lambdas if self.keywords.get('LAMBDAS') is None: self._exit("LAMBDAS needs to be specified") st_lambdas = self.keywords.get('LAMBDAS').split(',') if all([lambd != st_lambdas[0] for lambd in st_lambdas]): self.logger.warn("Not all starting lambdas are equal!") #lambda schedule if self.keywords.get('LAMBDA_SCHED') is None: self._exit("LAMBDA_SCHED needs to be specified") self.lambda_sched = self.keywords.get('LAMBDA_SCHED').split(',') #build parameters for the lambda/temperatures combined states self.nreplicas = self._buildBEDAMStates(st_lambdas, temperatures) #executive file's directory if self.keywords.get('JOB_TRANSPORT') is 'SSH': if self.keywords.get('EXEC_DIRECTORY') is None: self._exit("EXEC DIRECTORY needs to be specified") #schedule interval if self.keywords.get('SCHED_INTERVAL') is None: self._exit("SCHED_INTERVAL is a required parameter!") self.sched_interval = int(self.keywords.get('SCHED_INTERVAL')) if self.sched_interval < 1: self._exit("SCHED_INTERVAL must be > 0!")
def _checkInput(self): async_re._checkInput(self) #make sure BEDAM is wanted if self.keywords.get('RE_TYPE') != 'BEDAM': self._exit("RE_TYPE is not BEDAM") #BEDAM runs with IMPACT if self.keywords.get('ENGINE') != 'IMPACT': self._exit("ENGINE is not IMPACT") #input files # self.extfiles = self.keywords.get('ENGINE_INPUT_EXTFILES') # if not (self.extfiles is None): # if self.extfiles != '': # self.extfiles = self.extfiles.split(',') #list of lambdas if self.keywords.get('LAMBDAS') is None: self._exit("LAMBDAS needs to be specified") self.lambdas = self.keywords.get('LAMBDAS').split(',') self.nreplicas = len(self.lambdas) #simulation temperature if self.keywords.get('BEDAM_TEMPERATURE') is None: self._exit("BEDAM_TEMPERATURE is a required parameter") bedam_temperature = float(self.keywords.get('BEDAM_TEMPERATURE')) self.bedam_beta = 1./(0.0019872041*bedam_temperature)
def _checkInput(self): async_re._checkInput(self) #make sure BEDAM is wanted if self.keywords.get('RE_TYPE') != 'BEDAM': self._exit("RE_TYPE is not BEDAM") #BEDAM runs with IMPACT if self.keywords.get('ENGINE') != 'IMPACT': self._exit("ENGINE is not IMPACT") #input files # self.extfiles = self.keywords.get('ENGINE_INPUT_EXTFILES') # if not (self.extfiles is None): # if self.extfiles != '': # self.extfiles = self.extfiles.split(',') #list of lambdas if self.keywords.get('LAMBDAS') is None: self._exit("LAMBDAS needs to be specified") self.lambdas = self.keywords.get('LAMBDAS').split(',') self.nreplicas = len(self.lambdas) #simulation temperature if self.keywords.get('BEDAM_TEMPERATURE') is None: self._exit("BEDAM_TEMPERATURE is a required parameter") bedam_temperature = float(self.keywords.get('BEDAM_TEMPERATURE')) self.bedam_beta = 1. / (0.0019872041 * bedam_temperature)