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 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)
