schrodinger.application.desmond.extend

Class ExtensionWorkflow

object --+ | Workflow --+ | ExtensionWorkflow

Instance Methods

__init__(self, work_list, prep_only=False, force=False)
x.__init__(...) initializes x; see help(type(x)) for signature

bool

stageOne(self)
Remove units that are not properly initialized.

bool

stageTwo(self)
Prepare new input files for valid workunit objects @return : We return True if we successfully prepared a job, False otherwise

bool

createNewMsj(self, wu)
This is a bit complicated due to adding the ability to extend simulations multiple times.

prepNewTgz(self, wu, fn, remote_pert_dir)
This assumes that we only need the -out.cms files for the replicas from previous stage to run an extension job

processWorkList(self, remote_pert_dir)

Inherited from Workflow: crunch, initPrepDir, multisimLogPresent, prepForRemoteRun, preparePerturbDir, stageThree

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

init(self, work_list, prep_only=False, force=False)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

work_list - List containg Workunit objects to be sent to jobDJ
prep_only - This option can be used to prepare the launch file only
force - If set this will ignore the fact that a log is not present in the cwd and launch the job

Overrides: object.__init__

(inherited documentation)

stageOne(self)

Remove units that are not properly initialized. Return True if we have units to work on so we are gaurenteed to have at least one valid work unit to process if stageOne passes. @return : We return True if we successfully prepared a job, False otherwise

Returns: bool

createNewMsj(self, wu)

This is a bit complicated due to adding the ability to extend simulations multiple times. If we do not find the _extention.msj then we will use the original msj otherwise we will use the extension msj.

Parameters:

wu (Workunit) - a workunit for which we create a new msj

Returns: bool

True upon successful generation of the msj

prepNewTgz(self, wu, fn, remote_pert_dir)

This assumes that we only need the -out.cms files for the replicas from previous stage to run an extension job

Parameters:

wu (Workunit) - A work unit
fn (string) - filename of the tar.gz
remote_pert_dir (string) - The remote perturbation directory

processWorkList(self, remote_pert_dir)

Parameters:

remote_pert_dir (string) - The remote directory we will copy files to

Class ExtensionWorkflow

__init__(self, work_list, prep_only=False, force=False) (Constructor)

stageOne(self)

createNewMsj(self, wu)

prepNewTgz(self, wu, fn, remote_pert_dir)

processWorkList(self, remote_pert_dir)

init(self, work_list, prep_only=False, force=False)
(Constructor)