schrodinger.application.desmond.extend

Class Workunit

object --+ | Baseunit --+ | Workunit

This subclasses Baseunit and adds attributes specific to the workunit being created. The typical workunits will be "solvent" and "complex". If ext_time_ps or total_proc are set we will use those otherwise we will use the values found in the previous msj for the workunit. Maxjob should not be set to anything other than "1".

Instance Methods

[hide private]

__init__(self, edge, ext_type, master_checkpoint_fn, ext_time_ps=None, msj_fn=None, checkpoint_fn=None, prev_stage_tgz_fn=None, total_proc=None, maxjob='1', jobname=None, restart=False, host=None, subhost=None)
x.__init__(...) initializes x; see help(type(x)) for signature

initExtMSJ(self)
If a <>_extension.msj file is present in the stage_3 dir it will use this otherwise it will make a copy of the <>_complex.msj as a starting template for <>_extensiont.msj

initLastLambdaStage(self)
Will read the checkpoint file and count how many lambda stages are present

discoverTgz(self)
Will find the next stage in the workflow that we will need to copy over for extending i.e.

Inherited from Baseunit: discoverCheckpoint, discoverPerturbationDir, initializeWorkunit

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

Properties

[hide private]

Inherited from object: __class__

init(self, edge, ext_type, master_checkpoint_fn, ext_time_ps=None, msj_fn=None, checkpoint_fn=None, prev_stage_tgz_fn=None, total_proc=None, maxjob=`'1'`, jobname=None, restart=False, host=None, subhost=None)
(Constructor)

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

Parameters:

edge (Tuple containg strings i.e. (benzene, acetic_acid)) - This is a tuple which contains the two edges to be extended
ext_type - The simulation type "complex" or "solvent"
ext_type - string

Overrides: object.__init__

discoverTgz(self)

Will find the next stage in the workflow that we will need to copy over for extending i.e. stage 9 if it is a complex, but this will become stage 10 after the first extenstion stage 11 after the second, etc.

Class Workunit

__init__(self, edge, ext_type, master_checkpoint_fn, ext_time_ps=None, msj_fn=None, checkpoint_fn=None, prev_stage_tgz_fn=None, total_proc=None, maxjob='1', jobname=None, restart=False, host=None, subhost=None) (Constructor)

discoverTgz(self)

init(self, edge, ext_type, master_checkpoint_fn, ext_time_ps=None, msj_fn=None, checkpoint_fn=None, prev_stage_tgz_fn=None, total_proc=None, maxjob=`'1'`, jobname=None, restart=False, host=None, subhost=None)
(Constructor)