Package schrodinger :: Package application :: Package desmond :: Module extend_fep :: Class Baseunit

Class Baseunit

object --+
         |
        Baseunit

Known Subclasses:

Workunit

This contains info common to all work units, they should subclass this unit to get jobname, master_msj, and master_checkpoint_fn, and perturbation_dir

Instance Methods

[hide private]

__init__(self, master_checkpoint_fn, jobname=None, master_msj_fn=None, host=None, subhost=None, perturbation_dir=None, opls_dir=None, pkl_fn=None, cwd=None, complex_msj_fn=None, solvent_msj_fn=None)
x.__init__(...) initializes x; see help(type(x)) for signature

initializeWorkunit(self)

string or None

discoverCheckpoint(self, perturb_sim='')
This will automatically find a checkpoint file for the complex and solvent.

bool

discoverPerturbationDir(self)
This will automatically find the perturbation directory.

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, master_checkpoint_fn, jobname=None, master_msj_fn=None, host=None, subhost=None, perturbation_dir=None, opls_dir=None, pkl_fn=None, cwd=None, complex_msj_fn=None, solvent_msj_fn=None)
(Constructor)

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

Overrides: object.__init__

discoverCheckpoint(self, perturb_sim=`''`)

This will automatically find a checkpoint file for the complex and solvent. The master checkpoint has been implicitly discovered when finding the jobname. We also have a check for multiple master checkpoint files in case there are multiple files in the root dir.

Parameters:

perturb_sim (string) - simulation type e.g. "complex", "solvent", or ""

Returns: string or None

Name of the file if it was discovered

discoverPerturbationDir(self)

This will automatically find the perturbation directory. If this is not present then there is no simulation to extned. The PERTURBATION_STAGE is currently 3 if this changes in the workflow then we need to update it at the top of this file. @return : True if it was successfully discovered, False otherwise

Returns: bool

Class Baseunit

__init__(self, master_checkpoint_fn, jobname=None, master_msj_fn=None, host=None, subhost=None, perturbation_dir=None, opls_dir=None, pkl_fn=None, cwd=None, complex_msj_fn=None, solvent_msj_fn=None) (Constructor)

discoverCheckpoint(self, perturb_sim='')

discoverPerturbationDir(self)

init(self, master_checkpoint_fn, jobname=None, master_msj_fn=None, host=None, subhost=None, perturbation_dir=None, opls_dir=None, pkl_fn=None, cwd=None, complex_msj_fn=None, solvent_msj_fn=None)
(Constructor)

discoverCheckpoint(self, perturb_sim=`''`)