Package schrodinger :: Package application :: Package desmond :: Module stage :: Class LambdaHopping

Class LambdaHopping

         object --+                
                  |                
picklejar.Picklable --+            
                      |            
          cmj.StageBase --+        
                          |        
                   Simulate --+    
                              |    
                ReplicaExchange --+
                                  |
                                 LambdaHopping

Nested Classes

[hide private]

Inherited from cmj.StageBase: __metaclass__

Instance Methods

[hide private]

__init__(self, *arg, **kwarg)
x.__init__(...) initializes x; see help(type(x)) for signature

crunch(self)
This is where jobs of this stage are created.

restart_subjobs(self, jobs)
Subclass should override this if it supports subjob restarting.

hook_captured_successful_job(self, job)

Inherited from ReplicaExchange (private): _write_cfg

Inherited from Simulate (private): _create_job, _get_model, _write_cms

Inherited from cmj.StageBase: __getstate__, __setstate__, capture, check_param, describe, determine, pack_stage, poststage, prestage, push, release

Inherited from cmj.StageBase (private): _effect, _gen_unique_jobname, _get_jobname_and_dir, _get_macro_dict, _log, _param_jlaunch_opt_check, _print, _reg_param_postcheck, _reg_param_precheck, _set

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

Static Methods

[hide private]

Inherited from Simulate: check_cms_file

Class Variables

[hide private]

NAME = "lambda_hopping"

PARAM = cmj._create_param_when_needed([...

Inherited from Simulate: DESMOND_CMD

Inherited from cmj.StageBase: count, stage_cls, stage_obj

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, *arg, **kwarg)
(Constructor)

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

Overrides: object.__init__

crunch(self)

This is where jobs of this stage are created. This function should be overriden by the subclass.

Overrides: cmj.StageBase.crunch

restart_subjobs(self, jobs)

Subclass should override this if it supports subjob restarting.

Overrides: cmj.StageBase.restart_subjobs: (inherited documentation)

hook_captured_successful_job(self, job)

Overrides: cmj.StageBase.hook_captured_successful_job

Class Variable Details

[hide private]

PARAM

Value:

cmj._create_param_when_needed(["""
    DATA = {
    jobname          = "$MASTERJOBNAME_$STAGENO"
    dir              = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STA
GENO"
    fep.output.name  = "$JOBNAME$[_replica$REPLICA$].dE"
    should_sync      = yes
    solute_tempering = off
...

Class LambdaHopping

__init__(self, *arg, **kwarg) (Constructor)

crunch(self)

restart_subjobs(self, jobs)

hook_captured_successful_job(self, job)

PARAM

init(self, *arg, **kwarg)
(Constructor)