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

Class McproSystemBuilder

         object --+            
                  |            
picklejar.Picklable --+        
                      |        
          cmj.StageBase --+    
                          |    
             McproStageBase --+
                              |
                             McproSystemBuilder

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

_gen_model_sys(self, job)
Constructs a model system for MCPRO+ FEP simulations.

gen_model_sys(self, job)

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

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

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]

initialise(pertdb_file="", pertdb_type=None)

Inherited from McproStageBase: symlink_input

Class Variables

[hide private]

NAME = "mcpro_system_builder"

ZMAT_CMD = os.path.join(envir.CONST.SCHRODINGER_UTILITIES, "mc...

_PERT_ID = None, Picklable

_PERT_TRANS = None, Picklable

_is_inited = False, Picklable

PARAM = cmj._create_param_when_needed([...

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

Class Variable Details

[hide private]

ZMAT_CMD

Value:

os.path.join(envir.CONST.SCHRODINGER_UTILITIES, "mcpro_zmat")

PARAM

Value:

cmj._create_param_when_needed(["""
    DATA = {
    pertdb_file       = ""
    protein_trunc_rad = 12.0
    constraint        = 2        # Corresponds to the '-x' option.
    solvent_cap       = 1        # Corresponds to the '-c' option.
    bond_tolerance    = 0.1      # -bndTol
    angle_tolerance   = 180.0    # -angTol
...

Class McproSystemBuilder

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

crunch(self)

ZMAT_CMD

PARAM

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