Package schrodinger :: Package application :: Package phase :: Module input :: Class PhaseHypothesisInputConfig

Class PhaseHypothesisInputConfig

   object --+                
            |                
         dict --+            
                |            
configobj.Section --+        
                    |        
  configobj.ConfigObj --+    
                        |    
  inputconfig.InputConfig --+
                            |
                           PhaseHypothesisInputConfig

Settings/Validation InputConfig class for the Phase Hypothesis Driver.

The class acts as a container and validator for calling driver property setters through the (keyword, value) interface, or in the case of indexable attributes, the (keyword, index, value).

Instance Methods

[hide private]

new empty dictionary

__init__(self, input_file=None)
Initializes the inputconfig settings with a dictionary of options and corresponding validators.

namedtuple @return : cast of current (validated) settings as a namedtuple

asNamedTuple(self)
Returns the current settings as a validated namedtuple for driver use.

validateKeywords(self)
Validates that all set keywords are supported.

validateAll(self)
Validates all values and keywords, removing entries that are set to None

Inherited from inputconfig.InputConfig: getSpecsString, printout, validateValues, writeInputFile

Inherited from inputconfig.InputConfig (private): _quote

Inherited from configobj.ConfigObj: __repr__, reload, reset, validate, write

Inherited from configobj.ConfigObj (private): _a_to_u, _decode, _decode_element, _get_single_quote, _get_triple_quote, _handle_bom, _handle_comment, _handle_configspec, _handle_error, _handle_value, _initialise, _load, _match_depth, _multiline, _parse, _set_configspec, _str, _unquote, _write_line, _write_marker

Inherited from configobj.Section: __delitem__, __getitem__, __iter__, __reduce__, __setitem__, __setstate__, __str__, as_bool, as_float, as_int, as_list, clear, dict, get, items, iteritems, iterkeys, itervalues, keys, merge, pop, popitem, rename, restore_default, restore_defaults, setdefault, update, values, walk

Inherited from configobj.Section (private): _interpolate

Inherited from dict: __cmp__, __contains__, __eq__, __ge__, __getattribute__, __gt__, __le__, __len__, __lt__, __ne__, __new__, __sizeof__, copy, fromkeys, has_key, viewitems, viewkeys, viewvalues

Inherited from object: __delattr__, __format__, __reduce_ex__, __setattr__, __subclasshook__

Class Variables

[hide private]

PHASE_DEVELOP_HYPOTHESIS_SPEC = ['INPUT_STRUCTURE_FILE ...

Inherited from configobj.ConfigObj (private): _bools, _keyword, _listvalueexp, _multi_line_double, _multi_line_single, _nolistvalue, _sectionmarker, _single_line_double, _single_line_single, _triple_quote, _valueexp

Inherited from dict: __hash__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, input_file=None)
(Constructor)

Initializes the inputconfig settings with a dictionary of options and corresponding validators.

Parameters:

specs_list - list of ConfigObj keyword validators

Returns: new empty dictionary

Overrides: object.__init__

validateKeywords(self)

Validates that all set keywords are supported.

Raises:

ValueError - Error message if keyword is not supported

validateAll(self)

Validates all values and keywords, removing entries that are set to None

Raises:

ValueError - Error message if keyword is not supported

Class Variable Details

[hide private]

PHASE_DEVELOP_HYPOTHESIS_SPEC

Value:

['INPUT_STRUCTURE_FILE              = string()',
 'USE_PREALIGNED_LIGANDS            = boolean(default=False)',
 'ACTIVITY_PROPERTY                 = string(default=None)',
 'USE_GENERATED_CONFORMERS          = boolean(default=False)',
 'MAX_NUMBER_CONFORMERS             = integer(min=1, default=10)',
 'USE_CONFORMER_MINIMIZATION        = boolean(default=False)',
 'REQUIRED_MATCH_FRACTION           = float(min=0.0, max=1.0, default=
0.5)',
...

Class PhaseHypothesisInputConfig

__init__(self, input_file=None) (Constructor)

validateKeywords(self)

validateAll(self)

PHASE_DEVELOP_HYPOTHESIS_SPEC

init(self, input_file=None)
(Constructor)