Package schrodinger :: Package application :: Package prime :: Module input :: Class Prime

Class Prime

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

Known Subclasses:

bioluminate.protein.PrimeConfig

Class for reading and writing simplified Prime input files.

Example 1:

   config = Prime(keyword_dict)
   config.write("path.inp")

Example 2:

   config = Prime("path.inp")
   inpath = config['STRUCT_FILE']

Example 3:

   config = Prime()
   config['STRUCT_FILE'] = "path.mae"
   config.write("path.inp")

Instance Methods

[hide private]

new empty dictionary

__init__(self, kw=None)
Accepts one argument which is either a path or a keyword dictionary.

write(self, filename)
Writes a simplified input file to filename.

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

Inherited from inputconfig.InputConfig (private): _quote

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

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]

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, kw=None)
(Constructor)

Accepts one argument which is either a path or a keyword dictionary.

Parameters:

infile - The name of the input file.
specs - A list of strings, each in the format <keywordname> = <validator>(<validatoroptions>). An example string is NUM_RINGS = integer(min=1, max=100, default=1). For available validators, see: http://www.voidspace.org.uk/python/validate.html.

Returns: new empty dictionary

Overrides: object.__init__

write(self, filename)

Writes a simplified input file to filename.

This input file needs to be run via $SCHRODINGER/prime.

Overrides: configobj.ConfigObj.write

Class Prime

__init__(self, kw=None) (Constructor)

write(self, filename)

init(self, kw=None)
(Constructor)