Package schrodinger :: Package application :: Package glide :: Module glide :: Class Gridgen

Class Gridgen

   object --+                    
            |                    
         dict --+                
                |                
configobj.Section --+            
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  configobj.ConfigObj --+        
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  inputconfig.InputConfig --+    
                            |    
                     GlideJob --+
                                |
                               Gridgen

Class for writing Glide Grid Generation input files. Currently, the receptor input file for a Gridgen job (NOT created by this class) must be named "<jobname>.mae".

Instance Methods

[hide private]

new empty dictionary

__init__(self, keywords)
Specify a dictionary of keywords, where the key is the short keyword name and the value is what is should be set to.

string

setup(self)
Calls appropriate MMIM APIs for all keywords for this instance.

_parseHbondConstraint(self, cons_string)
Parse a string with the format "<label> <atom_index> [nosym]" and return the tuple (label, atomindex, symmetrize).

_setupHbondConstraints(self)

_setupConstraints(self)

cleanup(self)
Free the memory associated with constraings

Inherited from GlideJob: get, getAllowedRange, writeDice, writeSimplified

Inherited from GlideJob (private): _applyKeyword, _getAndApplyKeyword

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, 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, keywords)
(Constructor)


Specify a dictionary of keywords, where the key is the short keyword
name and the value is what is should be set to. For indexed keywords,
the value needs to be a list.
It is also possible to specify a file path to a simplified input file
that contains the keywords.

Constraint sites may be set via the following keywords:
    HBOND_CONSTRAINTS
    METAL_CONSTRAINTS
    POSIT_CONSTRAINTS
    NOE_CONSTRAINTS
    METCOORD_CONSTRAINTS
    METCOORD_SITES

@type keywords: dict or file path
@param keywords: Either a dictionary of keywords or a simplified input file path.

@raise RuntimeError: If no job name specified.

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__

setup(self)

Calls appropriate MMIM APIs for all keywords for this instance.

Returns: string

The input file name.

Raises:

RuntimeError - If the grid specification is incomplete or if there is a problem with a mm.mmim* call.

Overrides: GlideJob.setup

_parseHbondConstraint(self, cons_string)

Parse a string with the format "<label> <atom_index> [nosym]" and return the tuple (label, atomindex, symmetrize). Raises ValueError if the string is invalid for any reason.

cleanup(self)

Free the memory associated with constraings

Overrides: GlideJob.cleanup

Class Gridgen

__init__(self, keywords) (Constructor)

setup(self)

_parseHbondConstraint(self, cons_string)

cleanup(self)

init(self, keywords)
(Constructor)