Package schrodinger :: Package application :: Package glide :: Module glide :: Class Dock

Class Dock

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

Class for generating Glide docking input files.

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.

_mungeBeforeValidation(self)

setLigRange(self, start, end)
Shortcut for setting the range of ligands to be read from the LIGANDFILE.

_checkPeptide(self, val)
Return True if the PEPTIDE keyword is true or the grid archive is available and was generated using peptide mode.

_checkFlexOH(self)
Return True if the grid file for a docking job exists and was generated using rotatable hydroxyl groups.

_autoLigFormat(self, filename)

_defaultsTable(self)

_conflictsTable(self)

checkConflicts(self)
Check for invalid keyword combinations.

_setupCombiGlide(self, jsdict)
Copy the values from certain CG_* keywords to the equivalent "pure Glide" keyword.

applyContextDependentDefaults(self)
Apply context-dependent defaults for a Glide job.

_setupPhase(self, jsdict)
Make sure that the Phase keywords make sense before writing a JSON file.

setupJson(self, jsdict)
Additional setup to do before writing a JSON file.

_setupJsonTorcons(self, jsdict)

_gridfile(self)
Return the grid file to use, normally just the value of the GRIDFILE keyword, but sometimes based on legacy keywords for compatibility.

_featfile(self)

_setupConstraints(self, write_featfile=False)

cleanup(self)
Free up the group handles

addConstraintGroup(self, cons_labels, nrequired)
Add a new constraint group to this Docking instance.

useConstraint(self, label)
Adds specified constraint to the first group.

setNRequired(self, nrequired)
Set the minimum number of constraints required for the first group.

_setupTorCons(self)

Inherited from GlideJob: checkForceFieldLicense, get, getAllowedRange, validateValues, writeJSON, writeSimplified

Inherited from GlideJob (private): _applyKeyword, _getAndApplyKeyword

Inherited from inputconfig.InputConfig: getSpecsString, printout, 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.

Parameters:

keywords (dict or file path) - Either a dictionary of keywords or a simplified input file path.

Returns: new empty dictionary

Overrides: object.__init__

_mungeBeforeValidation(self)

Overrides: GlideJob._mungeBeforeValidation

setLigRange(self, start, end)

Shortcut for setting the range of ligands to be read from the LIGANDFILE.

Parameters:

end - If zero, means to go to the end of the file.

checkConflicts(self)

Check for invalid keyword combinations. Raises a ValueError if any are found.

Overrides: GlideJob.checkConflicts: (inherited documentation)

applyContextDependentDefaults(self)

Apply context-dependent defaults for a Glide job. It modifies the job object, but marks the modified keywords as "default" so they won't be written by writeSimplified().

Overrides: GlideJob.applyContextDependentDefaults: (inherited documentation)

setupJson(self, jsdict)

Additional setup to do before writing a JSON file. Base implementation does nothing. This method is expected not to modify 'self', but only jsdict, which is the dictionary of keywords that ultimately will be written to the JSON file.

Overrides: GlideJob.setupJson: (inherited documentation)

cleanup(self)

Free up the group handles

Overrides: GlideJob.cleanup

addConstraintGroup(self, cons_labels, nrequired)

Add a new constraint group to this Docking instance.

Parameters:

cons_labels - A list of labels for constraints to use.
nrequired - Minimum number of constraints required for match (Can be ALL).

useConstraint(self, label)

Adds specified constraint to the first group.

Default group is #1; constraint type determined automatically.

setNRequired(self, nrequired)

Set the minimum number of constraints required for the first group. A value of ALL means all constraints are required.

Class Dock

__init__(self, keywords) (Constructor)

_mungeBeforeValidation(self)

setLigRange(self, start, end)

checkConflicts(self)

applyContextDependentDefaults(self)

setupJson(self, jsdict)

cleanup(self)

addConstraintGroup(self, cons_labels, nrequired)

useConstraint(self, label)

setNRequired(self, nrequired)

init(self, keywords)
(Constructor)