Package schrodinger :: Package application :: Package bioluminate :: Module protein :: Class PrimeConfig

Class PrimeConfig

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

Class containing the methods to write Prime input files.

Instance Methods

[hide private]

new empty dictionary

__init__(self, st_filename, set_defaults=True, **kwargs)
Accepts one argument which is either a path or a keyword dictionary.

addResidues(self, residues=None)
Adds residues to consider for refinement.

prepEnergy(self)

prepMinimize(self, residues=None)

prepResidue(self, residues=None)

prepSidechain(self, residues=None)

prepSidechainCBeta(self, residues=None)

prepSidechainBB(self, residues=None)

prepActive(self, lig_id, residues=None)

prepLoop(self, start_res=None, end_res=None, res_sphere=7.5, maxcalpha=None, protocol='LOOP_BLD', loop2=None, max_jobs=0, residues=None)

prepAntibodyLoop(self, start_res=None, end_res=None, cpus=1, residues=None)

prepBldStruct(self, jobname, dirname)

Inherited from prime.input.Prime: write

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]

ALL_RESIDUES = 'all'

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, st_filename, set_defaults=True, **kwargs)
(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__

(inherited documentation)

addResidues(self, residues=None)

Adds residues to consider for refinement. The passed in argument can take the form of:

ASL expression
List of schrodinger.structure._Residue objects
'all'
None

prepLoop(self, start_res=None, end_res=None, res_sphere=7.5, maxcalpha=None, protocol=`'LOOP_BLD'`, loop2=None, max_jobs=0, residues=None)

Parameters:

start_res (string) - loop start residue, e.g. A:15
end_res (string) - loop start residue, e.g. A:20
res_sphere (float) - radius of nearby residue refinement
maxcalpha (float) - CA atom movement constraint
protocol (string) - loop refinement protocol
loop2 (list) - the definition of the second loop, e.g. ['A:4','A:6']
residues (None) - Unused, kept for API compatibility
max_jobs (int) - how many processes will be run simultaneously

Class PrimeConfig

__init__(self, st_filename, set_defaults=True, **kwargs) (Constructor)

addResidues(self, residues=None)

prepLoop(self, start_res=None, end_res=None, res_sphere=7.5, maxcalpha=None, protocol='LOOP_BLD', loop2=None, max_jobs=0, residues=None)

init(self, st_filename, set_defaults=True, **kwargs)
(Constructor)

prepLoop(self, start_res=None, end_res=None, res_sphere=7.5, maxcalpha=None, protocol=`'LOOP_BLD'`, loop2=None, max_jobs=0, residues=None)