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Package CHEM :: Package CombiCDB :: Module ReactionModel :: Class SMIRKSReagent
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Class SMIRKSReagent



           object --+            
                    |            
                 dict --+        
                        |        
Common.Model.RowItemModel --+    
                            |    
                  BaseReagent --+
                                |
                               SMIRKSReagent
Specific implementation of BaseReagent that uses SMIRKS string processing to execute the transformations.

Instance Methods [hide private]
 
__init__(self, initData=None, dataKeys=None)
Constructor, based on same dictionary arrangement of text-based key-value properties which are parsed by the loadTextProperties method.
 
loadTextProperties(self)
Parse text-based key-value properties into actual objects, numbers, lists, etc.
 
generateProducts(self, reactants, supplementalData=None)
Main method for generating / predicting products from some input reactants.
 
retro(self)
Return a new Reagent model which is the retro / inverse version of the current one.
 
__recursiveGeneration(self, reactants, depth=0, requiredReactant=None, trackingData=None, supplementalData=None)
Returns any products generated in this step AND all subsequent recursions requiredReactant: If specified, should match one of the provided reactants.
 
__singleStepGeneration(self, reactants, requiredReactant=None, trackingData=None, supplementalData=None)
Single reaction step vs.
 
__addToFinalProductList(self, product, productSmilesList, acceptedProductList, depth, trackingData=None, supplementalData=None)
 
__allComponentCombinations(self, componentSubProductsList, currentList=None)
componentSubProductsList is a list of sub product lists.
 
__worstWarningLevel(self, level1, message1, level2, message2)
Given a pair of warning_level_ids with their respective warning_messages, return the warning of greater severity, and combine the warning messages.

Inherited from BaseReagent: __call__, __str__, html, isRetro, postProcess, postProcessing

Inherited from Common.Model.RowItemModel: update, valuesByName

Inherited from dict: __cmp__, __contains__, __delitem__, __eq__, __ge__, __getattribute__, __getitem__, __gt__, __hash__, __iter__, __le__, __len__, __lt__, __ne__, __new__, __repr__, __setitem__, clear, copy, fromkeys, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, values

Inherited from object: __delattr__, __reduce__, __reduce_ex__, __setattr__

Static Methods [hide private]
 
loadDBInstances(reagentSearchModel=None, conn=None)
Return a list of reagent objects based on data loaded from the database.
Class Variables [hide private]
  reactionProfileList = <CHEM.DB.rdb.search.NameRxnPatternMatchi...
  reactionProcessor = <CHEM.DB.rdb.search.NameRxnPatternMatching...
  requiredAtomicNums = REQUIRED_ATOMIC_NUMS

Inherited from BaseReagent: countIntermediates, enforceRetroReactions, ignoreSelfReactions, inherentProductSmiSet, inherentProducts, inherentReactants, originalReagent, removeInherentProducts

Inherited from Common.Model.RowItemModel: childData, index, isNew, mol, newCount, tableName

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

loadDBInstances(reagentSearchModel=None, conn=None)
Static Method

  
Return a list of reagent objects based on data loaded from the database.  

reagentSearchModel
    Simple struct containing various query parameters

__init__(self, initData=None, dataKeys=None)
(Constructor)

 
Constructor, based on same dictionary arrangement of text-based key-value properties which are parsed by the loadTextProperties method.
Overrides: BaseReagent.__init__

loadTextProperties(self)

 
Parse text-based key-value properties into actual objects, numbers, lists, etc.
Overrides: BaseReagent.loadTextProperties

generateProducts(self, reactants, supplementalData=None)

 

Main method for generating / predicting products from some input reactants.

Although this can be called directly, it is advised to use the __call__ construct instead. That is a wrapper method with additional functions such as post-processing of generated products and automatic enumeration of reactant stereoisomers.
Overrides: BaseReagent.generateProducts

retro(self)

 
Return a new Reagent model which is the retro / inverse version of the current one. Will only produce meaningful results if the starting reagent is properly setup with "retro_ready" reaction profiles.
Overrides: BaseReagent.retro

__recursiveGeneration(self, reactants, depth=0, requiredReactant=None, trackingData=None, supplementalData=None)

  
Returns any products generated in this step AND all subsequent recursions

requiredReactant:
    If specified, should match one of the provided reactants.  Only accept
    reaction products where this reactant was used (i.e., where it does
    NOT appear UNmodified in the product).

__singleStepGeneration(self, reactants, requiredReactant=None, trackingData=None, supplementalData=None)

  
Single reaction step vs. general case which may have multiple recursions

requiredReactant:
    If specified, should match one of the provided reactants.  Only accept
    reaction products where this reactant was used (i.e., where it does
    NOT appear UNmodified in the product).

__allComponentCombinations(self, componentSubProductsList, currentList=None)

 
componentSubProductsList is a list of sub product lists. Pick one from each list, in every combination, to yield a composite product.

Class Variable Details [hide private]

reactionProfileList

Value:
None

reactionProcessor

Value:
None

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