bionetgen.atomizer.rulifier package
Submodules
bionetgen.atomizer.rulifier.arial10 module
Character width dictionary and convenience functions for column sizing with xlwt when Arial 10 is the standard font. Widths were determined experimentally using Excel 2000 on Windows XP. I have no idea how well these will work on other setups. For example, I don’t know if system video settings will affect the results. I do know for sure that this module won’t be applicable to other fonts in general. //John Yeung 2009-09-02
bionetgen.atomizer.rulifier.compareModels module
bionetgen.atomizer.rulifier.componentGroups module
- bionetgen.atomizer.rulifier.componentGroups.analyzeDependencies(componentStateCollection, state, moleculeName, molecules, dependencies)[source]
- bionetgen.atomizer.rulifier.componentGroups.askQuestions(inputfile, molecule, center, context=None)[source]
- bionetgen.atomizer.rulifier.componentGroups.componentStateSize(molecules, moleculeName, componentName)[source]
- bionetgen.atomizer.rulifier.componentGroups.defineConsole()[source]
defines the program console line commands
- bionetgen.atomizer.rulifier.componentGroups.extractCenterContext(rules, excludeReverse=False)[source]
- bionetgen.atomizer.rulifier.componentGroups.getChemicalStates(rules)[source]
goes through a list of rules and creates a dictionary (molecules) of possible chemical states of its components
- bionetgen.atomizer.rulifier.componentGroups.getContextRequirements(inputfile, collapse=True, motifFlag=False, excludeReverse=False)[source]
Receives a BNG-XML file and returns the contextual dependencies implied by this file
- bionetgen.atomizer.rulifier.componentGroups.getMotifRelationships(stateDictionary, molecules)[source]
- bionetgen.atomizer.rulifier.componentGroups.getMutualExclusions(stateDictionary, molecules)[source]
- bionetgen.atomizer.rulifier.componentGroups.getRestrictedChemicalStates(labelArray, products, contexts, doubleAction)[source]
goes through a list of reaction center and their associated context and creates a dictionary of molecules of possible chemical states
- bionetgen.atomizer.rulifier.componentGroups.molecule2stateTuples(molecule)[source]
Receives a molecule structure, returns a tuple detailing the state of the contained states
- bionetgen.atomizer.rulifier.componentGroups.removeIndirectDependencies(dependencies, stateSpace, motifFlag=False)[source]
goes through the list of dependencies and search for those states that requires more than 1 condition. If true, it will check if any of the set of prerequirements is a sufficient conditions for any of the other prerequirements to be valid. If true it will remove those redundant prerequirements them
bionetgen.atomizer.rulifier.parameterExtraction module
bionetgen.atomizer.rulifier.postAnalysis module
- class bionetgen.atomizer.rulifier.postAnalysis.ModelLearning(fileName, rawFileName=None)[source]
Bases:
object- analyzeRedundantBonds(assumptions)[source]
Analyzes a system of molecules with redundant bonds between them (more than one path between any two nodes in the system). The function attemps to score the bonds by looking out for partial competition relationships (e.g. the presence of one component excludes the activation of another, but in the other direction we see independence) which are less likely to occur than a fully independence relationship. The method will thus nominate such edges for deletion if the overall systems still forms a fully connected graph after the bond removal.
- classifyPairsByMotif(reverseDependencies)[source]
recives a dict arranged by molecule->componentPair->dependency
organizes molecule pairs by a concept called ‘motif’
- getContextMotifInformation()[source]
returns the reactions in the system classified by context-component motif pairs. e.g. a requirement,nullrequirement motif pair is a pair of components A->B such that B needs for A to be activated to activate, whereas A needs for B to be inactivated to activate.
- bionetgen.atomizer.rulifier.postAnalysis.defineConsole()[source]
defines the program console line commands
- bionetgen.atomizer.rulifier.postAnalysis.resolveEntry(dependencyGraph, moleculeSet)[source]
resolve an entry to its basic components according to dependency graph >>> dependencyGraph = {‘EGF_EGFR_2’:[[‘EGF_EGFR’,’EGF_EGFR’]],’EGF_EGFR’:[[‘EGF’,’EGFR’]],’EGFR’:[],’EGF’:[]} >>> resolveEntry(dependencyGraph, [‘EGF_EGFR_2’]) [‘EGF’, ‘EGFR’, ‘EGF’, ‘EGFR’]