Index

A

add_quotes_inside_brackets() (in module gMCSpy.Utilities)

B

buildDictionaryDossageNetwork() (in module gMCSpy.ProblemDefinitions) buildDictionaryFBA() (in module gMCSpy.ProblemDefinitions) buildDictionaryFBAWithDeletions() (in module gMCSpy.ProblemDefinitions) buildDictionaryMCSGeneProblem() (in module gMCSpy.ProblemDefinitions) buildDictionaryMCSGeneTargetedProblem() (in module gMCSpy.ProblemDefinitions) buildDictionaryMCSProblem() (in module gMCSpy.ProblemDefinitions)

buildDictionaryMCSTargetedProblem() (in module gMCSpy.ProblemDefinitions) buildDictionaryReactionsFBAWithDeletions() (in module gMCSpy.ProblemDefinitions) buildDictionaryRegNetwork() (in module gMCSpy.ProblemDefinitions) buildGMatrix() (in module gMCSpy.calculateGMCS) buildReactionFromBranch() (in module gMCSpy.calculateGMCS) buildRxnGeneMat() (in module gMCSpy.calculateGMCS)

C

calculate_GPR_MCS() (in module gMCSpy.calculateGMCS) calculateGeneMCS() (in module gMCSpy.calculateGMCS) calculateMCS() (in module gMCSpy.calculateMCS) calculateMCSForGPRs() (in module gMCSpy.calculateGMCS) checkFromReaction() (in module gMCSpy.Validations) checkGMCS() (in module gMCSpy.Validations)

checkGMCSChild() (in module gMCSpy.Validations) checkGMCSParallel() (in module gMCSpy.Validations) cplexProblemInterpreter() (in module gMCSpy.ProblemInterpreters) createLog() (in module gMCSpy.Utilities) createSparseMatrix() (in module gMCSpy.calculateGMCS) createToyModel() (in module gMCSpy.Utilities)

G

getGPRDict() (in module gMCSpy.calculateGMCS) gMCSpy.calculateGMCS module gMCSpy.calculateMCS module gMCSpy.ProblemDefinitions module

gMCSpy.ProblemInterpreters module gMCSpy.Utilities module gMCSpy.Validations module gurobiProblemInterpreter() (in module gMCSpy.ProblemInterpreters)

I

initiateLogger() (in module gMCSpy.calculateGMCS)

L

loadSolutions() (in module gMCSpy.Utilities)

M

mergeIsforms() (in module gMCSpy.calculateGMCS) module gMCSpy.calculateGMCS gMCSpy.calculateMCS gMCSpy.ProblemDefinitions gMCSpy.ProblemInterpreters gMCSpy.Utilities gMCSpy.Validations

P

parseGPRToModel() (in module gMCSpy.calculateGMCS)

R

read_sol_log() (in module gMCSpy.Utilities)

readjustmentProblem() (in module gMCSpy.ProblemDefinitions) relatedRows() (in module gMCSpy.calculateGMCS)

S

saveSolutionDict() (in module gMCSpy.Utilities) saveSolutions() (in module gMCSpy.Utilities)

scipProblemInterpreter() (in module gMCSpy.ProblemInterpreters) setSolver() (in module gMCSpy.Utilities) simplifyGMatrix() (in module gMCSpy.calculateGMCS)

T

transformReactionIdsIntoIndexes() (in module gMCSpy.calculateGMCS)