PySCes interface code for systems biology modeling and SBML model
markup.
This toolbox assumes you have PySCes installed.
R. Clewley, 2012
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acosh
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replaceSepStr
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newton_meth
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norm
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float96
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protected_randomnames
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ONES
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typeCounter
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specialfns
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ensuredecimalconst
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toCircumflexSyntax
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mathlookup
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Continuous = Continuous Domain
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toPowSyntax
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rerr = <PyDSTool.Redirector.Redirector object at 0x1686e50>
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sym2name
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sinh = <ufunc 'sinh'>
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getlftrtD
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doadd
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less_equal = <ufunc 'less_equal'>
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replaceCallsWithDummies
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randomlookup
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cPickle
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replaceSepQSpec
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feval_map_const
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protected_auxnamesDB = ModelSpec internal helper class: auxfnD...
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Inf = inf
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specTypes = ( ' RHSfuncSpec ' , ' ImpFuncSpec ' , ' ExpFuncSpec ' )
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MReg
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logical_or = <ufunc 'logical_or'>
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errorfields = { 0: [ ' t ' , ' error info ' ] , 10: [ ' t ' , ' event list ' ] }
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tan = <ufunc 'tan'>
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math_dir
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atanh
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name_chars_RE
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temp_macro_names_inv
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arccos = <ufunc 'arccos'>
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isVectorClause
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POW_STR
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convert_power_reserved_keywords
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W_NONTERMSTATEBD = 21
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predicate_op
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cosh = <ufunc 'cosh'>
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arcsinh = <ufunc 'arcsinh'>
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dsInterface
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inverseMathNameMap = { ' Random ' : ' Random ' , ' SystemRandom ' : ' Sys ...
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degrees = <ufunc 'degrees'>
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greater = <ufunc 'greater'>
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E_NONUNIQUETERM = 10
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radians = <ufunc 'radians'>
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sin = <ufunc 'sin'>
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symbolMapClass
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token
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API = API_class()
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fmod = <ufunc 'fmod'>
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ensureints
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API_class
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funcnames
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mathNameMap = { ' Abs ' : ' abs ' , ' Acos ' : ' acos ' , ' Asin ' : ' asin ' , ' ...
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alphabet_chars_RE
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re
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contained = contained
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toDoubleStarSyntax
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protected_allnames = [ ' acos ' , ' asin ' , ' atan ' , ' atan2 ' , ' ceil ' , ...
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ensureparen
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traceback
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math_globals
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ZEROS
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reserved_keywords
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arctan2 = <ufunc 'arctan2'>
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ldexp = <ufunc 'ldexp'>
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mapNames
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trysimple
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replaceSep
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complex192
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temp_macro_names
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arctanh = <ufunc 'arctanh'>
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string2ast
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W_UNCERTVAL = 0
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null_predicate_class
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rout = <PyDSTool.Redirector.Redirector object at 0x1686550>
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dodiv
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parserObject
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simplify
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minpack
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feature_node
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isNameToken
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W_TERMSTATEBD = 11
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fit_function
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exp = <ufunc 'exp'>
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DO_POW
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nameResolver = ModelSpec internal helper class: nameResolver o...
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DomainType
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findEndBrace
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frexp = <ufunc 'frexp'>
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simplify_str
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mapPowStr
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ceil = <ufunc 'ceil'>
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builtin_auxnames
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ensurebare
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regObject
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targetLangs = [ ' c ' , ' python ' , ' matlab ' ]
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allmathnames = [ ' acos ' , ' asin ' , ' atan ' , ' atan2 ' , ' ceil ' , ' cos ' ...
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isnan = <ufunc 'isnan'>
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strIfSeq
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feval_map_symb
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isIntegerToken
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protected_specialfns
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cos = <ufunc 'cos'>
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theGenSpecHelper = GenSpecHelper()
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feature_leaf
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whoQ
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dofun
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replaceSepListInv
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HAVE_PSYCO = True
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replaceSepInv
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protected_mathnames
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utils_info
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pi = 3.14159265359
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asinh
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arcsin = <ufunc 'arcsin'>
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doneg
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accrueCompTypes
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count_sep
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uncertain = uncertain
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protected_macronames
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tanh = <ufunc 'tanh'>
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DO_DEC
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builtinlookup
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getdim
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fabs = <ufunc 'fabs'>
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NaN = nan
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sqrt = <ufunc 'sqrt'>
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complex
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ensureparen_div
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LargestInt32 = 2147483647
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allCompTypes
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splitargs
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splitastLR
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dopower
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TENS
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processMultiDef
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W_NONTERMEVENT = 20
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joinStrs
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qtypes
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less = <ufunc 'less'>
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W_TERMEVENT = 10
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verstr_parts = [ ' 0 ' , ' 7 ' , ' 0 ' ]
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errmessages = { 0: ' Computation of trajectory failed ' , 10: ' Mor ...
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process_raw_residual
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W_BISECTLIMIT = 12
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isNumericToken
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isHierarchicalName
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genDB = Generator internal database class: []
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mod = <ufunc 'remainder'>
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builtinFnSigInfo
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warnfields = { 0: [ ' value ' , ' interval ' ] , 10: [ ' t ' , ' event list ' ...
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Macheps
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hypot = <ufunc 'hypot'>
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ast2string
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domul
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remove_indices_from_range
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null_predicate = null_predicate_class(None)
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collect_numbers
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modf = <ufunc 'modf'>
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power = <ufunc 'power'>
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syms
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Discrete = Discrete Domain
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findNumTailPos
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makeParList
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num_chars
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readArgs
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notcontained = notcontained
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symbolMapDict = { }
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resolveSpecTypeCombos
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joinAsStrs
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proper_match
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log = <ufunc 'log'>
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allmathnames_symbolic = [ ' Acos ' , ' Asin ' , ' Atan ' , ' Atan2 ' , ' Cei ...
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log10 = <ufunc 'log10'>
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ast2shortlist
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modlookup
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isToken
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replaceSepList
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dosub
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arccosh = <ufunc 'arccosh'>
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parser
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E_COMPUTFAIL = 0
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parseMatrixStrToDictStr
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warnmessages = { 0: ' Uncertain value computed ' , 10: ' Terminal e ...
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floor = <ufunc 'floor'>
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arctan = <ufunc 'arctan'>
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local_fndef
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protected_scipynames
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symbol
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e = 2.71828182846
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NAMESEP
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_seq_types = ( <type 'list'>, <type 'tuple'>, <type 'numpy.ndar...
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_num_types = ( <type 'float'>, <type 'int'>, <type 'numpy.float...
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isfinite = <ufunc 'isfinite'>
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sign = <ufunc 'sign'>
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allODEgens = [ ' Radau_ODEsystem ' , ' ADMC_ODEsystem ' , ' Vode_ODEsy ...
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_functions = [ ' get_nineml_model ' ]
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_classes = [ ' NineMLModel ' ]
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_features = [ ]
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ALLOW_THREADS = 1
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Abs = Abs (ModelSpec wrapper)
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Acos = Acos (ModelSpec wrapper)
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Asin = Asin (ModelSpec wrapper)
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Atan = Atan (ModelSpec wrapper)
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Atan2 = Atan2 (ModelSpec wrapper)
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BUFSIZE = 10000
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Betavariate = Betavariate (ModelSpec wrapper)
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CLIP = 0
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Ceil = Ceil (ModelSpec wrapper)
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Choice = Choice (ModelSpec wrapper)
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Cos = Cos (ModelSpec wrapper)
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Cosh = Cosh (ModelSpec wrapper)
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Degrees = Degrees (ModelSpec wrapper)
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E = QuantSpec e (ExpFuncSpec)
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ERR_CALL = 3
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ERR_DEFAULT = 0
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ERR_DEFAULT2 = 2084
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ERR_IGNORE = 0
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ERR_LOG = 5
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ERR_PRINT = 4
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ERR_RAISE = 2
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ERR_WARN = 1
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Exp = Exp (ModelSpec wrapper)
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Expovariate = Expovariate (ModelSpec wrapper)
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FLOATING_POINT_SUPPORT = 1
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FPE_DIVIDEBYZERO = 1
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FPE_INVALID = 8
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FPE_OVERFLOW = 2
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FPE_UNDERFLOW = 4
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Fabs = Fabs (ModelSpec wrapper)
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False_ = False
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Floor = Floor (ModelSpec wrapper)
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Fmod = Fmod (ModelSpec wrapper)
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Frexp = Frexp (ModelSpec wrapper)
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Gammavariate = Gammavariate (ModelSpec wrapper)
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Gauss = Gauss (ModelSpec wrapper)
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Getrandbits = Getrandbits (ModelSpec wrapper)
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Getstate = Getstate (ModelSpec wrapper)
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Hypot = Hypot (ModelSpec wrapper)
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Infinity = inf
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Jumpahead = Jumpahead (ModelSpec wrapper)
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Ldexp = Ldexp (ModelSpec wrapper)
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Log = Log (ModelSpec wrapper)
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Log10 = Log10 (ModelSpec wrapper)
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Lognormvariate = Lognormvariate (ModelSpec wrapper)
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MAXDIMS = 32
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Max = Max (ModelSpec wrapper)
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Min = Min (ModelSpec wrapper)
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Modf = Modf (ModelSpec wrapper)
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NAN = nan
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NINF = -inf
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NZERO = -0.0
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Normalvariate = Normalvariate (ModelSpec wrapper)
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PINF = inf
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PZERO = 0.0
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Paretovariate = Paretovariate (ModelSpec wrapper)
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Pi = QuantSpec pi (ExpFuncSpec)
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Pow = Pow (ModelSpec wrapper)
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RAISE = 2
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Radians = Radians (ModelSpec wrapper)
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Randint = Randint (ModelSpec wrapper)
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Random = Random (ModelSpec wrapper)
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Randrange = Randrange (ModelSpec wrapper)
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SHIFT_DIVIDEBYZERO = 0
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SHIFT_INVALID = 9
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SHIFT_OVERFLOW = 3
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SHIFT_UNDERFLOW = 6
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Sample = Sample (ModelSpec wrapper)
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ScalarType = ( <type 'int'>, <type 'float'>, <type 'complex'>, ...
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Seed = Seed (ModelSpec wrapper)
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Setstate = Setstate (ModelSpec wrapper)
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Shuffle = Shuffle (ModelSpec wrapper)
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Sin = Sin (ModelSpec wrapper)
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Sinh = Sinh (ModelSpec wrapper)
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Sqrt = Sqrt (ModelSpec wrapper)
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Sum = Sum (ModelSpec wrapper)
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Systemrandom = Systemrandom (ModelSpec wrapper)
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Tan = Tan (ModelSpec wrapper)
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Tanh = Tanh (ModelSpec wrapper)
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True_ = True
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UFUNC_BUFSIZE_DEFAULT = 10000
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UFUNC_PYVALS_NAME = ' UFUNC_PYVALS '
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Uniform = Uniform (ModelSpec wrapper)
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Vonmisesvariate = Vonmisesvariate (ModelSpec wrapper)
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WRAP = 1
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Weibullvariate = Weibullvariate (ModelSpec wrapper)
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Wichmannhill = Wichmannhill (ModelSpec wrapper)
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absolute = <ufunc 'absolute'>
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add = <ufunc 'add'>
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bitwise_and = <ufunc 'bitwise_and'>
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bitwise_not = <ufunc 'invert'>
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bitwise_or = <ufunc 'bitwise_or'>
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bitwise_xor = <ufunc 'bitwise_xor'>
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c_ = <numpy.lib.index_tricks.CClass object at 0x115c330>
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cast = {<type 'numpy.int64'>: <function <lambda> at 0x6d0c30>,...
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conj = <ufunc 'conjugate'>
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conjugate = <ufunc 'conjugate'>
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copysign = <ufunc 'copysign'>
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deg2rad = <ufunc 'deg2rad'>
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divide = <ufunc 'divide'>
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equal = <ufunc 'equal'>
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exp2 = <ufunc 'exp2'>
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expm1 = <ufunc 'expm1'>
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floor_divide = <ufunc 'floor_divide'>
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fmax = <ufunc 'fmax'>
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fmin = <ufunc 'fmin'>
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greater_equal = <ufunc 'greater_equal'>
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index_exp = <numpy.lib.index_tricks.IndexExpression object at ...
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inf = inf
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infty = inf
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invert = <ufunc 'invert'>
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isinf = <ufunc 'isinf'>
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left_shift = <ufunc 'left_shift'>
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little_endian = True
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log1p = <ufunc 'log1p'>
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logaddexp = <ufunc 'logaddexp'>
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logaddexp2 = <ufunc 'logaddexp2'>
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logical_and = <ufunc 'logical_and'>
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logical_not = <ufunc 'logical_not'>
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logical_xor = <ufunc 'logical_xor'>
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maximum = <ufunc 'maximum'>
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mgrid = <numpy.lib.index_tricks.nd_grid object at 0x1147490>
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minimum = <ufunc 'minimum'>
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multiply = <ufunc 'multiply'>
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n = 9
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nan = nan
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nbytes = {<type 'numpy.int64'>: 8, <type 'numpy.int16'>: 2, <t...
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negative = <ufunc 'negative'>
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newaxis = None
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nextafter = <ufunc 'nextafter'>
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not_equal = <ufunc 'not_equal'>
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ogrid = <numpy.lib.index_tricks.nd_grid object at 0x1147bb0>
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ones_like = <ufunc 'ones_like'>
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r_ = <numpy.lib.index_tricks.RClass object at 0x115c2f0>
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rad2deg = <ufunc 'rad2deg'>
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reciprocal = <ufunc 'reciprocal'>
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remainder = <ufunc 'remainder'>
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right_shift = <ufunc 'right_shift'>
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rint = <ufunc 'rint'>
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s_ = <numpy.lib.index_tricks.IndexExpression object at 0x115c3f0>
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sctypeDict = { 0: <type 'numpy.bool_'>, 1: <type 'numpy.int8'>, ...
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sctypeNA = { ' ? ' : ' Bool ' , ' B ' : ' UInt8 ' , ' Bool ' : <type 'numpy.bo...
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sctypes = { ' complex ' : [ <type 'numpy.complex64'>, <type 'numpy....
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signbit = <ufunc 'signbit'>
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spacing = <ufunc 'spacing'>
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square = <ufunc 'square'>
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subtract = <ufunc 'subtract'>
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t = ' 0 '
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true_divide = <ufunc 'true_divide'>
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trunc = <ufunc 'trunc'>
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typeDict = { 0: <type 'numpy.bool_'>, 1: <type 'numpy.int8'>, 2...
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typeNA = { ' ? ' : ' Bool ' , ' B ' : ' UInt8 ' , ' Bool ' : <type 'numpy.bool...
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typecodes = { ' All ' : ' ?bhilqpBHILQPfdgFDGSUVOMm ' , ' AllFloat ' : ' ...
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