libSBML Python API  5.11.0
libsbml.ASTNode Class Reference
Inheritance diagram for libsbml.ASTNode:
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Detailed Description

Abstract Syntax Trees for mathematical expressions.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

Abstract Syntax Trees (ASTs) are a simple kind of data structure used in libSBML for storing mathematical expressions. LibSBML ASTs provide a canonical, in-memory representation for all mathematical formulas regardless of their original format (which might be MathML or might be text strings).

An AST node in libSBML is a recursive tree structure; each node has a type, a pointer to a value, and a list of children nodes. Each ASTNode node may have none, one, two, or more children depending on its type. There are node types to represent numbers (with subtypes to distinguish integer, real, and rational numbers), names (e.g., constants or variables), simple mathematical operators, logical or relational operators and functions. The following diagram illustrates an example of how the mathematical expression '1 + 2' is represented as an AST with one plus node having two integer children nodes for the numbers 1 and 2. The figure also shows the corresponding MathML representation:
Example AST representation of a mathematical expression.
Infix AST MathML
1 + 2 <math xmlns="http://www.w3.org/1998/Math/MathML">
  <apply>
    <plus/>
    <cn type="integer"> 1 </cn>
    <cn type="integer"> 2 </cn>
  </apply>
</math>

The following are other noteworthy points about the AST representation in libSBML:

  • A numerical value represented in MathML as a real number with an exponent is preserved as such in the AST node representation, even if the number could be stored in a float data type. This is done so that when an SBML model is read in and then written out again, the amount of change introduced by libSBML to the SBML during the round-trip activity is minimized.
  • The children of an ASTNode are other ASTNode objects. The list of children is empty for nodes that are leaf elements, such as numbers. For nodes that are actually roots of expression subtrees, the list of children points to the parsed objects that make up the rest of the expression.

For many applications, the details of ASTs are irrelevant because libSBML provides text-string based translation functions such as formulaToL3String() and parseL3Formula(). If you find the complexity of using the AST representation of expressions too high for your purposes, perhaps the string-based functions will be more suitable.

The set of possible ASTNode types

Every ASTNode has an associated type code to indicate whether, for example, it holds a number or stands for an arithmetic operator.

The type is recorded as a value drawn from a set of static integer constants defined in the class libsbml. Their names begin with the characters AST_.The list of possible types is quite long, because it covers all the mathematical functions that are permitted in SBML. The values are shown in the following table:

AST_CONSTANT_E AST_FUNCTION_COT AST_LOGICAL_NOT
AST_CONSTANT_FALSE AST_FUNCTION_COTH AST_LOGICAL_OR
AST_CONSTANT_PI AST_FUNCTION_CSC AST_LOGICAL_XOR
AST_CONSTANT_TRUE AST_FUNCTION_CSCH AST_MINUS
AST_DIVIDE AST_FUNCTION_DELAY AST_NAME
AST_FUNCTION AST_FUNCTION_EXP AST_NAME_AVOGADRO (Level 3 only)
AST_FUNCTION_ABS AST_FUNCTION_FACTORIAL AST_NAME_TIME
AST_FUNCTION_ARCCOS AST_FUNCTION_FLOOR AST_PLUS
AST_FUNCTION_ARCCOSH AST_FUNCTION_LN AST_POWER
AST_FUNCTION_ARCCOT AST_FUNCTION_LOG AST_RATIONAL
AST_FUNCTION_ARCCOTH AST_FUNCTION_PIECEWISE AST_REAL
AST_FUNCTION_ARCCSC AST_FUNCTION_POWER AST_REAL_E
AST_FUNCTION_ARCCSCH AST_FUNCTION_ROOT AST_RELATIONAL_EQ
AST_FUNCTION_ARCSEC AST_FUNCTION_SEC AST_RELATIONAL_GEQ
AST_FUNCTION_ARCSECH AST_FUNCTION_SECH AST_RELATIONAL_GT
AST_FUNCTION_ARCSIN AST_FUNCTION_SIN AST_RELATIONAL_LEQ
AST_FUNCTION_ARCSINH AST_FUNCTION_SINH AST_RELATIONAL_LT
AST_FUNCTION_ARCTAN AST_FUNCTION_TAN AST_RELATIONAL_NEQ
AST_FUNCTION_ARCTANH AST_FUNCTION_TANH AST_TIMES
AST_FUNCTION_CEILING AST_INTEGER AST_UNKNOWN
AST_FUNCTION_COS AST_LAMBDA
AST_FUNCTION_COSH AST_LOGICAL_AND

The types have the following meanings:

  • If the node is a predefined function or operator from SBML Level 1 (in the string-based formula syntax used in Level 1) or SBML Level 2 and 3 (in the subset of MathML used in SBML Levels 2 and 3), then the node's type will be either AST_FUNCTION_X, AST_LOGICAL_X, or AST_RELATIONAL_X, as appropriate. (Examples: AST_FUNCTION_LOG, AST_RELATIONAL_LEQ.)
  • If the node refers to a user-defined function, the node's type will be AST_FUNCTION (because it holds the name of the function).
  • If the node is a lambda expression, its type will be AST_LAMBDA.
  • (Levels 2 and 3 only) If the node is the special MathML csymbol time, the value of the node will be AST_NAME_TIME. (Note, however, that the MathML csymbol delay is translated into a node of type AST_FUNCTION_DELAY. The difference is due to the fact that time is a single variable, whereas delay is actually a function taking arguments.)
  • (Level 3 only) If the node is the special MathML csymbol avogadro, the value of the node will be AST_NAME_AVOGADRO.

Converting between ASTs and text strings

The text-string form of mathematical formulas produced by formulaToString() and formulaToL3String(), and read by parseFormula() and parseL3Formula(), are in a simple C-inspired infix notation. A formula in one of these two text-string formats can be handed to a program that understands SBML mathematical expressions, or used as part of a translation system. The libSBML distribution comes with example programs in the 'examples' subdirectory that demonstrate such things as translating infix formulas into MathML and vice-versa.

Please see the documentation for the functions parseFormula() and parseL3Formula() for detailed explanations of the infix syntax they accept.

Historical notes

Readers may wonder why this part of libSBML uses a seemingly less object-oriented design than other parts. Originally, much of libSBML was written in C. All subsequent development was done in C++, but the complexity of some of the functionality for converting between infix, AST and MathML, coupled with the desire to maintain stability and backward compatibility, means that some of the underlying code is still written in C. This has lead to the exposed API being more C-like.

See also
parseL3Formula()
parseL3FormulaWithSettings()
parseL3FormulaWithModel()
parseFormula()
formulaToL3StringWithSettings()
formulaToL3String()
formulaToString()
getDefaultL3ParserSettings()

Public Member Functions

def __init__ (self, args)
  Abstract Syntax Trees for mathematical expressions. More...
 
def addChild (self, disownedChild)
 Adds the given node as a child of this ASTNode. More...
 
def addSemanticsAnnotation (self, disownedAnnotation)
 Adds the given XMLNode as a MathML <semantics> element to this ASTNode. More...
 
def canonicalize (self)
 Converts this ASTNode to a canonical form. More...
 
def deepCopy (self)
 Creates a recursive copy of this node and all its children. More...
 
def freeName (self)
 Frees the name of this ASTNode and sets it to None. More...
 
def getCharacter (self)
 Returns the value of this node as a single character. More...
 
def getChild (self, n)
 Returns the child at index n of this node. More...
 
def getClass (self)
 Returns the MathML class attribute value of this ASTNode. More...
 
def getDefinitionURL (self)
 Returns the MathML definitionURL attribute value. More...
 
def getDefinitionURLString (self)
 Returns the MathML definitionURL attribute value as a string. More...
 
def getDenominator (self)
 Returns the value of the denominator of this node. More...
 
def getExponent (self)
 Returns the exponent value of this ASTNode. More...
 
def getExtendedType (self)
 Returns the extended type of this ASTNode. More...
 
def getId (self)
 Returns the MathML id attribute value of this ASTNode. More...
 
def getInteger (self)
 Returns the value of this node as an integer. More...
 
def getLeftChild (self)
 Returns the left child of this node. More...
 
def getListOfNodes (self)
 Returns a list of nodes. More...
 
def getMantissa (self)
 Returns the mantissa value of this node. More...
 
def getName (self)
 Returns the value of this node as a string. More...
 
def getNumChildren (self)
 Returns the number of children of this node. More...
 
def getNumerator (self)
 Returns the value of the numerator of this node. More...
 
def getNumSemanticsAnnotations (self)
 Returns the number of MathML <semantics> element elements on this node. More...
 
def getOperatorName (self)
 Returns the value of this operator node as a string. More...
 
def getParentSBMLObject (self)
 Returns the parent SBML object. More...
 
def getPrecedence (self)
 Returns the precedence of this node in the infix math syntax of SBML Level 1. More...
 
def getReal (self)
 Returns the real-numbered value of this node. More...
 
def getRightChild (self)
 Returns the right child of this node. More...
 
def getSemanticsAnnotation (self, n)
 Returns the nth MathML <semantics> element on this ASTNode. More...
 
def getStyle (self)
 Returns the MathML style attribute value of this ASTNode. More...
 
def getType (self)
 Returns the type of this ASTNode. More...
 
def getUnits (self)
 Returns the units of this ASTNode. More...
 
def hasCorrectNumberArguments (self)
 Returns True if this ASTNode has the correct number of children for its type. More...
 
def hasTypeAndNumChildren (self, type, numchildren)
 Returns True if this node is of a certain type with a specific number of children. More...
 
def hasUnits (self)
 Returns True if this node or any of its children nodes have the attribute sbml:units. More...
 
def insertChild (self, n, disownedChild)
 Inserts the given ASTNode node at a given point in the current ASTNode's list of children. More...
 
def isAvogadro (self)
 Returns True if this node represents the predefined value for Avogadro's constant. More...
 
def isBoolean (self)
 Returns True if this node has a Boolean type. More...
 
def isConstant (self)
 Returns True if this node represents a MathML constant. More...
 
def isFunction (self)
 Returns True if this node represents a function. More...
 
def isInfinity (self)
 Returns True if this node represents the special IEEE 754 value for infinity. More...
 
def isInteger (self)
 Returns True if this node contains an integer value. More...
 
def isLambda (self)
 Returns True if this node is a MathML <lambda>. More...
 
def isLog10 (self)
 Returns True if this node represents a log10 function. More...
 
def isLogical (self)
 Returns True if this node is a MathML logical operator. More...
 
def isName (self)
 Returns True if this node is a user-defined variable name or the symbols for time or Avogadro's constant. More...
 
def isNaN (self)
 Returns True if this node represents the special IEEE 754 value 'not a number' (NaN). More...
 
def isNegInfinity (self)
 Returns True if this node represents the special IEEE 754 value 'negative infinity'. More...
 
def isNumber (self)
 Returns True if this node contains a number. More...
 
def isOperator (self)
 Returns True if this node is a mathematical operator. More...
 
def isPiecewise (self)
 Returns True if this node is the MathML <piecewise> construct. More...
 
def isQualifier (self)
 Predicate returning True if this node is a MathML qualifier. More...
 
def isRational (self)
 Returns True if this node represents a rational number. More...
 
def isReal (self)
 Returns True if this node can represent a real number. More...
 
def isRelational (self)
 Returns True if this node is a MathML relational operator. More...
 
def isSemantics (self)
 Predicate returning True if this node is a MathML semantics node. More...
 
def isSetClass (self)
 Returns True if this node has a value for the MathML attribute class. More...
 
def isSetId (self)
 Returns True if this node has a value for the MathML attribute id. More...
 
def isSetParentSBMLObject (self)
 Returns True if this node has a value for the parent SBML object. More...
 
def isSetStyle (self)
 Returns True if this node has a value for the MathML attribute style. More...
 
def isSetUnits (self)
 Returns True if this node has the attribute sbml:units. More...
 
def isSetUserData (self)
 Returns True if this node has a user data object. More...
 
def isSqrt (self)
 Returns True if this node represents a square root function. More...
 
def isUMinus (self)
 Returns True if this node is a unary minus operator. More...
 
def isUnknown (self)
 Returns True if this node has an unknown type. More...
 
def isUPlus (self)
 Returns True if this node is a unary plus operator. More...
 
def isWellFormedASTNode (self)
 Returns True or False depending on whether this ASTNode is well-formed. More...
 
def prependChild (self, disownedChild)
 Adds the given node as a child of this ASTNode. More...
 
def reduceToBinary (self)
 Reduces this ASTNode to a binary tree. More...
 
def removeChild (self, n)
 Removes the nth child of this ASTNode object. More...
 
def renameSIdRefs (self, oldid, newid)
 Renames all the SIdRef attributes on this node and its child nodes. More...
 
def renameUnitSIdRefs (self, oldid, newid)
 Renames all the UnitSIdRef attributes on this node and its child nodes. More...
 
def replaceArgument (self, bvar, arg)
 Replaces occurrences of a given name with a given ASTNode. More...
 
def replaceChild
 Replaces the nth child of this ASTNode with the given ASTNode. More...
 
def returnsBoolean
 Returns True if this node returns a Boolean value. More...
 
def setCharacter (self, value)
 Sets the value of this ASTNode to the given character. More...
 
def setClass (self, className)
 Sets the MathML attribute class of this ASTNode. More...
 
def setDefinitionURL (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setId (self, id)
 Sets the MathML attribute id of this ASTNode. More...
 
def setName (self, name)
 Sets the value of this ASTNode to the given name. More...
 
def setStyle (self, style)
 Sets the MathML attribute style of this ASTNode. More...
 
def setType (self, type)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setUnits (self, units)
 Sets the units of this ASTNode to units. More...
 
def setValue (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def swapChildren (self, that)
 Swaps the children of this node with the children of another node. More...
 
def unsetClass (self)
 Unsets the MathML class attribute of this ASTNode. More...
 
def unsetId (self)
 Unsets the MathML id attribute of this ASTNode. More...
 
def unsetParentSBMLObject (self)
 Unsets the parent SBML object. More...
 
def unsetStyle (self)
 Unsets the MathML style attribute of this ASTNode. More...
 
def unsetUnits (self)
 Unsets the units of this ASTNode. More...
 
def unsetUserData (self)
 Unsets the user data of this node. More...
 

Member Function Documentation

def libsbml.ASTNode.addChild (   self,
  disownedChild 
)

Adds the given node as a child of this ASTNode.

addChild(ASTNode disownedChild)   int

Child nodes are added in-order, from left to right.

Parameters
disownedChildthe ASTNode instance to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The method ASTNode.isWellFormedASTNode() may also be useful for checking the results of node modifications.
See also
prependChild()
replaceChild()
insertChild()
removeChild()
isWellFormedASTNode()
def libsbml.ASTNode.addSemanticsAnnotation (   self,
  disownedAnnotation 
)

Adds the given XMLNode as a MathML <semantics> element to this ASTNode.

addSemanticsAnnotation(XMLNode disownedAnnotation)   int

The <semantics> element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation> or <annotation-xml> elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.

Parameters
disownedAnnotationthe annotation to add.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Although SBML permits the use of the MathML <semantics> annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.
See also
ASTNode.getNumSemanticsAnnotations()
ASTNode.getSemanticsAnnotation()
def libsbml.ASTNode.canonicalize (   self)

Converts this ASTNode to a canonical form.

canonicalize()   bool

The rules determining the canonical form conversion are as follows:

  • If the node type is AST_NAME and the node name matches 'ExponentialE', 'Pi', 'True' or 'False' the node type is converted to the corresponding AST_CONSTANT_X type.
  • If the node type is an AST_FUNCTION and the node name matches an SBML (MathML) function name, logical operator name, or relational operator name, the node is converted to the corresponding AST_FUNCTION_X or AST_LOGICAL_X type.

SBML Level 1 function names are searched first; thus, for example, canonicalizing log will result in a node type of AST_FUNCTION_LN. (See the SBML Level 1 Version 2 Specification, Appendix C.)

Sometimes, canonicalization of a node results in a structural conversion of the node as a result of adding a child. For example, a node with the SBML Level 1 function name sqr and a single child node (the argument) will be transformed to a node of type AST_FUNCTION_POWER with two children. The first child will remain unchanged, but the second child will be an ASTNode of type AST_INTEGER and a value of 2. The function names that result in structural changes are: log10, sqr, and sqrt.

Returns
True if this node was successfully converted to canonical form, False otherwise.
def libsbml.ASTNode.deepCopy (   self)

Creates a recursive copy of this node and all its children.

deepCopy()   ASTNode
Returns
a copy of this ASTNode and all its children. The caller owns the returned ASTNode and is responsible for deleting it.
def libsbml.ASTNode.freeName (   self)

Frees the name of this ASTNode and sets it to None.

freeName()   int

This operation is only applicable to ASTNode objects corresponding to operators, numbers, or AST_UNKNOWN. This method has no effect on other types of nodes.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.getCharacter (   self)

Returns the value of this node as a single character.

getCharacter()   char

This function should be called only when ASTNode.getType() returns AST_MINUS, AST_TIMES, AST_DIVIDE or AST_POWER.

Returns
the value of this ASTNode as a single character
def libsbml.ASTNode.getChild (   self,
  n 
)

Returns the child at index n of this node.

getChild(long n)   ASTNode
Parameters
nthe index of the child to get
Returns
the nth child of this ASTNode or None if this node has no nth child (n > ASTNode.getNumChildren() - 1).
See also
getNumChildren()
getLeftChild()
getRightChild()
def libsbml.ASTNode.getClass (   self)

Returns the MathML class attribute value of this ASTNode.

getClass()   string
Returns
the MathML class of this ASTNode, if any exists.
See also
isSetClass()
setClass()
unsetClass()
def libsbml.ASTNode.getDefinitionURL (   self)

Returns the MathML definitionURL attribute value.

getDefinitionURL()   XMLAttributes
Returns
the value of the definitionURL attribute, in the form of a libSBML XMLAttributes object.
See also
setDefinitionURL()
setDefinitionURL()
getDefinitionURLString()
def libsbml.ASTNode.getDefinitionURLString (   self)

Returns the MathML definitionURL attribute value as a string.

getDefinitionURLString()   string
Returns
the value of the definitionURL attribute, as a string.
See also
getDefinitionURL()
setDefinitionURL()
setDefinitionURL()
def libsbml.ASTNode.getDenominator (   self)

Returns the value of the denominator of this node.

getDenominator()   long
Returns
the value of the denominator of this ASTNode, or 1 if this node has no numerical value.
Note
This function should be called only when ASTNode.getType() returns AST_RATIONAL. It will return 1 if the node type is another type, but since 1 may be a valid value for the denominator of a rational number, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.
def libsbml.ASTNode.getExponent (   self)

Returns the exponent value of this ASTNode.

getExponent()   long
Returns
the value of the exponent of this ASTNode, or 0 if this is not a type of node that has an exponent.
Note
This function should be called only when ASTNode.getType() returns AST_REAL_E. It will return 0 if the node type is another type, but since 0 may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.
def libsbml.ASTNode.getExtendedType (   self)

Returns the extended type of this ASTNode.

getExtendedType()   int

The type may be either a core integer type codeor a value of a type code defined by an SBML Level 3 package.

Returns
the type of this ASTNode.
Note
When the ASTNode is of a type from a package, the value returned by ASTNode.getType() will be AST_ORIGINATES_IN_PACKAGE and getExtendedType() will return a package-specific type code. To find out the possible package-specific types (if any), please consult the documentation for the particular package.
See also
getType()
def libsbml.ASTNode.getId (   self)

Returns the MathML id attribute value of this ASTNode.

getId()   string
Returns
the MathML id of this ASTNode.
See also
isSetId()
setId()
unsetId()
def libsbml.ASTNode.getInteger (   self)

Returns the value of this node as an integer.

getInteger()   long

If this node type is AST_RATIONAL, this method returns the value of the numerator.

Returns
the value of this ASTNode as a (long) integer.
Note
This function should be called only when ASTNode.getType() returns AST_INTEGER or AST_RATIONAL. It will return 0 if the node type is not one of these, but since 0 may be a valid value for integer, it is important to be sure that the node type is one of the expected types in order to understand if 0 is the actual value.
def libsbml.ASTNode.getLeftChild (   self)

Returns the left child of this node.

getLeftChild()   ASTNode
Returns
the left child of this ASTNode. This is equivalent to calling ASTNode.getChild() with an argument of 0.
See also
getNumChildren()
getChild()
getRightChild()
def libsbml.ASTNode.getListOfNodes (   self)

Returns a list of nodes.

getListOfNodes()   ASTNodeList

Unlike the equivalent method in the libSBML C/C++ interface, this method does not offer the ability to pass a predicate as an argument. The method always returns the list of all ASTNode objects.

Returns
the ASTNodeList of nodes.
Warning
The list returned is owned by the caller and should be deleted after the caller is done using it. The ASTNode objects in the list; however, are not owned by the caller (as they still belong to the tree itself), and therefore should not be deleted.
def libsbml.ASTNode.getMantissa (   self)

Returns the mantissa value of this node.

getMantissa()   float

If ASTNode.getType() returns AST_REAL, this method is identical to ASTNode.getReal().

Returns
the value of the mantissa of this ASTNode, or 0 if this node is not a type that has a real-numbered value.
Note
This function should be called only when ASTNode.getType() returns AST_REAL_E, AST_REAL or AST_NAME_AVOGADRO. It will return 0 if the node type is another type, but since 0 may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.
def libsbml.ASTNode.getName (   self)

Returns the value of this node as a string.

getName()   string

This function may be called on nodes that (1) are not operators, i.e., nodes for which ASTNode.isOperator() returns False, and (2) are not numbers, i.e., ASTNode.isNumber() returns False.

Returns
the value of this ASTNode as a string, or None if it is a node that does not have a name equivalent (e.g., if it is a number).
def libsbml.ASTNode.getNumChildren (   self)

Returns the number of children of this node.

getNumChildren()   long
Returns
the number of children of this ASTNode, or 0 is this node has no children.
def libsbml.ASTNode.getNumerator (   self)

Returns the value of the numerator of this node.

getNumerator()   long

This function should be called only when ASTNode.getType() returns AST_RATIONAL or AST_INTEGER.

Returns
the value of the numerator of this ASTNode.
def libsbml.ASTNode.getNumSemanticsAnnotations (   self)

Returns the number of MathML <semantics> element elements on this node.

getNumSemanticsAnnotations()   long

The <semantics> element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation> or <annotation-xml> elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.

Returns
the number of annotations of this ASTNode.
Note
Although SBML permits the use of the MathML <semantics> annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.
See also
ASTNode.addSemanticsAnnotation()
ASTNode.getSemanticsAnnotation()
def libsbml.ASTNode.getOperatorName (   self)

Returns the value of this operator node as a string.

getOperatorName()   string

This function may be called on nodes that are operators, i.e., nodes for which ASTNode.isOperator() returns True.

Returns
the name of this operator ASTNode as a string (or None if not an operator).
def libsbml.ASTNode.getParentSBMLObject (   self)

Returns the parent SBML object.

getParentSBMLObject()   SBase
Returns
the parent SBML object of this ASTNode.
See also
isSetParentSBMLObject()
def libsbml.ASTNode.getPrecedence (   self)

Returns the precedence of this node in the infix math syntax of SBML Level 1.

getPrecedence()   int

For more information about the infix syntax, see the discussion about text string formulas at the top of the documentation for ASTNode.

Returns
an integer indicating the precedence of this ASTNode
def libsbml.ASTNode.getReal (   self)

Returns the real-numbered value of this node.

getReal()   float

This function performs the necessary arithmetic if the node type is AST_REAL_E (mantissa * 10 exponent) or AST_RATIONAL (numerator / denominator).

Returns
the value of this ASTNode as a real (float), or 0 if this is not a node that holds a number.
Note
This function should be called only when this ASTNode has a numerical value type. It will return 0 if the node type is another type, but since 0 may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.
def libsbml.ASTNode.getRightChild (   self)

Returns the right child of this node.

getRightChild()   ASTNode
Returns
the right child of this ASTNode, or None if this node has no right child. If ASTNode.getNumChildren() > 1, then this is equivalent to:
getChild( getNumChildren() - 1 );
See also
getNumChildren()
getLeftChild()
getChild()
def libsbml.ASTNode.getSemanticsAnnotation (   self,
  n 
)

Returns the nth MathML <semantics> element on this ASTNode.

getSemanticsAnnotation(long n)   XMLNode

The <semantics> element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation> or <annotation-xml> elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.

Parameters
nthe index of the annotation to return. Callers should use ASTNode.getNumSemanticsAnnotations() to first find out how many annotations there are.
Returns
the nth annotation inside this ASTNode, or None if this node has no nth annotation (n > ASTNode.getNumSemanticsAnnotations() - 1).
Note
Although SBML permits the use of the MathML <semantics> annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.
See also
ASTNode.addSemanticsAnnotation()
ASTNode.getNumSemanticsAnnotations()
def libsbml.ASTNode.getStyle (   self)

Returns the MathML style attribute value of this ASTNode.

getStyle()   string
Returns
the MathML style of this ASTNode, if any exists.
See also
isSetStyle()
setStyle()
unsetStyle()
def libsbml.ASTNode.getType (   self)

Returns the type of this ASTNode.

getType()   long

The value returned is one of the Core AST type codes such as AST_LAMBDA, AST_PLUS, etc.

Returns
the type of this ASTNode.
Note
The introduction of extensibility in SBML Level 3 brings with it a need to allow for the possibility of node types that are defined by plug-ins implementing SBML Level 3 packages. If a given ASTNode is a construct created by a package rather than libSBML Core, then getType() will return AST_ORIGINATES_IN_PACKAGE. Callers can then obtain the package-specific type by calling getExtendedType().
See also
getExtendedType()
def libsbml.ASTNode.getUnits (   self)

Returns the units of this ASTNode.

getUnits()   string
SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Returns
the units of this ASTNode.
Note
The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.
See also
parseL3Formula()
def libsbml.ASTNode.hasCorrectNumberArguments (   self)

Returns True if this ASTNode has the correct number of children for its type.

hasCorrectNumberArguments()   bool

For example, an ASTNode with type AST_PLUS expects 2 child nodes.

Returns
True if this ASTNode has the appropriate number of children for its type, False otherwise.
Note
This function performs a check on the top-level node only. Child nodes are not checked.
See also
isWellFormedASTNode()
def libsbml.ASTNode.hasTypeAndNumChildren (   self,
  type,
  numchildren 
)

Returns True if this node is of a certain type with a specific number of children.

hasTypeAndNumChildren(int type, long numchildren)   int

Designed for use in cases where it is useful to discover if the node is a unary not or unary minus, or a times node with no children, etc.

Parameters
typethe type of ASTNode sought.
numchildrenthe number of child nodes sought.
Returns
True if this ASTNode is has the specified type and number of children, False otherwise.
def libsbml.ASTNode.hasUnits (   self)

Returns True if this node or any of its children nodes have the attribute sbml:units.

hasUnits()   bool
SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Returns
True if this ASTNode or its children has units associated with it, False otherwise.
Note
The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.
See also
isSetUnits()
setUnits()
def libsbml.ASTNode.insertChild (   self,
  n,
  disownedChild 
)

Inserts the given ASTNode node at a given point in the current ASTNode's list of children.

insertChild(long n, ASTNode disownedChild)   int
Parameters
nlong the index of the ASTNode being added
disownedChildASTNode to insert as the nth child
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The method ASTNode.isWellFormedASTNode() may also be useful for checking the results of node modifications.
See also
addChild()
prependChild()
replaceChild()
removeChild()
def libsbml.ASTNode.isAvogadro (   self)

Returns True if this node represents the predefined value for Avogadro's constant.

isAvogadro()   bool

SBML Level 3 introduced a predefined MathML <csymbol> for the value of Avogadro's constant. LibSBML stores this internally as a node of type AST_NAME_AVOGADRO. This method returns True if this node has that type.

Returns
True if this ASTNode is the special symbol avogadro, False otherwise.
See also
parseL3Formula()
def libsbml.ASTNode.isBoolean (   self)

Returns True if this node has a Boolean type.

isBoolean()   bool

The ASTNode objects that have Boolean types are the logical operators, relational operators, and the constants True or False.

Returns
True if this ASTNode has a Boolean type, False otherwise.
def libsbml.ASTNode.isConstant (   self)

Returns True if this node represents a MathML constant.

isConstant()   bool

Examples of MathML constants include such things as pi.

Returns
True if this ASTNode is a MathML constant, False otherwise.
Note
This function will also return True for nodes of type AST_NAME_AVOGADRO in SBML Level 3.
def libsbml.ASTNode.isFunction (   self)

Returns True if this node represents a function.

isFunction()   bool

The three types of functions in SBML are MathML functions (e.g., abs()), SBML Level 1 functions (in the SBML Level 1 math syntax), and user-defined functions (using FunctionDefinition in SBML Level 2 and 3).

Returns
True if this ASTNode is a function, False otherwise.
def libsbml.ASTNode.isInfinity (   self)

Returns True if this node represents the special IEEE 754 value for infinity.

isInfinity()   bool
Returns
True if this ASTNode is the special IEEE 754 value infinity, False otherwise.
def libsbml.ASTNode.isInteger (   self)

Returns True if this node contains an integer value.

isInteger()   bool
Returns
True if this ASTNode is of type AST_INTEGER, False otherwise.
def libsbml.ASTNode.isLambda (   self)

Returns True if this node is a MathML <lambda>.

isLambda()   bool
Returns
True if this ASTNode is of type AST_LAMBDA, False otherwise.
def libsbml.ASTNode.isLog10 (   self)

Returns True if this node represents a log10 function.

isLog10()   bool

More precisely, this predicate returns True if the node type is AST_FUNCTION_LOG with two children, the first of which is an AST_INTEGER equal to 10.

Returns
True if the given ASTNode represents a log10() function, False otherwise.
See also
parseL3Formula()
def libsbml.ASTNode.isLogical (   self)

Returns True if this node is a MathML logical operator.

isLogical()   bool

The possible MathML logical operators are and, or, not, and xor.

Returns
True if this ASTNode is a MathML logical operator, False otherwise.
def libsbml.ASTNode.isName (   self)

Returns True if this node is a user-defined variable name or the symbols for time or Avogadro's constant.

isName()   bool

SBML Levels 2 and 3 provides <csymbol> definitions for 'time' and 'avogadro', which can be used to represent simulation time and Avogadro's constant in MathML.

Returns
True if this ASTNode is a user-defined variable name in SBML or the special symbols for time or Avogadro's constant. It returns False otherwise.
def libsbml.ASTNode.isNaN (   self)

Returns True if this node represents the special IEEE 754 value 'not a number' (NaN).

isNaN()   bool
Returns
True if this ASTNode is the special IEEE 754 NaN, False otherwise.
def libsbml.ASTNode.isNegInfinity (   self)

Returns True if this node represents the special IEEE 754 value 'negative infinity'.

isNegInfinity()   bool
Returns
True if this ASTNode is the special IEEE 754 value negative infinity, False otherwise.
def libsbml.ASTNode.isNumber (   self)

Returns True if this node contains a number.

isNumber()   bool
Returns
True if this ASTNode is a number, False otherwise.
def libsbml.ASTNode.isOperator (   self)

Returns True if this node is a mathematical operator.

isOperator()   bool

The possible mathematical operators in the MathML syntax supported by SBML are +, -, *, / and ^ (power).

Returns
True if this ASTNode is an operator, False otherwise.
def libsbml.ASTNode.isPiecewise (   self)

Returns True if this node is the MathML <piecewise> construct.

isPiecewise()   bool
Returns
True if this ASTNode is a MathML piecewise function, False otherwise.
def libsbml.ASTNode.isQualifier (   self)

Predicate returning True if this node is a MathML qualifier.

isQualifier()   bool

The MathML qualifier node types are bvar, degree, base, piece, and otherwise.

Returns
True if this ASTNode is a MathML qualifier, False otherwise.
def libsbml.ASTNode.isRational (   self)

Returns True if this node represents a rational number.

isRational()   bool
Returns
True if this ASTNode is of type AST_RATIONAL, False otherwise.
def libsbml.ASTNode.isReal (   self)

Returns True if this node can represent a real number.

isReal()   bool

More precisely, this node must be of one of the following types: AST_REAL, AST_REAL_E or AST_RATIONAL.

Returns
True if the value of this ASTNode can represented as a real number, False otherwise.
def libsbml.ASTNode.isRelational (   self)

Returns True if this node is a MathML relational operator.

isRelational()   bool

The MathML relational operators are ==, >=, >, <, and !=.

Returns
True if this ASTNode is a MathML relational operator, False otherwise.
def libsbml.ASTNode.isSemantics (   self)

Predicate returning True if this node is a MathML semantics node.

isSemantics()   bool
Returns
True if this ASTNode is a MathML semantics node, False otherwise.
def libsbml.ASTNode.isSetClass (   self)

Returns True if this node has a value for the MathML attribute class.

isSetClass()   bool
Returns
true if this ASTNode has an attribute class, False otherwise.
See also
isSetId()
isSetStyle()
setClass()
unsetClass()
def libsbml.ASTNode.isSetId (   self)

Returns True if this node has a value for the MathML attribute id.

isSetId()   bool
Returns
true if this ASTNode has an attribute id, False otherwise.
See also
isSetClass()
isSetStyle()
setId()
unsetId()
def libsbml.ASTNode.isSetParentSBMLObject (   self)

Returns True if this node has a value for the parent SBML object.

isSetParentSBMLObject()   bool
Returns
true if this ASTNode has an parent SBML object set, False otherwise.
See also
getParentSBMLObject()
def libsbml.ASTNode.isSetStyle (   self)

Returns True if this node has a value for the MathML attribute style.

isSetStyle()   bool
Returns
true if this ASTNode has an attribute style, False otherwise.
See also
isSetClass()
isSetId()
setStyle()
unsetStyle()
def libsbml.ASTNode.isSetUnits (   self)

Returns True if this node has the attribute sbml:units.

isSetUnits()   bool
SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Returns
True if this ASTNode has units associated with it, False otherwise.
Note
The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.
See also
hasUnits()
setUnits()
def libsbml.ASTNode.isSetUserData (   self)

Returns True if this node has a user data object.

isSetUserData()   bool
Returns
true if this ASTNode has a user data object set, False otherwise.
def libsbml.ASTNode.isSqrt (   self)

Returns True if this node represents a square root function.

isSqrt()   bool

More precisely, the node type must be AST_FUNCTION_ROOT with two children, the first of which is an AST_INTEGER node having value equal to 2.

Returns
True if the given ASTNode represents a sqrt() function, False otherwise.
def libsbml.ASTNode.isUMinus (   self)

Returns True if this node is a unary minus operator.

isUMinus()   bool

A node is defined as a unary minus node if it is of type AST_MINUS and has exactly one child.

For numbers, unary minus nodes can be 'collapsed' by negating the number. In fact, parseFormula() does this during its parsing process, and parseL3Formula() has a configuration option that allows this behavior to be turned on or off. However, unary minus nodes for symbols (AST_NAME) cannot be 'collapsed', so this predicate function is necessary.

Returns
True if this ASTNode is a unary minus, False otherwise.
See also
parseL3Formula()
def libsbml.ASTNode.isUnknown (   self)

Returns True if this node has an unknown type.

isUnknown()   bool

'Unknown' nodes have the type AST_UNKNOWN. Nodes with unknown types will not appear in an ASTNode tree returned by libSBML based upon valid SBML input; the only situation in which a node with type AST_UNKNOWN may appear is immediately after having create a new, untyped node using the ASTNode constructor. Callers creating nodes should endeavor to set the type to a valid node type as soon as possible after creating new nodes.

Returns
True if this ASTNode is of type AST_UNKNOWN, False otherwise.
def libsbml.ASTNode.isUPlus (   self)

Returns True if this node is a unary plus operator.

isUPlus()   bool

A node is defined as a unary plus node if it is of type AST_PLUS and has exactly one child.

Returns
True if this ASTNode is a unary plus, False otherwise.
def libsbml.ASTNode.isWellFormedASTNode (   self)

Returns True or False depending on whether this ASTNode is well-formed.

isWellFormedASTNode()   bool
Note
An ASTNode may be well-formed, with each node and its children having the appropriate number of children for the given type, but may still be invalid in the context of its use within an SBML model.
Returns
True if this ASTNode is well-formed, False otherwise.
See also
hasCorrectNumberArguments()
def libsbml.ASTNode.prependChild (   self,
  disownedChild 
)

Adds the given node as a child of this ASTNode.

prependChild(ASTNode disownedChild)   int

This method adds child nodes from right to left.

Parameters
disownedChildthe ASTNode instance to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The method ASTNode.isWellFormedASTNode() may also be useful for checking the results of node modifications.
See also
addChild()
replaceChild()
insertChild()
removeChild()
def libsbml.ASTNode.reduceToBinary (   self)

Reduces this ASTNode to a binary tree.

reduceToBinary()

Example: if this ASTNode is and(x, y, z), then the formula of the reduced node is and(and(x, y), z). The operation replaces the formula stored in the current ASTNode object.

def libsbml.ASTNode.removeChild (   self,
  n 
)

Removes the nth child of this ASTNode object.

removeChild(long n)   int
Parameters
nlong the index of the child to remove
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The method ASTNode.isWellFormedASTNode() may also be useful for checking the results of node modifications.
See also
addChild()
prependChild()
replaceChild()
insertChild()
def libsbml.ASTNode.renameSIdRefs (   self,
  oldid,
  newid 
)

Renames all the SIdRef attributes on this node and its child nodes.

renameSIdRefs(string oldid, string newid)
Parameters
oldidthe old identifier.
newidthe new identifier.
def libsbml.ASTNode.renameUnitSIdRefs (   self,
  oldid,
  newid 
)

Renames all the UnitSIdRef attributes on this node and its child nodes.

renameUnitSIdRefs(string oldid, string newid)

The only place UnitSIDRefs appear in MathML <cn> elements, so the effects of this method are limited to that.

Parameters
oldidthe old identifier.
newidthe new identifier.
def libsbml.ASTNode.replaceArgument (   self,
  bvar,
  arg 
)

Replaces occurrences of a given name with a given ASTNode.

replaceArgument(string bvar, ASTNode arg)

For example, if the formula in this ASTNode is x + y, then the <bvar> is x and arg is an ASTNode representing the real value 3. This method substitutes 3 for x within this ASTNode object.

Parameters
bvara string representing the variable name to be substituted.
argan ASTNode representing the name/value/formula to use as a replacement.
def libsbml.ASTNode.replaceChild (   self,
  n,
  disownedChild,
  delreplaced = False 
)

Replaces the nth child of this ASTNode with the given ASTNode.

replaceChild(long n, ASTNode disownedChild, bool delreplaced=False)   int
replaceChild(long n, ASTNode disownedChild)   int
Parameters
nlong the index of the child to replace
disownedChildASTNode to replace the nth child
delreplacedboolean indicating whether to delete the replaced child.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The method ASTNode.isWellFormedASTNode() may also be useful for checking the results of node modifications.
See also
addChild()
prependChild()
insertChild()
removeChild()
def libsbml.ASTNode.returnsBoolean (   self,
  model = None 
)

Returns True if this node returns a Boolean value.

returnsBoolean(Model model=None)   bool
returnsBoolean()   bool

This function looks at the whole ASTNode rather than just the top level of the ASTNode. Thus, it will consider return values from piecewise statements. In addition, if this ASTNode uses a function call to a user-defined function, the return value of the corresponding FunctionDefinition object will be determined. Note that this is only possible where the ASTNode can trace its parent Model; that is, the ASTNode must represent the <math> element of some SBML object that has already been added to an instance of an SBMLDocument.

Parameters
modelthe Model to use as context
See also
isBoolean()
Returns
true if this ASTNode returns a boolean, False otherwise.
def libsbml.ASTNode.setCharacter (   self,
  value 
)

Sets the value of this ASTNode to the given character.

setCharacter(char value)   int

If character is one of +, -, *, / or ^, the node type will be set accordingly. For all other characters, the node type will be set to AST_UNKNOWN.

Parameters
valuethe character value to which the node's value should be set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.setClass (   self,
  className 
)

Sets the MathML attribute class of this ASTNode.

setClass(string className)   int
Parameters
classNamestring representing the MathML class for this node.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
isSetClass()
getClass()
unsetClass()
def libsbml.ASTNode.setDefinitionURL (   self,
  args 
)

This method has multiple variants; they differ in the arguments they accept.

setDefinitionURL(XMLAttributes url)   int
setDefinitionURL(string url)   int

Each variant is described separately below.


Method variant with the following signature:
setDefinitionURL(XMLAttributes url)

Sets the MathML attribute definitionURL.

Parameters
urlthe URL value for the definitionURL attribute.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setDefinitionURL()
getDefinitionURL()
getDefinitionURLString()

Method variant with the following signature:
setDefinitionURL(string url)

Sets the MathML attribute definitionURL.

Parameters
urlthe URL value for the definitionURL attribute.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setDefinitionURL()
getDefinitionURL()
getDefinitionURLString()
def libsbml.ASTNode.setId (   self,
  id 
)

Sets the MathML attribute id of this ASTNode.

setId(string id)   int
Parameters
idstring representing the identifier.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
isSetId()
getId()
unsetId()
def libsbml.ASTNode.setName (   self,
  name 
)

Sets the value of this ASTNode to the given name.

setName(string name)   int

As a side effect, this ASTNode object's type will be reset to AST_NAME if (and only if) the ASTNode was previously an operator (i.e.,ASTNode.isOperator() returns True), number (i.e., ASTNode.isNumber() returns True), or unknown. This allows names to be set for AST_FUNCTION nodes and the like.

Parameters
namethe string containing the name to which this node's value should be set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.setStyle (   self,
  style 
)

Sets the MathML attribute style of this ASTNode.

setStyle(string style)   int
Parameters
stylestring representing the identifier.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
isSetStyle()
getStyle()
unsetStyle()
def libsbml.ASTNode.setType (   self,
  type 
)

This method has multiple variants; they differ in the arguments they accept.

setType(int type)   int

Each variant is described separately below.


Method variant with the following signature:
setType(long type)

Sets the type of this ASTNode to the given type code.

Parameters
typethe type to which this node should be set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
A side-effect of doing this is that any numerical values previously stored in this node are reset to zero.
See also
getType()
setType()

Method variant with the following signature:
setType(int type)

Sets the type of this ASTNode.

This uses integer type codes, which may come from the set of static integer constants whose names begin with the prefix AST_ defined in the interface class libsbml or an enumeration of AST types in an SBML Level 3 package.

Parameters
typethe integer representing the type to which this node should be set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
A side-effect of doing this is that any numerical values previously stored in this node are reset to zero.
See also
getType()
setType()
def libsbml.ASTNode.setUnits (   self,
  units 
)

Sets the units of this ASTNode to units.

setUnits(string units)   int

The units will be set only if this ASTNode object represents a MathML <cn> element, i.e., represents a number. Callers may use ASTNode.isNumber() to inquire whether the node is of that type.

SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Parameters
unitsstring representing the unit identifier.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.
See also
isSetUnits()
hasUnits()
def libsbml.ASTNode.setValue (   self,
  args 
)

This method has multiple variants; they differ in the arguments they accept.

setValue(long value)   int
setValue(long numerator, long denominator)   int
setValue (float value)   int
setValue (float mantissa, long exponent)   int

Each variant is described separately below.


Method variant with the following signature:
setValue(int value)

Sets the value of this ASTNode to the given integer

As a side effect, this operation sets the node type to AST_INTEGER.

Parameters
valuethe integer to which this node's value should be set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

Method variant with the following signature:
setValue(long value)

Sets the value of this ASTNode to the given (long) integer

As a side effect, this operation sets the node type to AST_INTEGER.

Parameters
valuethe integer to which this node's value should be set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

Method variant with the following signature:
setValue(long numerator, long denominator)

Sets the value of this ASTNode to the given rational.

As a side effect, this operation sets the node type to AST_RATIONAL.

Parameters
numeratorthe numerator value of the rational.
denominatorthe denominator value of the rational.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

Method variant with the following signature:
setValue (float value)

Sets the value of this ASTNode to the given real (float).

As a side effect, this operation sets the node type to AST_REAL.

This is functionally equivalent to:

setValue(value, 0);
Parameters
valuethe float format number to which this node's value should be set.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

Method variant with the following signature:
setValue (float mantissa, long exponent)

Sets the value of this ASTNode to the given real (float)

As a side effet, this operation sets the node type to AST_REAL_E.

Parameters
mantissathe mantissa of this node's real-numbered value.
exponentthe exponent of this node's real-numbered value.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.swapChildren (   self,
  that 
)

Swaps the children of this node with the children of another node.

swapChildren(ASTNode that)   int
Parameters
thatthe other node whose children should be used to replace this node's children.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.unsetClass (   self)

Unsets the MathML class attribute of this ASTNode.

unsetClass()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.unsetId (   self)

Unsets the MathML id attribute of this ASTNode.

unsetId()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.unsetParentSBMLObject (   self)

Unsets the parent SBML object.

unsetParentSBMLObject()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
isSetParentSBMLObject()
getParentSBMLObject()
def libsbml.ASTNode.unsetStyle (   self)

Unsets the MathML style attribute of this ASTNode.

unsetStyle()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.unsetUnits (   self)

Unsets the units of this ASTNode.

unsetUnits()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.ASTNode.unsetUserData (   self)

Unsets the user data of this node.

unsetUserData()   int

The user data can be used by the application developer to attach custom information to the node. In case of a deep copy, this attribute will passed as it is. The attribute will be never interpreted by this class.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are: