libSBML Python API
5.11.0
|
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).
'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: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:
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.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 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:
'+'
), then the node's type will be AST_PLUS, AST_MINUS, AST_TIMES, AST_DIVIDE, or AST_POWER, as appropriate.AST_FUNCTION_
X, AST_LOGICAL_
X, or AST_RELATIONAL_
X, as appropriate. (Examples: AST_FUNCTION_LOG, AST_RELATIONAL_LEQ.)'ExponentialE'
, 'Pi'
, 'True'
or 'False'
), then the node's type will be AST_CONSTANT_E, AST_CONSTANT_PI, AST_CONSTANT_TRUE, or AST_CONSTANT_FALSE.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.)avogadro
, the value of the node will be AST_NAME_AVOGADRO.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.
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.
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... | |
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.
disownedChild | the ASTNode instance to add |
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.
disownedAnnotation | the annotation to add. |
<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.def libsbml.ASTNode.canonicalize | ( | self | ) |
Converts this ASTNode to a canonical form.
canonicalize() bool
The rules determining the canonical form conversion are as follows:
'ExponentialE'
, 'Pi'
, 'True'
or 'False'
the node type is converted to the corresponding AST_CONSTANT_
X type. 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
.
True
if this node was successfully converted to canonical form, False
otherwise. def libsbml.ASTNode.deepCopy | ( | self | ) |
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.
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.
def libsbml.ASTNode.getChild | ( | self, | |
n | |||
) |
Returns the child at index n of this node.
getChild(long n) ASTNode
n | the index of the child to get |
None
if this node has no nth child (n >
ASTNode.getNumChildren() - 1
).def libsbml.ASTNode.getClass | ( | self | ) |
Returns the MathML class
attribute value of this ASTNode.
getClass() string
def libsbml.ASTNode.getDefinitionURL | ( | self | ) |
Returns the MathML definitionURL
attribute value.
getDefinitionURL() XMLAttributes
definitionURL
attribute, in the form of a libSBML XMLAttributes object.def libsbml.ASTNode.getDefinitionURLString | ( | self | ) |
Returns the MathML definitionURL
attribute value as a string.
getDefinitionURLString() string
definitionURL
attribute, as a string.def libsbml.ASTNode.getDenominator | ( | self | ) |
Returns the value of the denominator of this node.
getDenominator() long
1
if this node has no numerical value.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
0
if this is not a type of node that has an exponent.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.
def libsbml.ASTNode.getId | ( | self | ) |
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.
long
) integer.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
0
.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.
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().
0
if this node is not a type that has a real-numbered value.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
.
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
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.
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.
<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.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
.
None
if not an operator). def libsbml.ASTNode.getParentSBMLObject | ( | self | ) |
Returns the parent SBML object.
getParentSBMLObject() SBase
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.
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).
0
if this is not a node that holds a number.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
None
if this node has no right child. If ASTNode.getNumChildren() > 1
, then this is equivalent to: getChild( getNumChildren() - 1 );
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.
n | the index of the annotation to return. Callers should use ASTNode.getNumSemanticsAnnotations() to first find out how many annotations there are. |
None
if this node has no nth annotation (n >
ASTNode.getNumSemanticsAnnotations() - 1
).<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.def libsbml.ASTNode.getStyle | ( | self | ) |
Returns the MathML style
attribute value of this ASTNode.
getStyle() string
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.
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>
sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.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.
True
if this ASTNode has the appropriate number of children for its type, False
otherwise.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.
type | the type of ASTNode sought. |
numchildren | the number of child nodes sought. |
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>
True
if this ASTNode or its children has units associated with it, False
otherwise.sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.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
n | long the index of the ASTNode being added |
disownedChild | ASTNode to insert as the nth child |
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.
True
if this ASTNode is the special symbol avogadro, False
otherwise.def libsbml.ASTNode.isBoolean | ( | self | ) |
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.
True
if this ASTNode is a MathML constant, False
otherwise.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).
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
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
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
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.
True
if the given ASTNode represents a log10()
function, False
otherwise.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
.
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.
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
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
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
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).
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
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
.
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
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.
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 !=
.
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
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
False
otherwise.def libsbml.ASTNode.isSetId | ( | self | ) |
Returns True
if this node has a value for the MathML attribute id
.
isSetId() bool
False
otherwise.def libsbml.ASTNode.isSetParentSBMLObject | ( | self | ) |
Returns True
if this node has a value for the parent SBML object.
isSetParentSBMLObject() bool
False
otherwise.def libsbml.ASTNode.isSetStyle | ( | self | ) |
Returns True
if this node has a value for the MathML attribute style
.
isSetStyle() bool
False
otherwise.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>
True
if this ASTNode has units associated with it, False
otherwise.sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.def libsbml.ASTNode.isSetUserData | ( | self | ) |
Returns True
if this node has a user data object.
isSetUserData() bool
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.
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.
True
if this ASTNode is a unary minus, False
otherwise.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.
True
if this ASTNode is of type AST_UNKNOWN, False
otherwise. def libsbml.ASTNode.isUPlus | ( | self | ) |
def libsbml.ASTNode.isWellFormedASTNode | ( | self | ) |
Returns True
or False
depending on whether this ASTNode is well-formed.
isWellFormedASTNode() bool
True
if this ASTNode is well-formed, False
otherwise.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.
disownedChild | the ASTNode instance to add |
def libsbml.ASTNode.reduceToBinary | ( | self | ) |
def libsbml.ASTNode.removeChild | ( | self, | |
n | |||
) |
Removes the nth child of this ASTNode object.
removeChild(long n) int
n | long the index of the child to remove |
def libsbml.ASTNode.renameSIdRefs | ( | self, | |
oldid, | |||
newid | |||
) |
Renames all the SIdRef attributes on this node and its child nodes.
renameSIdRefs(string oldid, string newid)
oldid | the old identifier. |
newid | the 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.
oldid | the old identifier. |
newid | the 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.
bvar | a string representing the variable name to be substituted. |
arg | an 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
n | long the index of the child to replace |
disownedChild | ASTNode to replace the nth child |
delreplaced | boolean indicating whether to delete the replaced child. |
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.
model | the Model to use as context |
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.
value | the character value to which the node's value should be set. |
def libsbml.ASTNode.setClass | ( | self, | |
className | |||
) |
Sets the MathML attribute class
of this ASTNode.
setClass(string className) int
className | string representing the MathML class for this node. |
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.
setDefinitionURL(XMLAttributes url)
Sets the MathML attribute definitionURL
.
url | the URL value for the definitionURL attribute. |
setDefinitionURL(string url)
Sets the MathML attribute definitionURL
.
url | the URL value for the definitionURL attribute. |
def libsbml.ASTNode.setId | ( | self, | |
id | |||
) |
Sets the MathML attribute id
of this ASTNode.
setId(string id) int
id | string representing the identifier. |
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.
name | the string containing the name to which this node's value should be set. |
def libsbml.ASTNode.setStyle | ( | self, | |
style | |||
) |
Sets the MathML attribute style
of this ASTNode.
setStyle(string style) int
style | string representing the identifier. |
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.
setType(long type)
Sets the type of this ASTNode to the given type code.
type | the type to which this node should be set. |
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.
type | the integer representing the type to which this node should be set. |
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: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>
units | string representing the unit identifier. |
sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.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.
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.
value | the integer to which this node's value should be set. |
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.
value | the integer to which this node's value should be set. |
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.
numerator | the numerator value of the rational. |
denominator | the denominator value of the rational. |
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);
value | the float format number to which this node's value should be set. |
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.
mantissa | the mantissa of this node's real-numbered value. |
exponent | the exponent of this node's real-numbered value. |
def libsbml.ASTNode.swapChildren | ( | self, | |
that | |||
) |
Swaps the children of this node with the children of another node.
swapChildren(ASTNode that) int
that | the other node whose children should be used to replace this node's children. |
def libsbml.ASTNode.unsetClass | ( | self | ) |
Unsets the MathML class
attribute of this ASTNode.
unsetClass() int
def libsbml.ASTNode.unsetId | ( | self | ) |
Unsets the MathML id
attribute of this ASTNode.
unsetId() int
def libsbml.ASTNode.unsetParentSBMLObject | ( | self | ) |
Unsets the parent SBML object.
unsetParentSBMLObject() int
def libsbml.ASTNode.unsetStyle | ( | self | ) |
Unsets the MathML style
attribute of this ASTNode.
unsetStyle() int
def libsbml.ASTNode.unsetUnits | ( | self | ) |
Unsets the units of this ASTNode.
unsetUnits() int
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.