Module Biocaml_sbml (.ml)

SBML file parser. Currently only level 2 version 4 is supported.

module Biocaml_sbml:

sig

exception Bad of string

type sb_math_operator =

| MPlus

| MMinus

| MTimes

| MDivide

| MPower

| MRoot

| MAbs

| MExp

| MLn

| MLog

| MFloor

| MCeiling

| MFactorial

| MEq

| MNeq

| MGt

| MLt

| MGeq

| MLeq

| MAnd

| MOr

| MXor

| MNot

| MSin

| MCos

| MTan

| MArcsin

| MArccos

| MArctan

| MDelay

| MFundef of string

type sb_math =

| MApply of sb_math_operator * sb_math list

| MLambda of string list * sb_math

| MPiecewise of (string * sb_math) list * string

| MFloatNumber of float

| MIntNumber of int

| MIdentifier of string

| MTime

| MTrue

| MFalse

| MNAN

| MPi

| MExponent

| MInfinity

| MNoMath

type sb_unit = {

unit_kind : string;

unit_exponent : int;

unit_scale : int;

unit_multiplier : float;

}

type sb_function_definition = {

fundef_id : string;

fundef_name : string;

fundef_math : sb_math ;

}

type sb_unit_definition = {

unitdef_id : string;

unitdef_name : string;

unitdef_unitlist : sb_unit list;

}

type sb_compartment = {

compart_id : string;

compart_name : string;

compart_spatialDimensions : int;

compart_size : float;

compart_units : string;

compart_outside : string;

compart_constant : bool;

}

type sb_species_ref = {

specref_species : string;

specref_id : string;

specref_name : string;

specref_stoichiometry : int;

}

type sb_species = {

species_id : string;

species_name : string;

species_type : string;

species_compartment : string;

species_initialAmount : float;

species_initialConcentration : float;

species_substanceUnits : string;

species_hasOnlySubstanceUnits : bool;

species_boundaryCondition : bool;

species_constant : bool;

}

type sb_parameter = {

param_id : string;

param_name : string;

param_value : float;

param_units : string;

param_constant : bool;

}

type sb_kinetic_law = {

klaw_math : sb_math ;

klaw_parameters : sb_parameter list;

}

type sb_reaction = {

react_id : string;

react_name : string;

react_boundaryCondition : bool;

react_fast : bool;

react_reactants : sb_species_ref list;

react_products : sb_species_ref list;

react_kineticLaw : sb_kinetic_law ;

}

type sb_initial_assignment = {

ia_symbol : string;

ia_math : sb_math ;

}

type sb_algebraic_rule = {

ar_math : sb_math ;

}

type sb_generic_rule = {

gr_variable : string;

gr_math : sb_math ;

}

type sb_rule =

| RateRule of sb_generic_rule

| AssignmentRule of sb_generic_rule

| AlgebraicRule of sb_algebraic_rule

type sb_math_container = {

math : sb_math ;

}

type sb_delay =

| Delay of sb_math_container

type sb_trigger =

| Trigger of sb_math_container

type sb_event_assignment = {

ea_variable : string;

ea_math : sb_math ;

}

type sb_event = {

event_id : string;

event_name : string;

event_useValuesFromTriggerTime : bool;

event_trigger : sb_trigger ;

event_delay : sb_delay ;

event_assignments : sb_event_assignment list;

}

type sb_model = {

sbm_id : string;

sbm_name : string;

sbm_functionDefinitions : sb_function_definition list;

sbm_unitDefinitions : sb_unit_definition list;

sbm_compartments : sb_compartment list;

sbm_species : sb_species list;

sbm_reactions : sb_reaction list;

sbm_parameters : sb_parameter list;

sbm_initialAssignments : sb_initial_assignment list;

sbm_rules : sb_rule list;

sbm_events : sb_event list;

}

val math_to_string  : sb_math -> string

Returns a string with sb_math converted into a S-expression

val in_sbml  : Pervasives.in_channel -> sb_model

Returns an sb_model read from input stream

end