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Module Biocaml.Sbml (.ml)

module Sbml: Biocaml_sbml

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