BiochemicalReaction#
- class biopax-explorer.biopax.biochemicalreaction.BiochemicalReaction(*args, **kwargs)[source]#
Bases:
ConversionClass BiochemicalReaction
Definition: A conversion in which molecules of one or more physicalEntity pools,
undergo covalent modifications and become a member of one or more other physicalEntity pools. The substrates of biochemical reactions are defined in terms of sums of species. This is a convention in biochemistry, and, in principle, all EC reactions should be biochemical reactions. Examples: ATP + H2O = ADP + Pi Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen. A better coverage for polymerization will be developed.
code generator : rdfobj (author F.Moreews 2023-2024).
Methods
get_availability()Attribute _availability getter
get_comment()Attribute _comment getter
get_conversionDirection()Attribute _conversionDirection getter
get_dataSource()Attribute _dataSource getter
Attribute _deltaG getter
Attribute _deltaH getter
Attribute _deltaS getter
get_displayName()Attribute _displayName getter
Attribute _eCNumber getter
get_evidence()Attribute _evidence getter
get_interactionType()Attribute _interactionType getter
get_kEQ()Attribute _kEQ getter
get_left()Attribute _left getter
get_name()Attribute _name getter
get_participant()Attribute _participant getter
get_participantStoichiometry()Attribute _participantStoichiometry getter
get_right()Attribute _right getter
get_spontaneous()Attribute _spontaneous getter
get_standardName()Attribute _standardName getter
get_xref()Attribute _xref getter
attribute_type_by_name
get_uri_string
object_attributes
set_availability
set_comment
set_conversionDirection
set_dataSource
set_deltaG
set_deltaH
set_deltaS
set_displayName
set_eCNumber
set_evidence
set_interactionType
set_kEQ
set_left
set_name
set_participant
set_participantStoichiometry
set_right
set_spontaneous
set_standardName
set_uri_string
set_xref
to_json
type_attributes
Methods Summary
Attribute _deltaG getter
Attribute _deltaH getter
Attribute _deltaS getter
Attribute _eCNumber getter
get_kEQ()Attribute _kEQ getter
set_deltaG(value)set_deltaH(value)set_deltaS(value)set_eCNumber(value)set_kEQ(value)set_uri_string(uristr)to_json()Methods Documentation
- get_deltaG()[source]#
- Attribute _deltaG getter
For biochemical reactions, this property refers to the standard transformed
Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G Since Delta-G can change based on multiple factors including ionic strength and temperature a reaction can have multiple DeltaG values.
- get_deltaH()[source]#
- Attribute _deltaH getter
For biochemical reactions, this property refers to the standard transformed
enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H’<sup>o</sup>. delta-G’<sup>o</sup> = delta-H’<sup>o</sup> - T delta-S’<sup>o</sup> Units: kJ/mole (This definition from EcoCyc)
- get_deltaS()[source]#
- Attribute _deltaS getter
For biochemical reactions, this property refers to the standard transformed
entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S’<sup>o</sup>. delta-G’<sup>o</sup> = delta-H’<sup>o</sup> - T delta-S’<sup>o</sup> (This definition from EcoCyc)
- get_eCNumber()[source]#
- Attribute _eCNumber getter
The unique number assigned to a reaction by the Enzyme Commission of the
International Union of Biochemistry and Molecular Biology. Note that not all biochemical reactions currently have EC numbers assigned to them.
- get_kEQ()[source]#
- Attribute _kEQ getter
This quantity is dimensionless and is usually a single number. The measured
equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K’. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K’ = [ADP][P<sub>i</sub>]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP<sup>4-</sup>] + [HATP<sup>3-</sup>] + [H<sub>2</sub>ATP<sup>2-</sup>] + [MgATP<sup>2-</sup>] + [MgHATP<sup>-</sup>] + [Mg<sub>2</sub>ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm<sup>3</sup>) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K’ T I pH pMg). This property may have multiple values, representing different measurements for K’ obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc)