4.1.1.1.1.1.1.4. datanator.api.lib.reaction package

4.1.1.1.1.1.1.4.1. Submodules

4.1.1.1.1.1.1.4.2. datanator.api.lib.reaction.manager module

Author:Yosef Roth <yosefdroth@gmail.com>
Author:Jonathan Karr <jonrkarr@gmail.com>
Author:Saahith Pochiraju <saahith116@gmail.com>
Date:2017-05-16
Copyright:2017, Karr Lab
License:MIT
class datanator.api.lib.reaction.manager.ReactionManager(cache_dirname='/root/.wc/data/datanator')[source]

Bases: datanator.api.lib.data_manager.BaseManager

Finds relevant kinetics observations for reactions

  1. Find kinetics observed for the reaction or similar reactions
  1. Find kinetics observed for the reaction
  1. Find the metabolite(s) of each participant
  2. Find the reaction(s) which contain all of these metabolites
  3. Find the kinetic laws associated with these reactions
  1. Find kinetics observed for similar reactions
  1. Find kinetics observed for the assigned EC number(s)
  2. Find kinetics observed for EC number(s) predicted by tools such as E-zyme
  1. Filter out observations from disimilar genetic and environmental conditions and rank the remaing observations by their similarity to the desired genetic and environmental conditions
  2. Calculate a statistical representation of the relevant observations
get_kinetic_laws_by_ec_numbers(ec_numbers, match_levels=4, select=<class 'datanator.core.models.KineticLaw'>)[source]

Get kinetic laws which have one of a list of EC numbers or, optionally, belong to one of a list of EC classes.

Parameters:
  • ec_numbers (list of str) – EC numbers to search for
  • match_levels (int) – number of EC levels that the EC number must match
Returns:

query for matching kinetic laws
Return type:

sqlalchemy.orm.query.Query
get_kinetic_laws_by_metabolite(metabolite, role='reactant', select=<class 'datanator.core.models.KineticLaw'>)[source]

Get kinetic laws that contain a structure in role role

Parameters:
  • structure (str) – InChI structure or formula and connectivity layers to search for
  • only_formula_and_connectivity (bool, optional) – if True, find kinetic laws which contain species with the same InChI formula and connectivity layers
  • role (str, optional) – role (reactant, or product) to search for species
Returns:

query for kinetic laws that contain the structure in role role
Return type:

sqlalchemy.orm.query.Query
get_kinetic_laws_by_participants(participants, only_formula_and_connectivity=False, include_water_hydrogen=False, select=<class 'datanator.core.models.KineticLaw'>)[source]

Get kinetic laws with the participants participants

Parameters:
  • participants (list of data_model.ReactionParticipant) – list of reaction participants
  • only_formula_and_connectivity (bool, optional) – if True, find kinetic laws which contain species with the same InChI formula and connectivity layers
  • include_water_hydrogen (bool, optional) – if True, restrict kinetic laws based on their water, hydroxide, and hydrogen participants
Returns:

a list kinetic laws that contain all of the participants
Return type:

list of models.KineticLaw
get_kinetic_laws_by_reaction(reaction, select=<class 'datanator.core.models.KineticLaw'>)[source]

Get kinetic laws that were observed for similar reactions (same participants or same EC class)

Parameters:reaction (data_model.Reaction) – reaction to find data for
Returns:a list kinetic laws that contain all of the participants
Return type:list of models.KineticLaw
get_kinetic_laws_by_structure(structure, only_formula_and_connectivity=False, role='reactant', select=<class 'datanator.core.models.KineticLaw'>)[source]

Get kinetic laws that contain a structure in role role

Parameters:
  • structure (str) – InChI structure or formula and connectivity layers to search for
  • only_formula_and_connectivity (bool, optional) – if True, find kinetic laws which contain species with the same InChI formula and connectivity layers
  • role (str, optional) – role (reactant, or product) to search for species
Returns:

query for kinetic laws that contain the structure in role role
Return type:

sqlalchemy.orm.query.Query
get_observed_parameter_value(reaction)[source]

Find observed kinetics for the reaction or similar reactions TODO: Add compartment infomrmation

  1. Find kinetics observed for the reaction
  1. Find the metabolite(s) of each participant
  2. Find the reaction(s) which contain all of these metabolites
  3. Find the kinetic laws associated with these reactions
  1. Find kinetics observed for similar reactions
  1. Find kinetics observed for the assigned EC number(s)
  2. Find kinetics observed for EC number(s) predicted by tools such as E-zyme
Parameters:reaction (data_model.Reaction) – reaction to find data for
Returns:list of relevant observed values
Return type:list of data_model.ObservedValue
get_reaction_by_kinetic_law_id(id)[source]
get_reaction_by_metabolite(metabolite, select=<class 'datanator.core.models.Reaction'>)[source]

Get reaction that contains the metabolite role models.Metabolite

Parameters:structure (models.Metabolite) – InChI structure or formula and connectivity layers to search for
Returns:reaction to find data for
Return type:data_model.Reaction

4.1.1.1.1.1.1.4.3. Module contents