msatpcorrection

MSATPCorrection

A class that corrects the ATP Hydrolysis reaction of a given model:

msatp = MSATPCorrection(model, core_template, atp_medias, compartment="c0", max_gapfilling=None, gapfilling_delta=0, atp_hydrolysis_id=None)

  • model cobra.core.model.Model: The model whose ATP Hydrolysis reaction will be corrected.

  • core_template modelseedpy.core.mstemplate.MSTemplate: The model template that is used to correct the model.

  • atp_medias modelseedpy.core.msmedia.MSMedia: The media that is associated with the growth phenotype.

  • compartment str: The compartment in which ATP will be added.

  • max_gapfilling float: The greatest extent of gapfilling for respective model.

  • gapfilling_delta int: The allowable margin above the best gapfilling score that permits selection of a growth media.

  • atp_hydrolysis_id str: The ID of the ATP Hydrolysis reaction, where None specifies a SEED reaction search.

atp_correction()

staticMethod Restores the bounds on all noncore reactions:

msatpobj = msatp.run_atp_correction(model, coretemplate, atp_medias = None, max_gapfilling = None, gapfilling_delta = 0)

  • model cobra.core.model.Model: The model whose ATP Hydrolysis reaction will be corrected.

  • coretemplate modelseedpy.core.mstemplate.MSTemplate: The template that consists of the reactions that be used to assess which reactions in the model are categorized as core.

  • atp_medias list: The collection of media whose gapfilling requirements to produce ATP will be examined.

  • max_gapfilling float: The maximal gapfilling score, where None defaults to the best score from gapfilling the provided media.

  • gapfilling_delta int: The allowable margin above the best gapfilling score that permits selection of a growth media.

Returns msatpobj modelseedpy.core.msatpcorrection.MSATPCorrection: The MSATPCorrection object that possesses the corrected model and all attributes of the correction process.