3.1. h1_hesc package¶

3.1.1. Subpackages¶

3.1.2. Submodules¶

3.1.3. h1_hesc.main module¶

Command line programs for generating random whole-cell models

Author: Jonathan Karr <karr@mssm.edu>
Date: 2018-05-15
Copyright: 2018, Karr Lab
License: MIT

class h1_hesc.__main__.App(label=None, **kw)[source]¶

Bases: cement.core.foundation.App

Command line application

class Meta[source]¶

Bases: object

base_controller = 'base'[source]¶

handlers = [<class 'h1_hesc.__main__.BaseController'>][source]¶

label = 'h1-hesc'[source]¶

class h1_hesc.__main__.BaseController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Base controller for command line application

class Meta[source]¶

Bases: object

arguments = [(['-v', '--version'], {'action': 'version', 'version': '0.0.1'})][source]¶

description = 'Whole-cell model of H1 human embryonic stem cells (hESCs)'[source]¶

label = 'base'[source]¶

decay()[source]¶

essential()[source]¶

growth_decay()[source]¶

kb()[source]¶

model()[source]¶

recal()[source]¶

sd_kb()[source]¶

sd_model()[source]¶

sd_sim()[source]¶

sim()[source]¶

h1_hesc.__main__.main()[source]¶

3.1.4. h1_hesc._version module¶

3.1.5. h1_hesc.utils module¶

A set of functions to support core functions

Author: Yin Hoon Chew <yinhoon.chew@mssm.edu>
Author: Jonathan Karr <jonrkarr@gmail.com>
Date: 2017-09-19
Copyright: 2017, Karr Lab
License: MIT

h1_hesc.utils.calc_eff_vmax(enzyme_kcats, prot_concs)[source]¶

Calculate the effective V_max of a reaction based on the kcats of each enzyme and the concentrations and stoichiometries of their subunits

Parameters

enzyme_kcats (dict) – a dictionary whose keys are enzymes (semicolon-separated list of the stoichiometry * the UniProt id of each subunit of the complex) and values are their k_{cat`s. See :obj:`calc_mean_kcat} for examples.
prot_concs (dict) – a dictionary whose keys are the UniProt ids of proteins and values are their concentrations

Returns

effective V_max

Return type

float

h1_hesc.utils.calc_median_kcat(reactions, enzyme_strs, kcats)[source]¶

Calculate the median k_cat for each enzyme of each reaction among a set of observed kcats

Parameters

reactions (list) – reaction ids
enzymes (list) –
enzyme compositions (semicolon-separated list of the stoichiometry * the UniProt id of each subunit of the complex), in the same order as the reaction list. Examples:
- A: monomer of A
- 2*A: homodimer of A
- A; B: heterodimer of A and B
- 2*A; 2*B: heterotetramer of A and B
kcats (list) – observed kcats, in the same order as the reaction and enzyme lists

Returns

a nested dictionary whose keys are reaction ids and values are dictionaries whose: keys are enzyme ids and values are the mean k_cat observed for the enzyme for the reaction

Return type

dict

h1_hesc.utils.create_conv_model(met_model)[source]¶

Convert a metabolism model into a linear programming model in conv_opt format

Parameters

met_model (wc_lang.Submodel) – metabolism submodel

Returns

a linear programming model in conv_opt format dict of str: conv_opt.Variable): a dictionary mapping

reaction IDs to their associated conv_opt.Variable objects

dict of str: list of conv_opt.LinearTerm: a: dictionary mapping species IDs to their associated list of conv_opt.LinearTerm objects representing their stoichiometry coefficients in reactions they participate in

Return type

conv_opt.Model

h1_hesc.utils.determine_bounds(met_model, cell_volume, scale_factor=None)[source]¶

Determine the bounds of a linear programming problem based on calculated rate laws or measured fluxes

Parameters

met_model (wc_lang.Submodel) – metabolism submodel
cell_volume (float) – cell volume
scale_factor (float, optional) – a scaling factor for the bounds; the default value is 1

Returns

tuple: a dictionary that maps reaction IDs: to (minimum bound, maximum bound) tuples

Return type

dict of str

h1_hesc.utils.eval_gene_reaction_rule(reaction, gene_expressions)[source]¶

Calculate the activity of a gene-reaction rule based on the expression of each gene

Parameters

reaction (cobra.Reaction) – COBRApy reaction
gene_expressions (dict) – dictionary whose keys are gene ids (str) and values are gene expressions (bool)

Returns

reaction activity

Return type

bool

h1_hesc.utils.extract_info_from_string(input_str, start_substr, end_substr, include_start=True)[source]¶

Parse strings to get metadata recorded in undefined format

Parameters

input_str (str) – input string
start_substr (str) – substring that indicates the metadata key
end_substr (str) – substring after the metadata value
include_start (bool, optional) – if False, the substring indicating the metadata key will be stripped out of the returned string, default = True

Returns

metadata value

Return type

str

h1_hesc.utils.get_complexes_from_gene_rule(rule)[source]¶

Get a list of all of the complexes that can catalyze a reaction from its gene-reaction rule

Parameters

rule (str) – gene-reaction rule (e.g. HGNC:8994 or HGNC:8995 or HGNC:8996)

Returns

list of complexes that can catalyze the reaction, with each complex listed: as a list of the names of the subunits

Return type

list of list of str

h1_hesc.utils.get_enzyme_equation(enzyme)[source]¶

Get a string representation of the subunits of an enzyme

Parameters: enzyme (list of dict) – enzyme
Returns: string representation of the subunits of the enzyme e.g. 2*subunit-A; subunit-B
Return type: str

h1_hesc.utils.get_reaction_equation(reaction)[source]¶

Create a string representation of the equation of a reaction

Parameters: reaction (dict) – dictionary that contains a key participants whose value is a list of participants, each of which is a dictionary with a species
Returns: string representation of the equation of the reaction
Return type: str

h1_hesc.utils.get_value_inchi_formula_connectivity(inchi_str)[source]¶

Get only the empirical formula and connectivity portion of an InChI string

Parameters: inchi_str (str) – InChI string
Returns: InchI string with only the the empirical formula and connectivity portion
Return type: str

h1_hesc.utils.has_all_inchi_structures(reaction)[source]¶

Determine if structures (in InChI format) are defined for all of a reaction’s participants

Parameters: reaction (dict) – dictionary that contains a key participants whose value is a list of participants, each of which is a dictionary with a species_type
Returns: True if structures (in InChI format) are defined for all of a reaction’s participants
Return type: bool

h1_hesc.utils.parse_cobra_reaction_equation(equation)[source]¶

Parse a COBRApy reaction equation

Parameters: equation (str) – a COBRApy reaction equation
Returns: dictionary whose keys are species ids (str) and values are stoichiometric coefficients (float) bool: reversibility of the reaction
Return type: dict

h1_hesc.utils.parse_cobra_reaction_equation_side(side)[source]¶

Parse a side of a COBRApy reaction equation

Parameters: side (str) – side of a COBRApy reaction equation
Returns: dictionary whose keys are species ids (str) and values are stoichiometric coefficients (float)
Return type: dict

h1_hesc.utils.remove_inchi_layer(inchi_structure, layer_to_remove, raise_error_if_no_layer=False)[source]¶

Remove a layer for an InChI-encoded chemical structure

Parameters

inchi_structure (str) – InChI-encoded chemical structure
layer_to_remove (str) – character code for the layer to remove
raise_error_if_no_layer (bool, optional) – if True, raise an error if the structure doesn’t contain the layer

Returns

InChI-encoded chemical structure with the specified layer removed

Return type

str

Raises

ValueError – if the raise_error_if_no_layer is True and the layer isn’t in the structure

3.1. h1_hesc package¶

3.1.1. Subpackages¶

3.1.2. Submodules¶

3.1.3. h1_hesc.__main__ module¶

3.1.4. h1_hesc._version module¶

3.1.5. h1_hesc.utils module¶

3.1.6. Module contents¶

3.1.3. h1_hesc.main module¶