From 53ca985343250835c85b3630be9ac4c857310bae Mon Sep 17 00:00:00 2001
From: Peter Schubert <Peter.Schubert@hhu.de>
Date: Thu, 5 Oct 2023 11:38:34 +0200
Subject: [PATCH] gba_stoic_problem solved via ipopt using jax autograd and jit
---
xbanalysis/model/fbc_gene_product.py | 5 ++++-
xbanalysis/model/fbc_objective.py | 9 ++++++---
xbanalysis/model/xba_compartment.py | 4 ++++
xbanalysis/model/xba_function.py | 4 ++++
xbanalysis/model/xba_model.py | 6 +++---
xbanalysis/model/xba_parameter.py | 5 ++++-
xbanalysis/model/xba_reaction.py | 5 ++++-
xbanalysis/model/xba_species.py | 11 +++++++++--
xbanalysis/model/xba_unit_def.py | 5 ++++-
xbanalysis/problems/fba_problem.py | 6 +++++-
10 files changed, 47 insertions(+), 13 deletions(-)
diff --git a/xbanalysis/model/fbc_gene_product.py b/xbanalysis/model/fbc_gene_product.py
index efd5477..2551c33 100644
--- a/xbanalysis/model/fbc_gene_product.py
+++ b/xbanalysis/model/fbc_gene_product.py
@@ -8,5 +8,8 @@ class FbcGeneProduct:
def __init__(self, s_fbc_gene_product):
self.id = s_fbc_gene_product.name
- self.name = s_fbc_gene_product.get('name', '')
+ if ('name' in s_fbc_gene_product) and (type(s_fbc_gene_product['name']) == str):
+ self.name = s_fbc_gene_product['name']
+ else:
+ self.name = self.id
self.label = s_fbc_gene_product['label']
diff --git a/xbanalysis/model/fbc_objective.py b/xbanalysis/model/fbc_objective.py
index 4db5d45..a0a8bd0 100644
--- a/xbanalysis/model/fbc_objective.py
+++ b/xbanalysis/model/fbc_objective.py
@@ -10,10 +10,13 @@ class FbcObjective:
def __init__(self, s_fbc_objective):
self.id = s_fbc_objective.name
- self.name = s_fbc_objective.get('name', '')
+ if ('name' in s_fbc_objective) and (type(s_fbc_objective['name']) == str):
+ self.name = s_fbc_objective['name']
+ else:
+ self.name = self.id
self.direction = s_fbc_objective['type']
self.active = s_fbc_objective['active']
- self.coefficiants = {}
+ self.coefficients = {}
for reac_ref in sbmlxdf.record_generator(s_fbc_objective['fluxObjectives']):
params = sbmlxdf.extract_params(reac_ref)
- self.coefficiants[params['reac']] = float(params['coef'])
+ self.coefficients[params['reac']] = float(params['coef'])
diff --git a/xbanalysis/model/xba_compartment.py b/xbanalysis/model/xba_compartment.py
index d243910..6fabc0e 100644
--- a/xbanalysis/model/xba_compartment.py
+++ b/xbanalysis/model/xba_compartment.py
@@ -13,6 +13,10 @@ class XbaCompartment:
def __init__(self, s_compartment):
self.id = s_compartment.name
+ if ('name' in s_compartment) and (type(s_compartment['name']) == str):
+ self.name = s_compartment['name']
+ else:
+ self.name = self.id
self.name = s_compartment.get('name', self.id)
if 'size' in s_compartment:
self.size = s_compartment['size']
diff --git a/xbanalysis/model/xba_function.py b/xbanalysis/model/xba_function.py
index 950bea1..ba93f1f 100644
--- a/xbanalysis/model/xba_function.py
+++ b/xbanalysis/model/xba_function.py
@@ -11,6 +11,10 @@ class XbaFunction:
def __init__(self, s_function):
self.id = s_function.name
+ if ('name' in s_function) and (type(s_function['name']) == str):
+ self.name = s_function['name']
+ else:
+ self.name = self.id
self.name = s_function.get('name', self.id)
self.math = s_function['math']
diff --git a/xbanalysis/model/xba_model.py b/xbanalysis/model/xba_model.py
index f4b3c54..f065b9c 100644
--- a/xbanalysis/model/xba_model.py
+++ b/xbanalysis/model/xba_model.py
@@ -33,18 +33,18 @@ class XbaModel:
print(f'{sbml_file} seems not to be a valid SBML model')
return
model_dict = sbml_model.to_df()
+ self.id = model_dict['modelAttrs'].id
+ self.name = model_dict['modelAttrs'].get('name', self.id)
self.unit_defs = {udid: XbaUnitDef(row)
for udid, row in model_dict['unitDefs'].iterrows()}
self.compartments = {cid: XbaCompartment(row)
for cid, row in model_dict['compartments'].iterrows()}
self.parameters = {pid: XbaParameter(row)
for pid, row in model_dict['parameters'].iterrows()}
+ self.functions = {}
if 'funcDefs' in model_dict:
self.functions = {fid: XbaFunction(row)
for fid, row in model_dict['funcDefs'].iterrows()}
- else:
- self.functions = {}
-
self.species = {sid: XbaSpecies(row)
for sid, row in model_dict['species'].iterrows()}
self.reactions = {rid: XbaReaction(row, self.species, self.functions, self.compartments)
diff --git a/xbanalysis/model/xba_parameter.py b/xbanalysis/model/xba_parameter.py
index b86a0c3..b73c077 100644
--- a/xbanalysis/model/xba_parameter.py
+++ b/xbanalysis/model/xba_parameter.py
@@ -9,7 +9,10 @@ class XbaParameter:
def __init__(self, s_parameter):
self.id = s_parameter.name
- self.name = s_parameter.get('name', self.id)
+ if ('name' in s_parameter) and (type(s_parameter['name']) == str):
+ self.name = s_parameter['name']
+ else:
+ self.name = self.id
self.value = s_parameter['value']
self.constant = s_parameter['constant']
self.units = s_parameter['units']
diff --git a/xbanalysis/model/xba_reaction.py b/xbanalysis/model/xba_reaction.py
index 619520b..20cb42c 100644
--- a/xbanalysis/model/xba_reaction.py
+++ b/xbanalysis/model/xba_reaction.py
@@ -14,7 +14,10 @@ class XbaReaction:
def __init__(self, s_reaction, species, functions, compartments):
self.id = s_reaction.name
- self.name = s_reaction.get('name', self.id)
+ if ('name' in s_reaction) and (type(s_reaction['name']) == str):
+ self.name = s_reaction['name']
+ else:
+ self.name = self.id
if ('sboterm' in s_reaction) and (type(s_reaction['sboterm']) is str):
self.sboterm = SboTerm(s_reaction['sboterm'])
self.reaction_string = s_reaction['reactionString']
diff --git a/xbanalysis/model/xba_species.py b/xbanalysis/model/xba_species.py
index 71706e7..f8f9449 100644
--- a/xbanalysis/model/xba_species.py
+++ b/xbanalysis/model/xba_species.py
@@ -12,7 +12,10 @@ class XbaSpecies:
def __init__(self, s_species):
self.id = s_species.name
- self.name = s_species.get('name', self.id)
+ if ('name' in s_species) and (type(s_species['name']) == str):
+ self.name = s_species['name']
+ else:
+ self.name = self.id
# set sboterm to 000247 to support Flux Balance Analysis
self.sboterm = SboTerm(s_species.get('sboterm', 'SBO:0000247'))
self.compartment = s_species['compartment']
@@ -20,8 +23,12 @@ class XbaSpecies:
self.boundary = s_species['boundaryCondition']
if 'initialConcentration' in s_species:
self.initial_conc = s_species['initialConcentration']
- if 'units' in s_species:
+ if 'substanceUnits' in s_species:
self.units = s_species['substanceUnits']
+ if 'fbcCharge' in s_species:
+ self.charge = s_species['fbcCharge']
+ if 'fbcChemicalFormula' in s_species:
+ self.formula = s_species['fbcChemicalFormula']
if 'xmlAnnotation' in s_species:
attrs = sbmlxdf.extract_xml_attrs(s_species['xmlAnnotation'], ns=xml_gba_ns, token='molecule')
if 'weight_Da' in attrs:
diff --git a/xbanalysis/model/xba_unit_def.py b/xbanalysis/model/xba_unit_def.py
index 5cd1326..72a1180 100644
--- a/xbanalysis/model/xba_unit_def.py
+++ b/xbanalysis/model/xba_unit_def.py
@@ -11,7 +11,10 @@ class XbaUnitDef:
def __init__(self, s_unit_def):
self.id = s_unit_def.name
- self.name = s_unit_def.get('name', self.id)
+ if ('name' in s_unit_def) and (type(s_unit_def['name']) == str):
+ self.name = s_unit_def['name']
+ else:
+ self.name = self.id
self.units = [XbaUnit(sbmlxdf.extract_params(u))
for u in sbmlxdf.record_generator(s_unit_def['units'])]
diff --git a/xbanalysis/problems/fba_problem.py b/xbanalysis/problems/fba_problem.py
index bebc68b..7c328c6 100644
--- a/xbanalysis/problems/fba_problem.py
+++ b/xbanalysis/problems/fba_problem.py
@@ -1,3 +1,7 @@
+"""Implementation of FbaProblem Class.
+
+Peter Schubert, HHU Duesseldorf, September 2022
+"""
import numpy as np
import math
from scipy import sparse
@@ -70,7 +74,7 @@ class FbaProblem:
if fbc_obj.active is True:
# self.obj_id = fbc_obj.id
self.obj_dir = fbc_obj.direction
- self.objective = fbc_obj.coefficiants
+ self.objective = fbc_obj.coefficients
break
# lp problem will only be created once required.
--
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