diff --git a/xbanalysis/model/fbc_gene_product.py b/xbanalysis/model/fbc_gene_product.py
new file mode 100644
index 0000000000000000000000000000000000000000..efd547704b0f24e93b972cd059221cafac9b9614
--- /dev/null
+++ b/xbanalysis/model/fbc_gene_product.py
@@ -0,0 +1,12 @@
+"""Implementation of FbcGeneProduct class.
+
+Peter Schubert, HHU Duesseldorf, July 2022
+"""
+
+
+class FbcGeneProduct:
+
+ def __init__(self, s_fbc_gene_product):
+ self.id = s_fbc_gene_product.name
+ self.name = s_fbc_gene_product.get('name', '')
+ self.label = s_fbc_gene_product['label']
diff --git a/xbanalysis/model/sbo_term.py b/xbanalysis/model/sbo_term.py
index 8272d072a9fb5c99d282a43ac6a465baa56384ad..52b5ace86069be7e01c5fea198dd4b20a66e8e6e 100644
--- a/xbanalysis/model/sbo_term.py
+++ b/xbanalysis/model/sbo_term.py
@@ -97,7 +97,7 @@ class SboTerm:
@property
def sbo_term(self):
- return self.__sbo_term
+ return re.sub('_', ':', self.__sbo_term)
@sbo_term.setter
def sbo_term(self, sbo_term):
diff --git a/xbanalysis/model/xba_model.py b/xbanalysis/model/xba_model.py
index 3f643b91d4d78fd51cb7b052768412c9161cb04f..29bcbccbd4b531cd1374efb9c81b6753d9f595eb 100644
--- a/xbanalysis/model/xba_model.py
+++ b/xbanalysis/model/xba_model.py
@@ -14,6 +14,7 @@ from .xba_parameter import XbaParameter
from .xba_reaction import XbaReaction
from .xba_species import XbaSpecies
from .fbc_objective import FbcObjective
+from .fbc_gene_product import FbcGeneProduct
# TODO: implement isGBAmodel(), isFBAmodel(), isRBAmodel()
@@ -51,6 +52,9 @@ class XbaModel:
if 'fbcObjectives' in model_dict:
self.fbc_objectives = {oid: FbcObjective(row)
for oid, row in model_dict['fbcObjectives'].iterrows()}
+ if 'fbcGeneProducts' in model_dict:
+ self.fbc_gene_products = {gp_id: FbcGeneProduct(row)
+ for gp_id, row in model_dict['fbcGeneProducts'].iterrows()}
def get_stoic_matrix(self, sids, rids):
"""retrieve stoichiometric sub-matrix [sids x rids].
diff --git a/xbanalysis/model/xba_reaction.py b/xbanalysis/model/xba_reaction.py
index 7bbc2b6a91966d0158da4532242de51ee835c9fd..e483fee3fccab608621b74d3038b5c5433a58f4d 100644
--- a/xbanalysis/model/xba_reaction.py
+++ b/xbanalysis/model/xba_reaction.py
@@ -47,6 +47,9 @@ class XbaReaction:
if self.reversible is False:
self.fbc_lb = max(0, self.fbc_lb)
self.fbc_ub = max(0, self.fbc_ub)
+ if 'fbcGeneProdAssoc' in s_reaction:
+ if type(s_reaction['fbcGeneProdAssoc']) == str:
+ self.fbc_gpa = re.sub(r'^assoc=', '', s_reaction['fbcGeneProdAssoc'])
if 'xmlAnnotation' in s_reaction:
attrs = sbmlxdf.extract_xml_attrs(s_reaction['xmlAnnotation'], ns=xml_rba_ns, token='kinetics')
if 'kapp_f_per_s' in attrs:
diff --git a/xbanalysis/model/xba_species.py b/xbanalysis/model/xba_species.py
index a7afc6243ca32b103050d35cd6f63842f9794459..71706e7cd7f43d3da3d8dd9201a765ce19fe7f34 100644
--- a/xbanalysis/model/xba_species.py
+++ b/xbanalysis/model/xba_species.py
@@ -34,7 +34,7 @@ class XbaSpecies:
if 'process_capacity_per_s' in attrs:
self.rba_process_capacity = float(attrs.pop('process_capacity_per_s'))
if len(attrs) > 0:
- self.rba_process_costs = attrs
+ self.rba_process_costs = {key: float(val) for key, val in attrs.items()}
self.ps_rid = None
self.m_reactions = {}
diff --git a/xbanalysis/problems/fba_problem.py b/xbanalysis/problems/fba_problem.py
index ed73a4b96a57819656ddfb09e67d624862bc6279..539a47a580e295352d6523897ae79884404c0538 100644
--- a/xbanalysis/problems/fba_problem.py
+++ b/xbanalysis/problems/fba_problem.py
@@ -143,7 +143,6 @@ class FbaProblem:
if lp is None:
return {'success': False, 'message': 'not an FBA model'}
res = lp.solve()
- del lp
res['x'] = self.combine_fwd_bwd(res['x'])
res['reduced_costs'] = self.combine_fwd_bwd(res['reduced_costs'])
return res
@@ -176,7 +175,6 @@ class FbaProblem:
res = lp.solve()
res['x'] = self.combine_fwd_bwd(res['x'])
res['reduced_costs'] = self.combine_fwd_bwd(res['reduced_costs'])
- del lp
return res
def fva_optimize(self, rids=None, fract_of_optimum=1.0):
@@ -231,7 +229,6 @@ class FbaProblem:
else:
print(f"FVA max failed for {rid}")
flux_ranges[1, idx] = np.nan
- del lp
res = {'rids': rids, 'min': flux_ranges[0], 'max': flux_ranges[1],
'obj_min': flux_ranges[2], 'obj_max': flux_ranges[3]}
diff --git a/xbanalysis/problems/rba_problem.py b/xbanalysis/problems/rba_problem.py
index 13433e9a0d679b3c00b08a2dca98fbdfeaeb8284..11c6dd7ecfd7686a1cc95e736fcbbb5d522e5b0b 100644
--- a/xbanalysis/problems/rba_problem.py
+++ b/xbanalysis/problems/rba_problem.py
@@ -24,6 +24,8 @@ class RbaProblem:
:param xba_model:
"""
+ self.xba_model = xba_model
+
# metabolic reactions and enzyme transitions (no FBA reactions, no protein synthesis, no degradation)
self.mr_rids = [r.id for r in xba_model.reactions.values() if r.sboterm.is_in_branch('SBO:0000167')
and r.sboterm.is_in_branch('SBO:0000179') is False]
@@ -145,7 +147,6 @@ class RbaProblem:
lp = LpProblem()
lp.configure(self.obj_coefs, constr_coefs, self.fix_row_bnds, self.col_bnds, self.obj_dir)
res = lp.solve(scaling=self.scaling)
- del lp
if res['success'] and res['fun'] > 1e-10:
gr['lb'] = gr['try']
gr['try'] *= 10
@@ -169,13 +170,19 @@ class RbaProblem:
lp = LpProblem()
lp.configure(self.obj_coefs, constr_coefs, self.fix_row_bnds, self.col_bnds, self.obj_dir)
res = lp.solve(scaling=self.scaling)
- del lp
if res['success'] and res['fun'] > 1e-10:
gr['lb'] = gr['try']
else:
gr['ub'] = gr['try']
if (gr['ub'] - gr['lb']) < gr['try'] * 1e-5:
break
+
+ # get optimum values for the final solution
+ gr['try'] = gr['lb']
+ constr_coefs = self.fix_mat + gr['try'] * self.var_mat
+ lp = LpProblem()
+ lp.configure(self.obj_coefs, constr_coefs, self.fix_row_bnds, self.col_bnds, self.obj_dir)
+ res = lp.solve(scaling=self.scaling)
res['fun'] = gr['try']
return res