From 19dd0cffd011dc2d73717633a3d609c7186c57d5 Mon Sep 17 00:00:00 2001
From: Peter Schubert <Peter.Schubert@hhu.de>
Date: Mon, 16 May 2022 14:58:33 +0200
Subject: [PATCH] protein syntheses reaction allow sboterm 589 and 205 for now.
---
xbanalysis/model/xba_reaction.py | 2 +-
xbanalysis/problems/gba_problem.py | 3 ++-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/xbanalysis/model/xba_reaction.py b/xbanalysis/model/xba_reaction.py
index 15edd1e..1303bf6 100644
--- a/xbanalysis/model/xba_reaction.py
+++ b/xbanalysis/model/xba_reaction.py
@@ -65,7 +65,7 @@ class XbaReaction:
# to species being consumed add the enzyme product with corresponding stoichiometry
# to species being produced add the enzyme product with corresponding stoichiometry, unless
# the species is itself the enzyme product, in which case we add the ps reaction producing it.
- if self.sboterm == 'SBO:0000589':
+ if (self.sboterm == 'SBO:0000589') or (self.sboterm == 'SBO:0000205') :
enz_sid = ''
for sid in self.products:
if (species[sid].sboterm == 'SBO:0000252') or (species[sid].sboterm == 'SBO:0000250'):
diff --git a/xbanalysis/problems/gba_problem.py b/xbanalysis/problems/gba_problem.py
index 0488eae..1f242fb 100644
--- a/xbanalysis/problems/gba_problem.py
+++ b/xbanalysis/problems/gba_problem.py
@@ -41,7 +41,8 @@ class GbaProblem:
if ((r.sboterm == 'SBO:0000167') or
(r.sboterm == 'SBO:0000179') or
(r.sboterm == 'SBO:0000182'))]
- self.ps_rids = [r.id for r in xba_model.reactions.values() if r.sboterm == 'SBO:0000589']
+ self.ps_rids = [r.id for r in xba_model.reactions.values()
+ if (r.sboterm == 'SBO:0000589') or (r.sboterm == 'SBO:0000205')]
spont_rids = [rid for rid in self.mr_rids if xba_model.reactions[rid].enzyme == '']
# calculate stoichiometric for mass balance equality constraints
--
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