From e6bf033af7c2afdf6230e75f53f5cbd20b436001 Mon Sep 17 00:00:00 2001 From: dtriadis Date: Thu, 19 Jun 2025 15:40:36 +1200 Subject: [PATCH 1/2] Update msbuilder.py Variable sn undefined in method: looks like it should be rn_norm. --- modelseedpy/core/msbuilder.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modelseedpy/core/msbuilder.py b/modelseedpy/core/msbuilder.py index 2b94352f..ae2f12cc 100755 --- a/modelseedpy/core/msbuilder.py +++ b/modelseedpy/core/msbuilder.py @@ -443,12 +443,12 @@ def _get_template_reaction_complexes(self, template_reaction): for role, (triggering, optional) in cpx.roles.items(): rn_norm = normalize_role(role.name) template_reaction_complexes[cpx.id][role.id] = [ - sn, + rn_norm, triggering, optional, set() - if sn not in self.search_name_to_genes - else set(self.search_name_to_genes[sn]), + if rn_norm not in self.search_name_to_genes + else set(self.search_name_to_genes[rn_norm]), ] return template_reaction_complexes From 84828f6d703884df8f2d1ae8b0f9631808031b1d Mon Sep 17 00:00:00 2001 From: dtriadis Date: Thu, 19 Jun 2025 16:42:21 +1200 Subject: [PATCH 2/2] Update msbuilder.py t[3] to complx[3] in _build_reaction_complex_get2 --- modelseedpy/core/msbuilder.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modelseedpy/core/msbuilder.py b/modelseedpy/core/msbuilder.py index ae2f12cc..0ce39e03 100755 --- a/modelseedpy/core/msbuilder.py +++ b/modelseedpy/core/msbuilder.py @@ -466,7 +466,7 @@ def _build_reaction_complex_gpr_sets2( complete &= len(complx[3]) > 0 or not complx[1] or complx[2] if len(complx[3]) > 0: roles.add(role_id) - role_genes[role_id] = t[3] + role_genes[role_id] = complx[3] # print(cpx_id, complete, roles) if len(roles) > 0 and (allow_incomplete_complexes or complete): complexes[cpx_id] = {}