From f72eff9bf767b2ec684c4a4114353780cb26650a Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Mon, 9 Dec 2024 12:59:15 -0600 Subject: [PATCH 1/2] feat: add boundary column --- .../boundary_rxns/naiveB_boundary_rxns.csv | 140 +++++++++--------- main/data/boundary_rxns/smB_boundary_rxns.csv | 140 +++++++++--------- 2 files changed, 140 insertions(+), 140 deletions(-) diff --git a/main/data/boundary_rxns/naiveB_boundary_rxns.csv b/main/data/boundary_rxns/naiveB_boundary_rxns.csv index 7130c9be..f9297391 100644 --- a/main/data/boundary_rxns/naiveB_boundary_rxns.csv +++ b/main/data/boundary_rxns/naiveB_boundary_rxns.csv @@ -1,70 +1,70 @@ -Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate -Exchange,glc_D,Extracellular,-100,1000 -Exchange,fe2,Extracellular,-1000,1000 -Exchange,gal,Extracellular,0,1000 -Exchange,zn2,Extracellular,-1000,1000 -Exchange,ca2,Extracellular,-1000,1000 -Exchange,na1,Extracellular,-1000,1000 -Exchange,cl,Extracellular,-1000,1000 -Exchange,k,Extracellular,-1000,1000 -Exchange,h,Extracellular,-1000,1000 -Exchange,h2o,Extracellular,-1000,1000 -Exchange,o2,Extracellular,-1000,1000 -Exchange,pi,Extracellular,-1000,1000 -Exchange,ppi,Extracellular,-1000,1000 -Exchange,co2,Extracellular,-1000,1000 -Exchange,nh4,Extracellular,-1000,1000 -Exchange,no2,Extracellular,-1000,1000 -Exchange,co,Extracellular,-1000,1000 -Exchange,asn_L,Extracellular,-1,1000 -Exchange,asp_L,Extracellular,-1,1000 -Exchange,glu_L,Extracellular,-1,1000 -Exchange,ile_L,Extracellular,-1,1000 -Exchange,leu_L,Extracellular,-1,1000 -Exchange,lys_L,Extracellular,-1,1000 -Exchange,met_L,Extracellular,-1,1000 -Exchange,pro_L,Extracellular,-1,1000 -Exchange,ser_L,Extracellular,-1,1000 -Exchange,val_L,Extracellular,-1,1000 -Exchange,gly,Extracellular,-1,1000 -Exchange,cys_L,Extracellular,-1,1000 -Exchange,ala_L,Extracellular,-1,1000 -Exchange,his_L,Extracellular,-1,1000 -Exchange,thr_L,Extracellular,-1,1000 -Exchange,gln_L,Extracellular,-1,1000 -Exchange,phe_L,Extracellular,-1,1000 -Exchange,tyr_L,Extracellular,-1,1000 -Exchange,arg_L,Extracellular,-1,1000 -Exchange,trp_L,Extracellular,-1,1000 -Exchange,eicostet,Extracellular,-1,1000 -Exchange,hdca,Extracellular,-1,1000 -Exchange,hdcea,Extracellular,-1,1000 -Exchange,lnlc,Extracellular,-1,1000 -Exchange,lnlnca,Extracellular,-1,1000 -Exchange,lnlncg,Extracellular,-1,1000 -Exchange,ocdca,Extracellular,-1,1000 -Exchange,ocdcea,Extracellular,-1,1000 -Exchange,thmmp,Extracellular,0,1000 -Exchange,thmtp,Extracellular,0,1000 -Exchange,ncam,Extracellular,0,1000 -Exchange,pnto_R,Extracellular,0,1000 -Exchange,pydxn,Extracellular,0,1000 -Exchange,pydx,Extracellular,0,1000 -Exchange,pydam,Extracellular,0,1000 -Exchange,btn,Extracellular,0,1000 -Exchange,fol,Extracellular,-10,1000 -Exchange,aqcobal,Extracellular,0,1000 -Exchange,vitd3,Extracellular,-1,1000 -Exchange,ascb_L,Extracellular,0,1000 -Exchange,retinol,Extracellular,-10,1000 -Exchange,retinal,Extracellular,-10,1000 -Exchange,ala_B,Extracellular,-1,1000 -Exchange,ala_D,Extracellular,-1,1000 -Exchange,h2co3,Extracellular,-1000,1000 -Exchange,h2o2,Extracellular,-1000,1000 -Exchange,hco3,Extracellular,-1000,1000 -Exchange,orn,Extracellular,-1,1000 -Exchange,orn_D,Extracellular,-1,1000 -Exchange,so4,Extracellular,-1000,1000 -Exchange,ribflv,Extracellular,-1,1000 -Exchange,Lcystin,Extracellular,-1,1000 \ No newline at end of file +Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate +Demand,Exchange,glc_D,Extracellular,-100,1000 +Demand,Exchange,fe2,Extracellular,-1000,1000 +Demand,Exchange,gal,Extracellular,0,1000 +Demand,Exchange,zn2,Extracellular,-1000,1000 +Demand,Exchange,ca2,Extracellular,-1000,1000 +Demand,Exchange,na1,Extracellular,-1000,1000 +Demand,Exchange,cl,Extracellular,-1000,1000 +Demand,Exchange,k,Extracellular,-1000,1000 +Demand,Exchange,h,Extracellular,-1000,1000 +Demand,Exchange,h2o,Extracellular,-1000,1000 +Demand,Exchange,o2,Extracellular,-1000,1000 +Demand,Exchange,pi,Extracellular,-1000,1000 +Demand,Exchange,ppi,Extracellular,-1000,1000 +Demand,Exchange,co2,Extracellular,-1000,1000 +Demand,Exchange,nh4,Extracellular,-1000,1000 +Demand,Exchange,no2,Extracellular,-1000,1000 +Demand,Exchange,co,Extracellular,-1000,1000 +Demand,Exchange,asn_L,Extracellular,-1,1000 +Demand,Exchange,asp_L,Extracellular,-1,1000 +Demand,Exchange,glu_L,Extracellular,-1,1000 +Demand,Exchange,ile_L,Extracellular,-1,1000 +Demand,Exchange,leu_L,Extracellular,-1,1000 +Demand,Exchange,lys_L,Extracellular,-1,1000 +Demand,Exchange,met_L,Extracellular,-1,1000 +Demand,Exchange,pro_L,Extracellular,-1,1000 +Demand,Exchange,ser_L,Extracellular,-1,1000 +Demand,Exchange,val_L,Extracellular,-1,1000 +Demand,Exchange,gly,Extracellular,-1,1000 +Demand,Exchange,cys_L,Extracellular,-1,1000 +Demand,Exchange,ala_L,Extracellular,-1,1000 +Demand,Exchange,his_L,Extracellular,-1,1000 +Demand,Exchange,thr_L,Extracellular,-1,1000 +Demand,Exchange,gln_L,Extracellular,-1,1000 +Demand,Exchange,phe_L,Extracellular,-1,1000 +Demand,Exchange,tyr_L,Extracellular,-1,1000 +Demand,Exchange,arg_L,Extracellular,-1,1000 +Demand,Exchange,trp_L,Extracellular,-1,1000 +Demand,Exchange,eicostet,Extracellular,-1,1000 +Demand,Exchange,hdca,Extracellular,-1,1000 +Demand,Exchange,hdcea,Extracellular,-1,1000 +Demand,Exchange,lnlc,Extracellular,-1,1000 +Demand,Exchange,lnlnca,Extracellular,-1,1000 +Demand,Exchange,lnlncg,Extracellular,-1,1000 +Demand,Exchange,ocdca,Extracellular,-1,1000 +Demand,Exchange,ocdcea,Extracellular,-1,1000 +Demand,Exchange,thmmp,Extracellular,0,1000 +Demand,Exchange,thmtp,Extracellular,0,1000 +Demand,Exchange,ncam,Extracellular,0,1000 +Demand,Exchange,pnto_R,Extracellular,0,1000 +Demand,Exchange,pydxn,Extracellular,0,1000 +Demand,Exchange,pydx,Extracellular,0,1000 +Demand,Exchange,pydam,Extracellular,0,1000 +Demand,Exchange,btn,Extracellular,0,1000 +Demand,Exchange,fol,Extracellular,-10,1000 +Demand,Exchange,aqcobal,Extracellular,0,1000 +Demand,Exchange,vitd3,Extracellular,-1,1000 +Demand,Exchange,ascb_L,Extracellular,0,1000 +Demand,Exchange,retinol,Extracellular,-10,1000 +Demand,Exchange,retinal,Extracellular,-10,1000 +Demand,Exchange,ala_B,Extracellular,-1,1000 +Demand,Exchange,ala_D,Extracellular,-1,1000 +Demand,Exchange,h2co3,Extracellular,-1000,1000 +Demand,Exchange,h2o2,Extracellular,-1000,1000 +Demand,Exchange,hco3,Extracellular,-1000,1000 +Demand,Exchange,orn,Extracellular,-1,1000 +Demand,Exchange,orn_D,Extracellular,-1,1000 +Demand,Exchange,so4,Extracellular,-1000,1000 +Demand,Exchange,ribflv,Extracellular,-1,1000 +Demand,Exchange,Lcystin,Extracellular,-1,1000 \ No newline at end of file diff --git a/main/data/boundary_rxns/smB_boundary_rxns.csv b/main/data/boundary_rxns/smB_boundary_rxns.csv index 9f0f9385..f9297391 100644 --- a/main/data/boundary_rxns/smB_boundary_rxns.csv +++ b/main/data/boundary_rxns/smB_boundary_rxns.csv @@ -1,70 +1,70 @@ -Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate -Exchange,glc_D,Extracellular,-100,1000 -Exchange,fe2,Extracellular,-1000,1000 -Exchange,gal,Extracellular,0,1000 -Exchange,zn2,Extracellular,-1000,1000 -Exchange,ca2,Extracellular,-1000,1000 -Exchange,na1,Extracellular,-1000,1000 -Exchange,cl,Extracellular,-1000,1000 -Exchange,k,Extracellular,-1000,1000 -Exchange,h,Extracellular,-1000,1000 -Exchange,h2o,Extracellular,-1000,1000 -Exchange,o2,Extracellular,-1000,1000 -Exchange,pi,Extracellular,-1000,1000 -Exchange,ppi,Extracellular,-1000,1000 -Exchange,co2,Extracellular,-1000,1000 -Exchange,nh4,Extracellular,-1000,1000 -Exchange,no2,Extracellular,-1000,1000 -Exchange,co,Extracellular,-1000,1000 -Exchange,asn_L,Extracellular,-1,1000 -Exchange,asp_L,Extracellular,-1,1000 -Exchange,glu_L,Extracellular,-1,1000 -Exchange,ile_L,Extracellular,-1,1000 -Exchange,leu_L,Extracellular,-1,1000 -Exchange,lys_L,Extracellular,-1,1000 -Exchange,met_L,Extracellular,-1,1000 -Exchange,pro_L,Extracellular,-1,1000 -Exchange,ser_L,Extracellular,-1,1000 -Exchange,val_L,Extracellular,-1,1000 -Exchange,gly,Extracellular,-1,1000 -Exchange,cys_L,Extracellular,-1,1000 -Exchange,ala_L,Extracellular,-1,1000 -Exchange,his_L,Extracellular,-1,1000 -Exchange,thr_L,Extracellular,-1,1000 -Exchange,gln_L,Extracellular,-1,1000 -Exchange,phe_L,Extracellular,-1,1000 -Exchange,tyr_L,Extracellular,-1,1000 -Exchange,arg_L,Extracellular,-1,1000 -Exchange,trp_L,Extracellular,-1,1000 -Exchange,eicostet,Extracellular,-1,1000 -Exchange,hdca,Extracellular,-1,1000 -Exchange,hdcea,Extracellular,-1,1000 -Exchange,lnlc,Extracellular,-1,1000 -Exchange,lnlnca,Extracellular,-1,1000 -Exchange,lnlncg,Extracellular,-1,1000 -Exchange,ocdca,Extracellular,-1,1000 -Exchange,ocdcea,Extracellular,-1,1000 -Exchange,thmmp,Extracellular,0,1000 -Exchange,thmtp,Extracellular,0,1000 -Exchange,ncam,Extracellular,0,1000 -Exchange,pnto_R,Extracellular,0,1000 -Exchange,pydxn,Extracellular,0,1000 -Exchange,pydx,Extracellular,0,1000 -Exchange,pydam,Extracellular,0,1000 -Exchange,btn,Extracellular,0,1000 -Exchange,fol,Extracellular,-10,1000 -Exchange,aqcobal,Extracellular,0,1000 -Exchange,vitd3,Extracellular,-1,1000 -Exchange,ascb_L,Extracellular,0,1000 -Exchange,retinol,Extracellular,-10,1000 -Exchange,retinal,Extracellular,-10,1000 -Exchange,ala_B,Extracellular,-1,1000 -Exchange,ala_D,Extracellular,-1,1000 -Exchange,h2co3,Extracellular,-1000,1000 -Exchange,h2o2,Extracellular,-1000,1000 -Exchange,hco3,Extracellular,-1000,1000 -Exchange,orn,Extracellular,-1,1000 -Exchange,orn_D,Extracellular,-1,1000 -Exchange,so4,Extracellular,-1000,1000 -Exchange,ribflv,Extracellular,-1,1000 -Exchange,Lcystin,Extracellular,-1,1000 +Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate +Demand,Exchange,glc_D,Extracellular,-100,1000 +Demand,Exchange,fe2,Extracellular,-1000,1000 +Demand,Exchange,gal,Extracellular,0,1000 +Demand,Exchange,zn2,Extracellular,-1000,1000 +Demand,Exchange,ca2,Extracellular,-1000,1000 +Demand,Exchange,na1,Extracellular,-1000,1000 +Demand,Exchange,cl,Extracellular,-1000,1000 +Demand,Exchange,k,Extracellular,-1000,1000 +Demand,Exchange,h,Extracellular,-1000,1000 +Demand,Exchange,h2o,Extracellular,-1000,1000 +Demand,Exchange,o2,Extracellular,-1000,1000 +Demand,Exchange,pi,Extracellular,-1000,1000 +Demand,Exchange,ppi,Extracellular,-1000,1000 +Demand,Exchange,co2,Extracellular,-1000,1000 +Demand,Exchange,nh4,Extracellular,-1000,1000 +Demand,Exchange,no2,Extracellular,-1000,1000 +Demand,Exchange,co,Extracellular,-1000,1000 +Demand,Exchange,asn_L,Extracellular,-1,1000 +Demand,Exchange,asp_L,Extracellular,-1,1000 +Demand,Exchange,glu_L,Extracellular,-1,1000 +Demand,Exchange,ile_L,Extracellular,-1,1000 +Demand,Exchange,leu_L,Extracellular,-1,1000 +Demand,Exchange,lys_L,Extracellular,-1,1000 +Demand,Exchange,met_L,Extracellular,-1,1000 +Demand,Exchange,pro_L,Extracellular,-1,1000 +Demand,Exchange,ser_L,Extracellular,-1,1000 +Demand,Exchange,val_L,Extracellular,-1,1000 +Demand,Exchange,gly,Extracellular,-1,1000 +Demand,Exchange,cys_L,Extracellular,-1,1000 +Demand,Exchange,ala_L,Extracellular,-1,1000 +Demand,Exchange,his_L,Extracellular,-1,1000 +Demand,Exchange,thr_L,Extracellular,-1,1000 +Demand,Exchange,gln_L,Extracellular,-1,1000 +Demand,Exchange,phe_L,Extracellular,-1,1000 +Demand,Exchange,tyr_L,Extracellular,-1,1000 +Demand,Exchange,arg_L,Extracellular,-1,1000 +Demand,Exchange,trp_L,Extracellular,-1,1000 +Demand,Exchange,eicostet,Extracellular,-1,1000 +Demand,Exchange,hdca,Extracellular,-1,1000 +Demand,Exchange,hdcea,Extracellular,-1,1000 +Demand,Exchange,lnlc,Extracellular,-1,1000 +Demand,Exchange,lnlnca,Extracellular,-1,1000 +Demand,Exchange,lnlncg,Extracellular,-1,1000 +Demand,Exchange,ocdca,Extracellular,-1,1000 +Demand,Exchange,ocdcea,Extracellular,-1,1000 +Demand,Exchange,thmmp,Extracellular,0,1000 +Demand,Exchange,thmtp,Extracellular,0,1000 +Demand,Exchange,ncam,Extracellular,0,1000 +Demand,Exchange,pnto_R,Extracellular,0,1000 +Demand,Exchange,pydxn,Extracellular,0,1000 +Demand,Exchange,pydx,Extracellular,0,1000 +Demand,Exchange,pydam,Extracellular,0,1000 +Demand,Exchange,btn,Extracellular,0,1000 +Demand,Exchange,fol,Extracellular,-10,1000 +Demand,Exchange,aqcobal,Extracellular,0,1000 +Demand,Exchange,vitd3,Extracellular,-1,1000 +Demand,Exchange,ascb_L,Extracellular,0,1000 +Demand,Exchange,retinol,Extracellular,-10,1000 +Demand,Exchange,retinal,Extracellular,-10,1000 +Demand,Exchange,ala_B,Extracellular,-1,1000 +Demand,Exchange,ala_D,Extracellular,-1,1000 +Demand,Exchange,h2co3,Extracellular,-1000,1000 +Demand,Exchange,h2o2,Extracellular,-1000,1000 +Demand,Exchange,hco3,Extracellular,-1000,1000 +Demand,Exchange,orn,Extracellular,-1,1000 +Demand,Exchange,orn_D,Extracellular,-1,1000 +Demand,Exchange,so4,Extracellular,-1000,1000 +Demand,Exchange,ribflv,Extracellular,-1,1000 +Demand,Exchange,Lcystin,Extracellular,-1,1000 \ No newline at end of file From 7b581470111243532e9dc17b2a74490a30384d32 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Mon, 9 Dec 2024 13:00:20 -0600 Subject: [PATCH 2/2] fix: allow new boundary column --- main/como/create_context_specific_model.py | 1 + 1 file changed, 1 insertion(+) diff --git a/main/como/create_context_specific_model.py b/main/como/create_context_specific_model.py index 373dab92..896c90cc 100644 --- a/main/como/create_context_specific_model.py +++ b/main/como/create_context_specific_model.py @@ -550,6 +550,7 @@ def _collect_boundary_reactions(path: Path) -> _BoundaryReactions: df = _create_df(path) for column in df.columns: if column not in [ + "boundary", "reaction", "abbreviation", "compartment",