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KennetLindquist merged 2 commits into from
Jan 21, 2026
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feat: reverse directionality of HSDy #35

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f4fb931
feat: reverse directionality of HSDy
KennetLindquist Oct 30, 2025
08fff45
chore: add macaw test result
KennetLindquist Oct 30, 2025
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18 changes: 9 additions & 9 deletions data/testResults/macaw_results.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -623,7 +623,7 @@ CYSItpp,cysi__L_c --> cysi__L_p,cysi__L_c;cysi__L_p,ok,ok,ok,N/A
CYSS,acser_c + h2s_c --> ac_c + cys__L_c + h_c,ok,ok,ok,ok,N/A
CYSSADS,3sala_c + 2.0 h_c --> ala__L_c + so2_c,3sala_c;so2_c,ok,ok,ok,N/A
CYSTA,akg_c + cys__L_c --> glu__L_c + mercppyr_c,mercppyr_c,ok,ok,ok,N/A
CYSTL,cyst__L_c + h2o_c --> hcys__L_c + nh4_c + pyr_c,cyst__L_c,ok,ok,ok,N/A
CYSTL,cyst__L_c + h2o_c --> hcys__L_c + nh4_c + pyr_c,ok,ok,ok,ok,N/A
CYSabc2pp,atp_c + cys__L_c + h2o_c --> adp_c + cys__L_p + h_c + pi_c,ok,ok,ok,CYSabcpp,N/A
CYSabcpp,atp_c + cys__L_p + h2o_c --> adp_c + cys__L_c + h_c + pi_c,ok,ok,ok,CYSabc2pp,N/A
CYStex,cys__L_e <=> cys__L_p,only when going forwards,ok,ok,ok,N/A
Expand Down Expand Up @@ -1037,7 +1037,7 @@ EX_hdca_e,hdca_e --> ,hdca_e,ok,ok,ok,N/A
EX_hdcea_e,hdcea_e --> ,hdcea_e,ok,ok,ok,N/A
EX_hg2_e,hg2_e --> ,hg2_e,ok,ok,ok,N/A
EX_his__L_e,his__L_e --> ,ok,ok,ok,ok,N/A
EX_hom__L_e,hom__L_e --> ,hom__L_e,ok,ok,ok,N/A
EX_hom__L_e,hom__L_e --> ,ok,ok,ok,ok,N/A
EX_hxa_e,hxa_e --> ,ok,ok,ok,ok,N/A
EX_hxan_e,hxan_e --> ,ok,ok,ok,ok,N/A
EX_idon__L_e,idon__L_e --> ,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -1589,8 +1589,8 @@ HKNDDH,h2o_c + hkndd_c --> h_c + op4en_c + succ_c,hkndd_c;op4en_c,ok,ok,ok,N/A
HKNTDH,h2o_c + hkntd_c --> fum_c + h_c + op4en_c,hkntd_c;op4en_c,ok,ok,ok,N/A
HMBS,h2o_c + 4.0 ppbng_c --> hmbil_c + 4.0 nh4_c,ok,ok,ok,ok,N/A
HMPK1,4ahmmp_c + atp_c --> 4ampm_c + adp_c + h_c,4ahmmp_c,ok,ok,ok,N/A
HOMt2pp,h_p + hom__L_c --> h_c + hom__L_p,hom__L_c;hom__L_p,ok,ok,ok,N/A
HOMtex,hom__L_e <=> hom__L_p,hom__L_e;hom__L_p,ok,ok,ok,N/A
HOMt2pp,h_p + hom__L_c --> h_c + hom__L_p,ok,ok,ok,ok,N/A
HOMtex,hom__L_e <=> hom__L_p,only when going forwards,ok,ok,ok,N/A
HOPNTAL,4h2opntn_c --> acald_c + pyr_c,4h2opntn_c,ok,ok,ok,N/A
HPACOAT,34dphacoa_c + h2o_c --> 34dhpha_c + coa_c + h_c,34dhpha_c;34dphacoa_c,ok,ok,ok,N/A
HPPK2,6hmhpt_c + atp_c --> 6hmhptpp_c + amp_c + h_c,ok,ok,ok,ok,N/A
Expand All @@ -1601,9 +1601,9 @@ HPYRI,hpyr_c <=> 2h3oppan_c,ok,ok,ok,ok,N/A
HPYRP,3php_c + h2o_c --> hpyr_c + pi_c,ok,ok,ok,ok,N/A
HPYRRx,h_c + hpyr_c + nadh_c --> glyc__R_c + nad_c,ok,ok,ok,ok,N/A
HPYRRy,h_c + hpyr_c + nadph_c --> glyc__R_c + nadp_c,ok,ok,ok,ok,N/A
HSDy,hom__L_c + nadp_c --> aspsa_c + h_c + nadph_c,hom__L_c,ok,ok,ok,N/A
HSK,atp_c + hom__L_c --> adp_c + h_c + phom_c,hom__L_c;phom_c,ok,ok,ok,N/A
HSST,hom__L_c + succoa_c --> coa_c + suchms_c,hom__L_c;suchms_c,ok,ok,ok,N/A
HSDy,aspsa_c + h_c + nadph_c --> hom__L_c + nadp_c,ok,ok,ok,ok,N/A
HSK,atp_c + hom__L_c --> adp_c + h_c + phom_c,ok,ok,ok,ok,N/A
HSST,hom__L_c + succoa_c --> coa_c + suchms_c,ok,ok,ok,ok,N/A
HSTPT,glu__L_c + imacp_c --> akg_c + hisp_c,ok,ok,ok,ok,N/A
HXAND,h2o_c + hxan_c + nad_c --> h_c + nadh_c + xan_c,ok,ok,ok,ok,N/A
HXAtex,hxa_e <=> hxa_p,only when going forwards,ok,ok,ok,N/A
Expand Down Expand Up @@ -2472,7 +2472,7 @@ SHCHF,fe2_c + scl_c --> 3.0 h_c + sheme_c,ok,ok,ok,ok,N/A
SHGO,S2hglut_c + o2_c --> akg_c + h2o2_c,ok,ok,ok,ok,N/A
SHK3Dr,3dhsk_c + h_c + nadph_c <=> nadp_c + skm_c,only when going backwards,ok,ok,ok,N/A
SHKK,atp_c + skm_c --> adp_c + h_c + skm5p_c,ok,ok,ok,ok,N/A
SHSL1,cys__L_c + suchms_c --> cyst__L_c + h_c + succ_c,cyst__L_c;suchms_c,ok,ok,ok,N/A
SHSL1,cys__L_c + suchms_c --> cyst__L_c + h_c + succ_c,ok,ok,ok,ok,N/A
SKMt2pp,h_p + skm_p --> h_c + skm_c,skm_p,ok,ok,ok,N/A
SKMtex,skm_e <=> skm_p,skm_e;skm_p,ok,ok,ok,N/A
SLNTabcpp,atp_c + h2o_c + slnt_p --> adp_c + h_c + pi_c + slnt_c,slnt_c;slnt_p,ok,ok,ok,N/A
Expand Down Expand Up @@ -2552,7 +2552,7 @@ THRA2,athr__L_c --> acald_c + gly_c,ok,ok,ok,ok,N/A
THRD,nad_c + thr__L_c --> 2aobut_c + h_c + nadh_c,ok,ok,ok,ok,N/A
THRD_L,thr__L_c --> 2obut_c + nh4_c,ok,ok,ok,ok,N/A
THRPtex,thrp_e <=> thrp_p,thrp_e;thrp_p,ok,ok,ok,N/A
THRS,h2o_c + phom_c --> pi_c + thr__L_c,phom_c,ok,ok,ok,N/A
THRS,h2o_c + phom_c --> pi_c + thr__L_c,ok,ok,ok,ok,N/A
THRabcpp,atp_c + h2o_c + thr__L_p --> adp_c + h_c + pi_c + thr__L_c,ok,ok,ok,ok,N/A
THRt2pp,h_p + thr__L_c --> h_c + thr__L_p,ok,ok,ok,THRt2rpp,N/A
THRt2rpp,h_p + thr__L_p --> h_c + thr__L_c,ok,ok,ok,THRt2pp,N/A
Expand Down
6 changes: 3 additions & 3 deletions data/testResults/macaw_summary.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Starting dead-end test...
- Found 688 dead-end metabolites.
- Found 875 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 244 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
- Found 682 dead-end metabolites.
- Found 866 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 245 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
- Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
- Found 77 reactions that were some type of duplicate:
Expand Down
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