feat: reaction mass balance and metabolite charge and formula

[sulheim]

Description of the issue:

From the Memote report we get that there are 1284 unconserved metabolites and 357 reactions not mass balanced. This should be fixed. Most of the unconserved metabolites are probably because one metabolite in a reaction is missing the chemical formula.

357 unbalanced reactions

["3T3LPROD","THYDNAPO","CBMD","THYDNAPS","GALOO","OCTSYN","24DCLPMO","44DPCDH","PPNAD2OR","S7PI","45DOPA","NSHDDS","24DCOAR","XLLGXYL","ALPHNH","DHICONF","GDCARBM","GDP64HRD","4HYBUT","TRYP2MO","TBFORMD","NHHAAH","TCLBZRED","TRYPYRAT","GDPMANDH","4HYDPRO","DPCOX","SCB11","DHYDTHYM","FHL","DPMSYN","COSPERDH","PROLRM","PROP2MO","SCB14","SUCOAICT","SCB15","FLAVMO","DPROLORED","SCB21a","5CM2HMUCI","FORHOPS","HCSUCT","FRD3","PTC6MT","SORBDH","PTLACS","HDXSQLS","ADOXFUTS","DARGO","5METDA","DGLUCYC","FENTON","PPTRIAT","UDPGDC","PPTSERDC","FEROXCYC","NADPHXE","2K3DRHAM","ONTROOXR","OPHBDC","2METBOD","CYSBLY","ADAPAT","MPAHYD","3AIBUTS","CDP4DGNOy","MPL","MPML","3CLBZADH","CEPSPORDA","3CLBZDH","CHO43OR","ACTS18","DCYCHEX","45SDOPs","FALDH3","FALGTHLs","RHAMFs","RIB1MPTS","4C4HX2OA","DDALLO","4CMCOAS","DDGALK","FARNDPPS","IPAXYL","MANISOs","ASCORPO","CINNCOAL","AHOPS","24DHX5M6OI","CINNDOX","25DBUT","LALDD2","LAURAT","MMSYNB","MMSYNA","2A3MUCSD","GALURDH","XLXG","5OP3TCCL","4IP7MO2H__R","6ADOFUT","DXYLDH","4IP7MO2H__S","6HEXHYD","4IZPHYDs","CARBMODH","ACCAHh","VNDH","CARBPHOL","VNDH_4","AC1MO","VNDH_2","CARNMOx","CARNMOy","PHYSYN","ACTCOAT","PSEUDO_ACCEPTOR_NAD","ARABDH","PHYTDES","PSEUDO_ACCEPTOR_NADP","PSEUDO_DONOR_NADH","ACTCOAT2","ARABLAC","ARABISOs","DRIB2FUR","GLYCTO4","PSEUDO_DONOR_NADPH","AMBACS","PHYTES","GEOSMS","11OXPENT","3HCINNMH","URECARB","AMBCOAL","DRIBPA","PICDDHs","3DM4HXPPO","SAMAAT","BFORCL","GERDH","BUPN","P2OLDH","SAMAT","BFORMDC","3DMA4HMO","AMID","ARAT","BUTCOAL","4COXADH","GGHCSH","ACNMS","TYRMO","GGLACOX","GGLUPUT","MGLYXOX","4HBHYOX","TRE6PPP","MGSDGS","TREPP","4HDAPMO","PGLYCP","NICMO","PTRCAT1","DMETMO","GADECARB","DHBD","O4OXOCYR","PU5PG","GALACDH","DHBS","DHPD","O426ISO","THPAT","SCB21b","2ABZMOx","4MBZALDH","CELLUL_DEGe","HEP7PHOK","2OGLUAH","FRUISOs","THPICHYDs","MAHYD","ULA4NFT","4MBZDH","SCB24","2OH3EDISO","HERCOX","2ABZMOy","GUL14LACDH","GUDBUTNAH","SCB31","4NIPHOM","SCB32","3OCHOCDH","3OXCOADH","SUCOMALT","AAAHYD","SULFPDH","ACETDH","ENTERt","CUMALDH","LLYXDH","CYANST","CREATA","CREATDA","CYCHEX_2","CYC1CCDH","CYCHEXDH","BZALDH","LYS6MO","BZDH","CYCHEXMO","ORNHYDXy","LCYB","AP2EISOs","CLADHAL","MMYSYN1","LCYG","MMYSYN2","APATT","MMYSYN3","ORNHYDXx","DGALACYC","CHOLOX","4HPROOR","3HPPPNH","GLULACIs","NADH8","BMMCOAL","3HXACOADH","FBA4","3HXKYN","1P4H2CDA","I3PYRMO","RBTDG","DTDP26DGR","NADH9","NADHXDH","23DHBZS","RE0691C","NADHXSs__R","NADHXE","GLNLASE","XGLCOLIG","23LGALAC","MYCARSL","QUINHYDs","GERDPM","AMID3","GERISOs","GLYOX","AMID5","4NITROB","GHBDHy","ZCAROTDH2","FEROXG1S","GMGGDCAP","XYLLAC","4OT","FORGLUIH","GALCTD","33BIFLAV","P4CADH","UAAGLS2","G3PD7","PYACOADH","UDPAGACA","AATA","UDPAMALA","AATC","UNDCAPPT","2AMUCSAD","GUL5DH","UNDEGLCT","SARCOX","CAT23DOX","SSBUTDH","CMCMSAD","GCGBGE","HBZOPT","2CLRED","HMMSHALDs","GCGUAIDH","STRP6K","GCL","2D3DGLUCDH","FALDH2","TMETMO","PPPNDO","DORNO","3K5AHC","3MBZALDH","FUMAH","4HXBOPT","ADXFUTNS","HEXHYD","3MBZDH","SLD","CHORDH","CHTNDG","DGLYHRED","DGLUC4KR","DGLUCMT","CDP4DGNOx","MCOALY","TAG6ISOs","FCLPA","CSPMDDH","CYCOADH","NADPHQR4","NADPHXD","MMSAD1","CTPGNAC","MNNH","36AHDGALC","MSUCOADH","SCB34","38BIFLAVS","4SBZADH","DCPEPFU","SCB35","LGALACD","AHLGAL","CYT5MONP","4SULFADH","LHISTMT","AHLGALb","MTBUTEMO","MALPYRISO","MYCFORM","NABTNO","NADHXSs__S","MALTHIK","BCOADH","BALDHs","KHK2","BSUZCOAD","ZCARDS","LACDHCYT","PHYFLUDS","BTCOAR","GMHEPAT","ARUH","BZSCT","C7AHXDH","2DHGLCK","HMSD","CADHX","ASCISOs","2FURAPS","ACITRULD","ASCOROX","CAFFCOA","GLUCORDH","GGGABADH"]

644 metabolites don't have a charge

12da3oaglcpyr_c, 12dgr120_c, 12dgr140_c, 12dgr141_c, 12dgr150_c, 12dgr160_c, 12dgr161_c, 12dgr170_c, 12dgr180_c, 12dgr181_c, 12dgrai150_c, 12dgrai170_c, 12dgri140_c, 12dgri150_c, 12dgri160_c, 12dgri170_c, 12dgri180_c, 14glucan_c, 14glucan_e, 14hdphet_c, 15cphyt_c, 1Dgali_c, 1Dgali_e, 1acpc_c, 23btd_c, 24dab_c, 24dclphen_c, 24dtcho_c, 25dc25chx_c, 25dclpql_c, 26dap_LL_c, 26dap_LL_e, 26dap__M_c, 26dap__M_e, 26hxcho_c, 2aobut_c, 2dmmql9_c, 2hxmp_e, 2hymeph_c, 2ins_c, 2mborn_c, 2mop_c, 2o3pop3odn_c, 2o3pp8m3onn_c, 2oph_c, 2ppoh_c, 36ahgalfur_c, 36ahgalpyr_c, 3aib_c, 3clbxal_c, 3clbzal_c, 3dclcatc_c, 3fe4s_c, 3hanthrn_c, 3mbzalc_c, 3metbzal_c, 44dpcop_c, 465mo5othf3mdhp_c, 46mo5o25dhf3mdhp_c, 4abut_c, 4abut_e, 4ahmmp_c, 4ahmmp_e, 4crsol_c, 4gglutbut_c, 4guanbut_c, 4hbald_c, 4hdthbiop_c, 4hglusa_c, 4hm36modhf2o_c, 4hm3odhf2o_c, 4hpgly_c, 4hpro_LT_c, 4hthr_c, 4ip7moxo_c, 4ipropmo_c, 4mbzalc_c, 4mbzald_c, 4nitrocc_c, 4o5odhmdhp_c, 4o5othf3mdp_c, 4r5au_c, 56dthm_c, 56dura_c, 5a2opntn_c, 5am3ohex_c, 5aop_c, 5aptn_c, 5drib_c, 5g2oxpt_c, 5hiu_c, 5mcsn_c, 5mta_c, 5mtho_c, 5mtr_c, 5mtr_e, 6apa_c, 6hmhpt_c, 8aonn_c, ACPmmy_c, C21565_c, CE2705_c, ETFred_c, KSredX_c, Lfmkynr_c, Lkynr_c, N6liplys_c, XXXGsacch_c, aa_c, abt__D_c, abt__D_e, abt_c, acald_c, acald_e, acceptor_c, accp_c, accys_c, accys_e, acetoin__S_c, acetoin_c, acetol_c, acetone_c, acgam_c, acgam_e, acglc__D_c, achms_c, acmalt_c, acmana_c, acorn_c, acser_c, acser_e, adcobhex_c, add26810t5o_c, ade_c, ade_e, adhlam_c, adn_c, adn_e, adocbl_c, afactor_c, ahcys_c, ahmann_c, ahop_c, aic_c, ala_B_c, ala_B_e, ala__D_c, ala__D_e, ala__L_c, ala__L_e, alaala_c, alaala_e, albflol__R_c, albflol__S_c, albflon_c, alltn_c, alltn_e, alpam_c, amob_c, apoACP_c, apoACPact_c, apoACPcda_c, apoACPredL_c, apoACPredN_c, apoACPredQ_c, apoPCPredO_c, arab__D_c, arab__D_e, arab__L_c, arab__L_e, arabinofur__L_c, arb14lac__L_c, asn__L_c, asn__L_e, aspsa_c, asptrna_c, at44dcop_c, athr__L_c, atphyflu_c, bfrn_c, bglycogen_c, btal_c, btnCCP_c, bzal_c, bzalc_c, bzamid_c, carb_c, carnitine_c, caro_c, catechol_c, cbi_c, cbi_e, cellb_c, cellb_e, cellul_e, cellwall_c, cgly_c, chdpro__D_c, chitin_e, chol4e3o_c, chsterol_c, chtbs_c, chtbs_e, cigam_c, citr__L_c, citr__L_e, co2_c, co2_e, co_c, cpkepox_c, cpkepox_e, creat_c, crn_c, crtn_c, csn_c, csn_e, cyan_c, cychex_c, cychxaol_c, cys__L_c, cys__L_e, cyst__L_c, cytd_c, cytd_e, dad_2_c, dad_2_e, dad_5_c, dalua_c, dcyt_c, dcyt_e, ddhrb_c, dgsn_c, dgsn_e, dha_c, dha_e, dhdascb_c, dhdcarn_c, dhiconfa_c, dhlam_c, dhlpro_c, dhmpt_c, dhnpt_c, dim1oct_c, din_c, din_e, dmbzid_c, dmlz_c, dmppat_c, dna_c, dolichol_c, dolmanp_c, dopa__L_c, drib_c, drib_e, duri_c, duri_e, dxyl_c, ecaplac_c, enter_c, enter_e, episz_c, epm_c, epm_e, etf_ox_c, etoh_c, etoh_e, f420ox_c, f420red_c, fald_c, fald_e, fcoelchl_c, fcoelchl_e, fdxrd_c, feroxBfe_c, feroxBfe_e, feroxEfe_c, feroxEfe_e, feroxG1_c, fldox_c, fldrd_c, fmettrna_c, formhop_c, formyct_c, frmd_c, fru_B_c, fru_c, fru_e, fruur_c, g15lac_c, g3pc_c, g3pc_e, g3pe_c, g3pe_e, gact_e, gal__L_c, gal_aD_c, gal_c, gal_e, galac14lac_c, galac15lac_c, gcald_c, gcarote_c, gcgguaiac_c, gcgguaiace_c, geosmin_c, geranial_c, geraniol_c, germicidinA_c, germicidinB_c, germicidinC_c, germicidinD_c, ggl_c, ggl_e, glc__D_c, glc__D_e, glc__bD_c, gln__L_c, gln__L_e, glu1sa_c, glu5sa_c, glutADP_c, glutrna_c, gly_c, gly_e, glyald_c, glyald_e, glyb_c, glyb_e, glyc_c, glyc_e, glycogen_c, gmhep7p_c, grmcrnd_c, grmcrol_c, gsn_c, gsn_e, gtca2_c, gua_c, gua_e, gullac_c, h2_c, h2o2_c, h2o2_e, h2o_c, h2o_e, h2s_c, h2s_e, hLkynr_c, haphenon_c, hbc_c, hbm_c, hccystox_c, hcys__L_c, hdd2610t_c, hdhk_c, hercyn_c, his__L_c, his__L_e, hmmsh_c, hom__L_c, hom__L_e, hop22en_c, hop22ol_c, hpglu_c, hqn_c, hsql_c, hxan_c, hxan_e, hycorn_c, hyxsuccad_c, iacgam_c, iad_c, ile__L_c, ile__L_e, indole_c, indole_e, inost_c, inost_e, ins_c, ins_e, iprimev_c, iscs_c, iscssh_c, lald__D_c, lald__L_c, lcts_c, lcts_e, leu__L_c, leu__L_e, lipid_c, lipoate_c, lipoate_e, lipopb_c, lpam_c, lpro_c, lycop_c, lyx__D_c, lyx__D_e, lyx__L_c, lyx__L_e, malACPmmy_c, malt_c, malt_e, malthp_c, malthp_e, malthx_c, malthx_e, maltpt_c, maltpt_e, malttr_c, malttr_e, maltttr_c, maltttr_e, man_c, man_e, mbc_c, mbm_c, melib_c, melib_e, melt_c, melt_e, meoh_c, meoh_e, met__L_c, met__L_e, metac_c, metbute_c, methydan_c, metsox_R__L_c, metsox_S__L_c, mh5odhfmdp_c, mh5othfmdp_c, mhpglu_c, misc_c, mmyA_c, mmyB_c, mmyC_c, mmyint1_c, mmyint2_c, mnl_c, mnl_e, moadcosh_c, mparathion_c, mphpv__R_c, mphpv__S_c, mql9_c, mqn9_c, msh_c, mssg_c, mthgxl_c, myarso_c, n2o_c, n2o_e, n4abutn_c, n6hxlys_c, nac24dab_c, ncam_c, neral_c, neuspn_c, nic1ox_c, nicrns_c, nndmyani_c, no_c, no_e, nphtatt_c, o2_c, o2_e, ohrad_c, pacald_c, pacald_e, pcumald_c, pe120_c, pe140_c, pe141_c, pe150_c, pe160_c, pe161_c, pe170_c, pe180_c, pe181_c, peai150_c, peai170_c, pei140_c, pei150_c, pei160_c, pei170_c, pei180_c, phe__L_c, phe__L_e, ppdyletamin_c, pprdn_c, proPCPredO_c, pro__D_c, pro__L_c, pro__L_e, proamp_c, progly_c, propane_c, protein_c, protein_tRNA_c, pydx_c, pydx_e, pydxn_c, pydxn_e, pyrKSredX_c, pyrgal_c, q8_c, q8h2_c, qnon_c, raffin_c, raffin_e, rbflvrd_c, rbl__D_c, rbl__L_c, rbt_c, rdmbzi_c, red_c, red_e, rib__D_c, rib__D_e, ribflv_c, ribsylo_c, rml_c, rmn_c, rmn_e, rmnf_c, rna_c, salcn_e, sarcs_c, sbt__D_c, sbt__D_e, scb1_c, scb1_e, scb2_c, scb2_e, scb3_c, scb3_e, sdhliplys_c, ser__D_c, ser__D_e, ser__L_c, ser__L_e, sorb14lac_c, sql_c, strprub_c, stys_c, sucr_c, sucr_e, sufbcd_c, sufse_c, sufsesh_c, t3hdprol_c, tag120_c, tag140_c, tag141_c, tag150_c, tag160_c, tag161_c, tag170_c, tag180_c, tag181_c, tagai150_c, tagai170_c, tagi140_c, tagi150_c, tagi160_c, tagi170_c, tagi180_c, taur_c, taur_e, tbutalc_c, tbutfor_c, tbutmet_c, tc12dhdol_c, tcl14bzq_c, tcynt_c, thchd_c, thr__L_c, thr__L_e, thym_c, thym_e, thymd_c, thymd_e, tmao_c, tol_c, trdox_c, trdrd_c, tre_c, tre_e, trnaala_c, trnaarg_c, trnaasn_c, trnaasp_c, trnacys_c, trnagln_c, trnaglu_c, trnagly_c, trnahis_c, trnaile_c, trnaleu_c, trnalys_c, trnamet_c, trnaphe_c, trnapro_c, trnaser_c, trnathr_c, trnatrp_c, trnatyr_c, trnaval_c, trp__L_c, trp__L_e, tyr__L_c, tyr__L_e, up_c, upn_c, ura_c, ura_e, urate_c, urdgci_c, urea_c, urea_e, uri_c, uri_e, val__L_c, val__L_e, vanln_c, xan_c, xan_e, xllgsacc_c, xlxgxgsac_c, xtsn_c, xtsn_e, xxlgsacc_c, xyhex3u14lac_c, xyl__D_c, xyl__D_e, xylan_e, xylnact__D_c, xylt_c, xylt_e, xylu__D_c, xylu__L_c, ycpk_e, zcarote_c

399 metabolites don't have a chemical formula

12da3oaglcpyr_c, 14hdphet_c, 15cphyt_c, 1acpc_c, 1p4h2cbxl_c, 23btd_c, 23dahxoc_c, 23ddhb_c, 23dhb_c, 23dhba_c, 24dclphen_c, 24ddhrham_c, 24dh5m6o24d_c, 24dtcho_c, 25dc25chx_c, 25dclpql_c, 26hxcho_c, 2a5ocyc1eccoa_c, 2amac_c, 2chloacr_c, 2clprop_c, 2cm3hppc_c, 2ddara__L_c, 2ddara_c, 2dg25hbz_c, 2dh3dgal6p_c, 2dh3dogal_c, 2dh3dorham_c, 2dhglcn_c, 2h4oxbut_c, 2hdhepdd_c, 2hmc_c, 2hmcnsad_c, 2improp_c, 2kmb_c, 2mborn_c, 2mfumcoa_c, 2mop_c, 2mygydpp_c, 2ohed_c, 2oph_c, 2oxalc_c, 2pglyc_c, 2ppoh_c, 2pyr46dcox_c, 33biflav_c, 34dhcinm_c, 36ahgalfur_c, 36ahgalpyr_c, 38biflav_c, 3aib_c, 3ambutcoa_c, 3clbxal_c, 3clbzal_c, 3clbzat_c, 3dclcatc_c, 3dm4hdppyr_c, 3dma4hbz_c, 3dma4hma_c, 3h4oxbut_c, 3hcinnm_c, 3hd4oxhxcoa_c, 3hd5ohexa_c, 3hdkynu_c, 3hpppn_c, 3hxquin_c, 3mbzalc_c, 3metbzal_c, 3oc4en24ocoa_c, 3ocd26ocoa_c, 3ocdncoa_c, 3oce26ocoa_c, 3ocl4e26ocoa_c, 3ophb_c, 3ovobenz_c, 3spyr_c, 3sulfcat_c, 3sulflac_c, 3sulprop_c, 3uribut_c, 44dpcop_c, 44dpcopd_c, 45secdop_c, 4aabutn_c, 4carbzal_c, 4cboxald_c, 4gglutbut_c, 4guanbut_c, 4gubuty_c, 4h2mohexn_c, 4hambz_c, 4hbald_c, 4hbutcoa_c, 4hbz_c, 4hdthbiop_c, 4hphac_c, 4ip7moxo_c, 4ipropmo_c, 4mbzalc_c, 4mbzald_c, 4nitrobz_c, 4nitrocc_c, 4nitroph_c, 4sulbza_c, 4sulfbenz_c, 4sulfbzalc_c, 56dthm_c, 56dura_c, 5a2opntn_c, 5am3ohex_c, 5c2oh3ed_c, 5cmhm_c, 5cmhmsa_c, 5g2oxpt_c, 5mtho_c, 5oxhlnitro_c, 6a6doxf_c, 6h3iphep_c, 6hd3iphep_c, 6hdhx_c, 6mpttmide_c, 6p2dgluc_c, CE1944_c, CE2705_c, ETFred_c, HC00591_c, HC01115_c, L2aadp_c, Lcyst_c, Nforglu_c, Sfglutth_c, T4hcinnm_c, XXXGsacch_c, aa_c, aaekpim_c, aahxioct_c, abacptri_c, acarbmucosad_c, acetoin__S_c, acetoin_c, acetol_c, acmana_c, acnam__B_c, acryl_c, adphep_DD_c, agdppdtundec_c, agppcap_c, ahgalac__L_c, ahmann_c, ahop_c, allphn_c, amuco_c, amucsam_c, anthrancoa_c, ap4a_c, aprut_c, arabat__L_c, arabinofur__L_c, arb14lac__L_c, arg__D_c, ascb__L_c, at44dcop_c, atphyflu_c, betahyd_c, betalm_c, bgalac__D_c, bmmcoa_c, btal_c, butanoate_c, bz_c, bzal_c, bzalc_c, bzamid_c, bzsucc_c, bzsuccoa__R_c, bzsuccoa_c, cacodylate_c, caffcoa_c, cala_c, caro_c, cbm_c, cdp4dh36ddglc_c, cdp4dh6doglc_c, cechddd_c, cepspoc_c, ch15deccoa_c, chdpro__D_c, chlorac_c, chol4e3o_c, cholate_c, chsterol_c, cinnm_c, cmpacna_c, cmpglna_c, co_c, coucoa_c, coxsperm_c, creat_c, crn_c, crtn_c, cspmd_c, cyccarcoa_c, cychex1coa_c, cychex_c, cychxaol_c, d11oxpen_c, dacepspo_c, dddeccoa_c, decda_tb_c, dh7oxcho_c, dhcinnm_c, dhdascb_c, dhiconf_c, dhiconfa_c, dhpppn_c, dim1oct_c, dmppat_c, dmthiopp_c, dolichol_c, dolmanp_c, dopa__L_c, dpperypfur_c, dtdp26ddgh2e2u_c, dtdp34dh26doglc_c, dtdp4dh26dall_c, dtdp4dh3m26ddglc_c, dtdp4h26dthp_c, dtdpaoliv_c, ecaplac_c, ecinncoa_c, enter_c, enter_e, etf_ox_c, f420ox_c, f420red_c, fc1p_c, feroxG1_c, flaviolin_c, forfurmpp_c, foriglut_c, formhop_c, formyct_c, frdp_2_c, fru_B_c, fruur_c, fumpyr_c, g1p_B_c, ga_c, gal14lac__D_c, gal15lac_c, gal__L_c, galac14lac_c, galac15lac_c, galct__D_c, gcarote_c, gcgguaiac_c, gcgguaiace_c, gdp6dklh_c, gdp6domanhep_c, gdpmannur_c, geranial_c, geraniol_c, gg4abut_c, ggaggdcap_c, ggcysto_c, ggputresc_c, ghb_c, gluca14lac_c, gluca15lac_c, glucor__bD_c, glucys_c, gmhep17bp__B_c, gmhep1p_c, gmhep7p_c, gpdtoucap_c, gullac_c, guln__L_c, h2_c, haphenon_c, hccystox_c, hdoxcad_c, hercyn_c, hmgth_c, hmmsh_c, hosuprop_c, hsql_c, hycorn_c, hyxsuccad_c, iad_c, ind3ac_c, indpyr_c, iprimev_c, itaccoa_c, itacon_c, kdo2laur_c, kdo2lipid4_c, lald__D_c, lgt__S_c, lycop_c, lyxat__L_c, m_tol_c, malpyr_c, malylcoa_c, mana_c, marsonate_c, metac_c, metbute_c, methydan_c, mompain_c, mparathion_c, mphpv__R_c, mphpv__S_c, mppate_c, mppp9_c, mthgxl_c, myarso_c, mycthigpyrpp_c, n4abutn_c, n6all26d_c, n6hxlys_c, nacitrul__L_c, nacpphin_c, nadhx__R_c, nadhx__S_c, nadphx__R_c, nadphx__S_c, nal2a6o_c, ncrbmsar_c, neral_c, neuspn_c, nic1ox_c, nico__S_c, nisirhcl_c, nndmyani_c, nphtatt_c, nsirhcda_c, o3n54ocyo_c, o54ocyo_c, oh1_c, ohrad_c, orn__D_c, p_tol_c, paolac_c, pcumald_c, pcumat_c, pentlacF_c, pentlacd_c, phgkyx_c, phitcoa_c, picoln_c, pp2slac_c, ppdyletamin_c, pphinit_c, pppn_c, prephytedp_c, pro__D_c, propane_c, prp13da_c, prp2enoate_c, pttamid_c, puri4pp_c, pyr2cbox_c, pyrgal_c, rbl__D_c, rbt_c, rib1mpp5tpp_c, ribsylo_c, rmnf_c, ru1p__D_c, sarcs_c, sl__L_c, sorb14lac_c, stmyn_c, strep6p_c, t3hdprol_c, tag6p_c, tbutalc_c, tbutfor_c, tbutmet_c, tcl14bzq_c, tclhqn_c, tma_c, tmao_c, todcpribfur_c, uGgl_c, uGgla_c, udpLa4fn_c, udpLa4n_c, udpLa4o_c, unaga_c, vanln_c, xllgsacc_c, xlxgxgsac_c, xu1p__D_c, xxlgsacc_c, xyhex3u14lac_c, xylnact__D_c, xylonate__D_c, zcarote_c, 

Expected feature/value/output:

All metabolites should have both a charge and mass balance

Reproducing these results:

n_charge = 0
n_formula= 0
print("Metabolites missing formula:")
for m in model.metabolites:
    if not m.formula:
        n_formula += 1
        print(m)
print(n_formula)
print("Metabolites missing charge:")
for m in model.metabolites:
    if not m.charge:
        n_charge += 1
        print(m)
print(n_charge)

n_reactions = 0
for r in model.reactions:
    if not r.boundary and len(r.check_mass_balance()):
        print(r)
        n_reactions += 1
print(n_reactions)

To do:

• Add chemical formula and charge to all metabolites
• Check that all reactions except boundaries and biomass-reactions are charge and mass-balanced

I hereby confirm that:

• This problem persists in the master branch of the repository
• A similar issue does not already exist
• I've considered asking this first in the Gitter chat room

[edkerk]

Do these metabolites have annotations that can be queried to get the formulae and charges?