fix: mass- and charge balance reactions

[edkerk]

Description of the issue:

Various reactions are chemically unbalanced. Many are caused by H⁺, but this is not the only culprit (see list below). In some cases, the metFormula should be modified.

Expected feature/value/output:

Example:

1. r_2126: sedoheptulose 1,7-bisphosphate[c] + H2O[c] => phosphate[c] + sedoheptulose 7-phosphate[c] link. Was missing H2O.

2. r_2116: acetaldehyde[c] + H2O[c] + NAD[c] => acetate[c] + 2 H+[c] + NADH[c]; link. Instead only produced 1 H+[c].

3. GTP: C10H12N5O14P3: link. In yeast-GEM the nucleotides are in their deprotonated state, while the chemical formula of GTP was still in the fully protonated state (C10H16N5O14P3). This causes an imbalance in e.g. r_0800: ATP[c] + GDP[c] => ADP[c] + GTP[c].

Reproducing these results:

In RAVEN, it identifies 1517 unbalanced reactions in yeast-GEM 8.3.3, and this is excluding cases where balance cannot be calculated because of absent chemical formulae:

>> bs=getElementalBalance(model);
>> length(find(bs.balanceStatus==0))

ans =

        1517

List of unbalanced reactions, note that the problem can be in the reaction, or in the chemical formula!

>> bs  = getElementalBalance(model);
>> idx = find(bs.balanceStatus==0)
>> out = model.rxns(idx);
>> for i=1:length(idx)
>>     dif = bs.leftComp(idx(i),:) - bs.rightComp(idx(i),:);
>>     mets = find(~dif==0);
>>     difference = '';
>>     for j=1:length(mets)
>>         difference = strcat(difference,bs.elements.abbrevs(mets(j)));
>>         difference = strcat(difference,num2str(dif(mets(j))));
>>     end
>>     out(i,2) = difference;
>> end
>> out

'r_0014'	'H2'
'r_0015'	'H-2'
'r_0034'	'H1'
'r_0035'	'H1'
'r_0038'	'H-2'
'r_0041'	'H1'
'r_0043'	'H1'
'r_0045'	'H1'
'r_0063'	'H-2'
'r_0066'	'H1'
'r_0067'	'H-1'
'r_0073'	'H12'
'r_0074'	'O-1H-1'
'r_0080'	'H1'
'r_0082'	'H-1'
'r_0083'	'H1'
'r_0088'	'H-13'
'r_0089'	'H-13'
'r_0092'	'H12'
'r_0093'	'O-1H-1'
'r_0094'	'H-5'
'r_0100'	'H4'
'r_0105'	'H4'
'r_0106'	'H4'
'r_0107'	'H4'
'r_0123'	'H-4'
'r_0124'	'H-4'
'r_0146'	'H2'
'r_0150'	'H1'
'r_0153'	'H1'
'r_0189'	'H-1'
'r_0195'	'H2'
'r_0215'	'H1'
'r_0219'	'H-1'
'r_0223'	'H-3'
'r_0224'	'H1'
'r_0228'	'C10H17'
'r_0234'	'C1O-1H2'
'r_0240'	'C-1O1H-2'
'r_0263'	'H4'
'r_0264'	'H4'
'r_0265'	'H3'
'r_0266'	'H3'
'r_0271'	'H-1'
'r_0274'	'H-1'
'r_0282'	'H-3'
'r_0312'	'H-1'
'r_0315'	'H1'
'r_0319'	'H1'
'r_0322'	'H2'
'r_0335'	'H-2'
'r_0340'	'O1H2'
'r_0341'	'O1H2'
'r_0342'	'O-1H-1'
'r_0343'	'O-1H-1'
'r_0344'	'H-2'
'r_0345'	'H-2'
'r_0357'	'H10'
'r_0358'	'H-10'
'r_0360'	'H-2'
'r_0361'	'H1'
'r_0363'	'H2'
'r_0364'	'H1'
'r_0365'	'H1'
'r_0441'	'H-1'
'r_0442'	'H-1'
'r_0446'	'H2'
'r_0447'	'H2'
'r_0449'	'H4'
'r_0450'	'H4'
'r_0454'	'H1'
'r_0455'	'H1'
'r_0457'	'H-1'
'r_0461'	'H-3'
'r_0465'	'H1'
'r_0466'	'H2'
'r_0467'	'H2'
'r_0477'	'H-1'
'r_0490'	'H-1'
'r_0499'	'H-2'
'r_0501'	'H2'
'r_0502'	'H2'
'r_0503'	'H2'
'r_0504'	'H1'
'r_0506'	'C4N2O3H6R1'
'r_0507'	'H1'
'r_0508'	'C-4N-2O-3H-5R-1'
'r_0509'	'H1'
'r_0518'	'H-1'
'r_0524'	'H1'
'r_0525'	'H1'
'r_0530'	'H1'
'r_0531'	'H-2'
'r_0534'	'H-2'
'r_0535'	'H-2'
'r_0545'	'H-1'
'r_0550'	'N-1H-1R-2'
'r_0551'	'N-1H-1R-2'
'r_0552'	'N-1H-1R-2'
'r_0555'	'H2'
'r_0558'	'H5'
'r_0559'	'H-5'
'r_0560'	'H-5'
'r_0571'	'H2'
'r_0572'	'H2'
'r_0573'	'H2'
'r_0574'	'H2'
'r_0575'	'H2'
'r_0616'	'H2'
'r_0617'	'H2'
'r_0618'	'H2'
'r_0619'	'H2'
'r_0620'	'H2'
'r_0621'	'H2'
'r_0622'	'H2'
'r_0623'	'H2'
'r_0624'	'H2'
'r_0625'	'H2'
'r_0646'	'H2'
'r_0647'	'H2'
'r_0648'	'H2'
'r_0649'	'H2'
'r_0650'	'H2'
'r_0651'	'H2'
'r_0652'	'H2'
'r_0653'	'H2'
'r_0654'	'H2'
'r_0655'	'H2'
'r_0672'	'H-1'
'r_0673'	'H-1'
'r_0681'	'H1'
'r_0682'	'H1'
'r_0683'	'H1'
'r_0687'	'O1'
'r_0690'	'H1'
'r_0695'	'H-3'
'r_0703'	'H-1'
'r_0704'	'H-1'
'r_0705'	'H-1'
'r_0706'	'H-1'
'r_0722'	'H3'
'r_0723'	'H2'
'r_0727'	'H-3'
'r_0728'	'H-3'
'r_0737'	'H1'
'r_0747'	'H1'
'r_0748'	'H1'
'r_0749'	'H1'
'r_0750'	'H1'
'r_0751'	'H1'
'r_0752'	'H1'
'r_0753'	'H1'
'r_0754'	'H1'
'r_0755'	'H1'
'r_0756'	'H1'
'r_0758'	'H2'
'r_0760'	'H1'
'r_0763'	'H4'
'r_0768'	'H3'
'r_0769'	'H3'
'r_0785'	'H-3'
'r_0797'	'H-1'
'r_0798'	'H-1'
'r_0799'	'H-1'
'r_0800'	'H-1'
'r_0802'	'H3'
'r_0803'	'H-1'
'r_0804'	'H1'
'r_0813'	'H-1'
'r_0831'	'H1'
'r_0832'	'H-1'
'r_0842'	'H-3'
'r_0855'	'H-1'
'r_0882'	'H-2'
'r_0883'	'N-1H-2R-2'
'r_0886'	'H-4'
'r_0888'	'H2'
'r_0890'	'H-1'
'r_0905'	'H3'
'r_0907'	'H-2'
'r_0911'	'H2'
'r_0912'	'H-2'
'r_0916'	'H2'
'r_0919'	'O1H1'
'r_0920'	'O1H1'
'r_0921'	'H1'
'r_0922'	'H1'
'r_0941'	'H-1'
'r_0967'	'H3'
'r_0968'	'H-1'
'r_0969'	'H-2'
'r_0970'	'N-1H-1R-2'
'r_0971'	'N-1H-2R-2'
'r_0972'	'N-1H-1R-2'
'r_0973'	'N-1H-2R-2'
'r_0974'	'N-1H-1R-2'
'r_0975'	'N-1H-1R-2'
'r_0976'	'N-1H-1R-2'
'r_0977'	'N-1H-1R-2'
'r_0978'	'N-1H-1R-2'
'r_0979'	'N-1H-1R-2'
'r_0982'	'H-2'
'r_0993'	'H-1'
'r_0998'	'H1'
'r_0999'	'H-1'
'r_1000'	'H1'
'r_1004'	'H2'
'r_1006'	'H-2'
'r_1027'	'H2'
'r_1029'	'H-1'
'r_1031'	'H-1'
'r_1032'	'H2'
'r_1033'	'H2'
'r_1034'	'H-2'
'r_1035'	'H2'
'r_1036'	'H-2'
'r_1037'	'N-1H-1R-2'
'r_1038'	'N1H1R2'
'r_1039'	'N1H1R2'
'r_1045'	'H-2'
'r_1049'	'H2'
'r_1069'	'H2'
'r_1076'	'H1'
'r_1078'	'H1'
'r_1095'	'H2'
'r_2112'	'O1H1'
'r_2113'	'O1'
'r_2116'	'H1'
'r_2126'	'O-1H-2'
'r_2147'	'C-10H-20R1'
'r_2154'	'H-4'
'r_2156'	'H-4'
'r_2157'	'H-4'
'r_2162'	'H-4'
'r_2168'	'H4'
'r_2172'	'C10H20'
'r_2176'	'H4'
'r_2177'	'H4'
'r_2179'	'C-10H-20'
'r_2209'	'H-4'
'r_2210'	'H-4'
'r_2211'	'H-4'
'r_2212'	'H-4'
'r_2213'	'H-4'
'r_2214'	'H-4'
'r_2215'	'H-4'
'r_2216'	'H-4'
'r_2217'	'H-4'
'r_2218'	'H-4'
'r_2232'	'H4'
'r_2233'	'H4'
'r_2238'	'H-4'
'r_2240'	'C10H20'
'r_2242'	'H-4'
'r_2245'	'H-4'
'r_2248'	'H-4'
'r_2249'	'H-4'
'r_2250'	'H-4'
'r_2258'	'C-10H-16'
'r_2260'	'C-2H-4'
'r_2268'	'H4'
'r_2271'	'H4'
'r_2275'	'H-4'
'r_2277'	'C2O1H2'
'r_2280'	'O1H-2'
'r_2281'	'O1H-2'
'r_2282'	'O1H-2'
'r_2286'	'H4'
'r_2289'	'O-1H2'
'r_2290'	'O-1H2'
'r_2292'	'O-1H2'
'r_2293'	'O-1H2'
'r_2294'	'O-1H2'
'r_2295'	'H4'
'r_2297'	'H4'
'r_2298'	'H4'
'r_2300'	'H4'
'r_2302'	'H4'
'r_2304'	'H-4'
'r_2308'	'H-2'
'r_2309'	'H-2'
'r_2310'	'H-2'
'r_2311'	'H-2'
'r_2312'	'H-2'
'r_2313'	'H-2'
'r_2315'	'C-14O-1H-28'
'r_2316'	'H-2'
'r_2317'	'H-2'
'r_2318'	'H-2'
'r_2319'	'H-2'
'r_2320'	'H-2'
'r_2321'	'H-2'
'r_2323'	'C-14O-1H-28'
'r_2326'	'H-2'
'r_2327'	'C14O1H26'
'r_2330'	'H-2'
'r_2331'	'C14O1H26'
'r_2332'	'H2'
'r_2344'	'H-2'
'r_2345'	'H2'
'r_2346'	'H2'
'r_2347'	'H2'
'r_2348'	'H2'
'r_2349'	'H2'
'r_2350'	'H2'
'r_2351'	'H2'
'r_2352'	'H-2'
'r_2353'	'H2'
'r_2354'	'H2'
'r_2355'	'H2'
'r_2356'	'H2'
'r_2357'	'H2'
'r_2358'	'H2'
'r_2359'	'H2'
'r_2360'	'H-2'
'r_2361'	'H2'
'r_2362'	'H2'
'r_2363'	'H2'
'r_2364'	'H2'
'r_2365'	'H2'
'r_2366'	'H2'
'r_2367'	'H2'
'r_2368'	'H2'
'r_2376'	'H2'
'r_2384'	'H2'
'r_2392'	'H2'
'r_2400'	'H2'
'r_2408'	'H2'
'r_2416'	'H2'
'r_2424'	'H2'
'r_2432'	'H-2'
'r_2438'	'H4'
'r_2440'	'H-2'
'r_2446'	'H1'
'r_2447'	'H1'
'r_2448'	'H1'
'r_2449'	'H1'
'r_2450'	'H1'
'r_2451'	'H1'
'r_2452'	'H-3'
'r_2453'	'H1'
'r_2454'	'H1'
'r_2455'	'H1'
'r_2456'	'H1'
'r_2457'	'H1'
'r_2458'	'H1'
'r_2459'	'H1'
'r_2460'	'H-3'
'r_2461'	'H1'
'r_2462'	'H-6'
'r_2463'	'H-6'
'r_2464'	'H1'
'r_2465'	'H1'
'r_2466'	'H1'
'r_2467'	'H1'
'r_2468'	'H1'
'r_2469'	'H1'
'r_2470'	'H1'
'r_2471'	'H1'
'r_2472'	'H1'
'r_2473'	'H1'
'r_2474'	'H1'
'r_2475'	'H1'
'r_2476'	'H1'
'r_2477'	'H1'
'r_2478'	'H1'
'r_2479'	'H1'
'r_2480'	'H1'
'r_2481'	'H1'
'r_2482'	'H1'
'r_2483'	'H1'
'r_2484'	'H1'
'r_2485'	'H1'
'r_2486'	'H1'
'r_2487'	'H1'
'r_2506'	'O1'
'r_2507'	'O1'
'r_2510'	'O1'
'r_2511'	'O1'
'r_2512'	'H2'
'r_2513'	'H-2'
'r_2514'	'H-2'
'r_2515'	'H-2'
'r_2516'	'H-2'
'r_2517'	'H-2'
'r_2518'	'H-2'
'r_2519'	'H-2'
'r_2520'	'H2'
'r_2528'	'H3'
'r_2529'	'H1'
'r_2530'	'O1H1'
'r_2531'	'O1H1'
'r_2532'	'H1'
'r_2533'	'H1'
'r_2534'	'O1H1'
'r_2535'	'O1H1'
'r_2536'	'C-2H-1'
'r_2537'	'C-2H-1'
'r_2538'	'C-2H1'
'r_2539'	'C-2H1'
'r_2540'	'C-2H1'
'r_2541'	'C-2H1'
'r_2542'	'C2H2'
'r_2543'	'C2H2'
'r_2544'	'C2'
'r_2545'	'C2'
'r_2546'	'C2'
'r_2547'	'C2'
'r_2548'	'H-1'
'r_2549'	'H1'
'r_2550'	'H-1'
'r_2551'	'H1'
'r_2552'	'H-1'
'r_2553'	'H1'
'r_2554'	'H-1'
'r_2555'	'H1'
'r_2556'	'H-1'
'r_2557'	'H1'
'r_2558'	'H-1'
'r_2559'	'H1'
'r_2560'	'H-1'
'r_2561'	'H1'
'r_2562'	'H-1'
'r_2563'	'H1'
'r_2564'	'H-1'
'r_2565'	'H1'
'r_2566'	'H-1'
'r_2567'	'H1'
'r_2568'	'H-1'
'r_2569'	'H1'
'r_2570'	'H-1'
'r_2571'	'H1'
'r_2572'	'H-1'
'r_2573'	'H1'
'r_2574'	'H-1'
'r_2575'	'H1'
'r_2576'	'H-1'
'r_2577'	'H1'
'r_2578'	'H-1'
'r_2579'	'H1'
'r_2580'	'H-1'
'r_2581'	'H1'
'r_2582'	'H-1'
'r_2583'	'H1'
'r_2584'	'H2'
'r_2586'	'H2'
'r_2588'	'H2'
'r_2590'	'H2'
'r_2592'	'H2'
'r_2594'	'H2'
'r_2596'	'H2'
'r_2598'	'H2'
'r_2600'	'H2'
'r_2602'	'H2'
'r_2603'	'H2'
'r_2604'	'H2'
'r_2605'	'H2'
'r_2606'	'H2'
'r_2607'	'H2'
'r_2608'	'H2'
'r_2609'	'H2'
'r_2610'	'H2'
'r_2611'	'H2'
'r_2612'	'H2'
'r_2613'	'H2'
'r_2614'	'H2'
'r_2615'	'H2'
'r_2616'	'H2'
'r_2617'	'H2'
'r_2618'	'H2'
'r_2619'	'H2'
'r_2620'	'H-3'
'r_2621'	'H-3'
'r_2622'	'O-1H-3'
'r_2623'	'O-1H-3'
'r_2624'	'H-3'
'r_2625'	'H-3'
'r_2626'	'O-1H-3'
'r_2627'	'O-1H-3'
'r_2628'	'H-1'
'r_2629'	'H-1'
'r_2630'	'O-1H-1'
'r_2631'	'O-1H-1'
'r_2632'	'H-1'
'r_2633'	'H-1'
'r_2634'	'O-1H-1'
'r_2635'	'O-1H-1'
'r_2636'	'H-3'
'r_2637'	'H-3'
'r_2638'	'O-1H-3'
'r_2639'	'O-1H-3'
'r_2640'	'H-3'
'r_2641'	'H-3'
'r_2642'	'O-1H-3'
'r_2643'	'O-1H-3'
'r_2644'	'H-1'
'r_2645'	'H-1'
'r_2646'	'O-1H-1'
'r_2647'	'O-1H-1'
'r_2648'	'H-1'
'r_2649'	'H-1'
'r_2650'	'O-1H-1'
'r_2651'	'O-1H-1'
'r_2652'	'H-3'
'r_2653'	'H-3'
'r_2654'	'O-1H-3'
'r_2655'	'O-1H-3'
'r_2656'	'H-3'
'r_2657'	'H-3'
'r_2658'	'O-1H-3'
'r_2659'	'O-1H-3'
'r_2660'	'H-1'
'r_2661'	'H-1'
'r_2662'	'O-1H-1'
'r_2663'	'O-1H-1'
'r_2664'	'H-1'
'r_2665'	'H-1'
'r_2666'	'O-1H-1'
'r_2667'	'O-1H-1'
'r_2668'	'H-3'
'r_2669'	'H-3'
'r_2670'	'O-1H-3'
'r_2671'	'O-1H-3'
'r_2672'	'H-3'
'r_2673'	'H-3'
'r_2674'	'O-1H-3'
'r_2675'	'O-1H-3'
'r_2676'	'H-1'
'r_2677'	'H-1'
'r_2678'	'O-1H-1'
'r_2679'	'O-1H-1'
'r_2680'	'H-1'
'r_2681'	'H-1'
'r_2682'	'O-1H-1'
'r_2683'	'O-1H-1'
'r_2684'	'H-3'
'r_2685'	'H-3'
'r_2686'	'O-1H-3'
'r_2687'	'O-1H-3'
'r_2688'	'H-3'
'r_2689'	'H-3'
'r_2690'	'O-1H-3'
'r_2691'	'O-1H-3'
'r_2692'	'H-1'
'r_2693'	'H-1'
'r_2694'	'O-1H-1'
'r_2695'	'O-1H-1'
'r_2696'	'H-1'
'r_2697'	'H-1'
'r_2698'	'O-1H-1'
'r_2699'	'O-1H-1'
'r_2700'	'H-3'
'r_2701'	'H-3'
'r_2702'	'O-1H-3'
'r_2703'	'O-1H-3'
'r_2704'	'H-3'
'r_2705'	'H-3'
'r_2706'	'O-1H-3'
'r_2707'	'O-1H-3'
'r_2708'	'H-1'
'r_2709'	'H-1'
'r_2710'	'O-1H-1'
'r_2711'	'O-1H-1'
'r_2712'	'H-1'
'r_2713'	'H-1'
'r_2714'	'O-1H-1'
'r_2715'	'O-1H-1'
'r_2716'	'H-1'
'r_2717'	'H-1'
'r_2718'	'O-1H-1'
'r_2719'	'O-1H-1'
'r_2720'	'H-1'
'r_2721'	'H-1'
'r_2722'	'O-1H-1'
'r_2723'	'O-1H-1'
'r_2724'	'H-1'
'r_2725'	'H-1'
'r_2726'	'O-1H-1'
'r_2727'	'O-1H-1'
'r_2728'	'H-1'
'r_2729'	'H-1'
'r_2730'	'O-1H-1'
'r_2731'	'O-1H-1'
'r_2732'	'H-1'
'r_2733'	'H-1'
'r_2734'	'O-1H-1'
'r_2735'	'O-1H-1'
'r_2736'	'H-1'
'r_2737'	'H-1'
'r_2738'	'O-1H-1'
'r_2739'	'O-1H-1'
'r_2740'	'H-1'
'r_2741'	'H-1'
'r_2742'	'O-1H-1'
'r_2743'	'O-1H-1'
'r_2744'	'H-1'
'r_2745'	'H-1'
'r_2746'	'O-1H-1'
'r_2747'	'O-1H-1'
'r_2748'	'H-1'
'r_2749'	'H-1'
'r_2750'	'O-1H-1'
'r_2751'	'O-1H-1'
'r_2752'	'H-1'
'r_2753'	'H-1'
'r_2754'	'O-1H-1'
'r_2755'	'O-1H-1'
'r_2756'	'H-1'
'r_2757'	'H-1'
'r_2758'	'O-1H-1'
'r_2759'	'O-1H-1'
'r_2760'	'H-1'
'r_2761'	'H-1'
'r_2762'	'O-1H-1'
'r_2763'	'O-1H-1'
'r_2764'	'H-1'
'r_2765'	'H-1'
'r_2766'	'O-1H-1'
'r_2767'	'O-1H-1'
'r_2768'	'H-1'
'r_2769'	'H-1'
'r_2770'	'O-1H-1'
'r_2771'	'O-1H-1'
'r_2772'	'H-1'
'r_2773'	'H-1'
'r_2774'	'O-1H-1'
'r_2775'	'O-1H-1'
'r_2776'	'H-1'
'r_2777'	'H-1'
'r_2778'	'O-1H-1'
'r_2779'	'O-1H-1'
'r_2780'	'H-1'
'r_2781'	'H-1'
'r_2782'	'O-1H-1'
'r_2783'	'O-1H-1'
'r_2784'	'H-1'
'r_2785'	'H-1'
'r_2786'	'O-1H-1'
'r_2787'	'O-1H-1'
'r_2788'	'H-1'
'r_2789'	'H-1'
'r_2790'	'O-1H-1'
'r_2791'	'O-1H-1'
'r_2792'	'H-1'
'r_2793'	'H-1'
'r_2794'	'O-1H-1'
'r_2795'	'O-1H-1'
'r_2796'	'H-1'
'r_2797'	'H-1'
'r_2798'	'O-1H-1'
'r_2799'	'O-1H-1'
'r_2800'	'H-1'
'r_2801'	'H-1'
'r_2802'	'O-1H-1'
'r_2803'	'O-1H-1'
'r_2804'	'H-1'
'r_2805'	'H-1'
'r_2806'	'O-1H-1'
'r_2807'	'O-1H-1'
'r_2808'	'H-1'
'r_2809'	'H-1'
'r_2810'	'O-1H-1'
'r_2811'	'O-1H-1'
'r_2820'	'H-2'
'r_2821'	'H-2'
'r_2822'	'H-2'
'r_2823'	'H-2'
'r_2824'	'H-2'
'r_2825'	'H-2'
'r_2826'	'H-2'
'r_2827'	'H-2'
'r_2828'	'H-2'
'r_2829'	'H-2'
'r_2830'	'H-2'
'r_2831'	'H-2'
'r_2832'	'H-2'
'r_2833'	'H-2'
'r_2834'	'H-2'
'r_2835'	'H-2'
'r_2836'	'H-2'
'r_2837'	'H-2'
'r_2838'	'H-2'
'r_2839'	'H-2'
'r_2840'	'H-2'
'r_2841'	'H-2'
'r_2842'	'H-2'
'r_2843'	'H-2'
'r_2844'	'H-2'
'r_2845'	'H-2'
'r_2846'	'H-2'
'r_2847'	'H-2'
'r_2848'	'H-2'
'r_2849'	'H-2'
'r_2850'	'H-2'
'r_2851'	'H-2'
'r_2852'	'H-2'
'r_2853'	'H-2'
'r_2854'	'H-2'
'r_2855'	'H-2'
'r_2856'	'H-2'
'r_2857'	'H-2'
'r_2858'	'H-2'
'r_2859'	'H-2'
'r_2860'	'H-2'
'r_2861'	'H-2'
'r_2862'	'H-2'
'r_2863'	'H-2'
'r_2864'	'H-2'
'r_2865'	'H-2'
'r_2866'	'H-2'
'r_2867'	'H-2'
'r_2868'	'H-2'
'r_2869'	'H-2'
'r_2870'	'H-2'
'r_2871'	'H-2'
'r_2872'	'H-2'
'r_2873'	'H-2'
'r_2874'	'H-2'
'r_2875'	'H-2'
'r_2876'	'H-2'
'r_2877'	'H-2'
'r_2878'	'H-2'
'r_2879'	'H-2'
'r_2880'	'H-2'
'r_2881'	'H-2'
'r_2882'	'H-2'
'r_2883'	'H-2'
'r_2884'	'H2'
'r_2885'	'H2'
'r_2886'	'H2'
'r_2887'	'H2'
'r_2888'	'H2'
'r_2889'	'H2'
'r_2890'	'H2'
'r_2891'	'H2'
'r_2948'	'H1'
'r_2949'	'H1'
'r_2950'	'O-1H1'
'r_2951'	'O-1H1'
'r_2952'	'H1'
'r_2953'	'H1'
'r_2954'	'O-1H1'
'r_2955'	'O-1H1'
'r_2956'	'H-1'
'r_2957'	'H-1'
'r_2958'	'O-1H-1'
'r_2959'	'O-1H-1'
'r_2960'	'H-1'
'r_2961'	'H-1'
'r_2962'	'O-1H-1'
'r_2963'	'O-1H-1'
'r_2964'	'H-1'
'r_2965'	'H-1'
'r_2966'	'O-1H-1'
'r_2967'	'O-1H-1'
'r_2968'	'H-1'
'r_2969'	'H-1'
'r_2970'	'O-1H-1'
'r_2971'	'O-1H-1'
'r_2972'	'H-1'
'r_2973'	'H-1'
'r_2974'	'O-1H-1'
'r_2975'	'O-1H-1'
'r_2976'	'H-1'
'r_2977'	'H-1'
'r_2978'	'O-1H-1'
'r_2979'	'O-1H-1'
'r_2980'	'H-1'
'r_2981'	'H-1'
'r_2982'	'O-1H-1'
'r_2983'	'O-1H-1'
'r_2984'	'H-1'
'r_2985'	'H-1'
'r_2986'	'O-1H-1'
'r_2987'	'O-1H-1'
'r_2988'	'H-1'
'r_2989'	'H-1'
'r_2990'	'O-1H-1'
'r_2991'	'O-1H-1'
'r_2992'	'H-1'
'r_2993'	'H-1'
'r_2994'	'O-1H-1'
'r_2995'	'O-1H-1'
'r_2996'	'H-1'
'r_2997'	'H-1'
'r_2998'	'O-1H-1'
'r_2999'	'O-1H-1'
'r_3000'	'H-1'
'r_3001'	'H-1'
'r_3002'	'O-1H-1'
'r_3003'	'O-1H-1'
'r_3004'	'H-1'
'r_3005'	'H-1'
'r_3006'	'O-1H-1'
'r_3007'	'O-1H-1'
'r_3008'	'H-1'
'r_3009'	'H-1'
'r_3010'	'O-1H-1'
'r_3011'	'O-1H-1'
'r_3022'	'H-1'
'r_3023'	'H-1'
'r_3024'	'O-1H-1'
'r_3025'	'O-1H-1'
'r_3026'	'H-1'
'r_3027'	'H-1'
'r_3028'	'O-1H-1'
'r_3029'	'O-1H-1'
'r_3030'	'H1'
'r_3031'	'H1'
'r_3032'	'H1'
'r_3033'	'H1'
'r_3034'	'H-1'
'r_3035'	'H-1'
'r_3036'	'O-1H-1'
'r_3037'	'O-1H-1'
'r_3038'	'H-1'
'r_3039'	'H-1'
'r_3040'	'O-1H-1'
'r_3041'	'O-1H-1'
'r_3042'	'H1'
'r_3043'	'H1'
'r_3044'	'H1'
'r_3045'	'H1'
'r_3078'	'H1'
'r_3079'	'H1'
'r_3080'	'H1'
'r_3081'	'H1'
'r_3082'	'H3'
'r_3083'	'H5'
'r_3084'	'H5'
'r_3085'	'H5'
'r_3086'	'H5'
'r_3087'	'H5'
'r_3088'	'H5'
'r_3089'	'H5'
'r_3090'	'H3'
'r_3091'	'H5'
'r_3092'	'H5'
'r_3093'	'H5'
'r_3094'	'H5'
'r_3095'	'H5'
'r_3096'	'H5'
'r_3097'	'H5'
'r_3098'	'H-1'
'r_3099'	'H1'
'r_3100'	'H1'
'r_3101'	'H1'
'r_3102'	'H1'
'r_3103'	'H1'
'r_3105'	'H-2'
'r_3106'	'O-1H-2'
'r_3107'	'O-1H-2'
'r_3108'	'H-2'
'r_3109'	'H-2'
'r_3110'	'O-1H-2'
'r_3111'	'O-1H-2'
'r_3112'	'H2'
'r_3113'	'H2'
'r_3114'	'H2'
'r_3115'	'H2'
'r_3116'	'H2'
'r_3117'	'H2'
'r_3118'	'H2'
'r_3119'	'H2'
'r_3120'	'H2'
'r_3121'	'H2'
'r_3122'	'H2'
'r_3123'	'H2'
'r_3124'	'H2'
'r_3125'	'H2'
'r_3126'	'H2'
'r_3127'	'H2'
'r_3128'	'H2'
'r_3129'	'H2'
'r_3130'	'H2'
'r_3131'	'H2'
'r_3132'	'H2'
'r_3133'	'H2'
'r_3134'	'H2'
'r_3135'	'H2'
'r_3136'	'H2'
'r_3137'	'H2'
'r_3138'	'H2'
'r_3139'	'H2'
'r_3140'	'H2'
'r_3141'	'H2'
'r_3142'	'H2'
'r_3143'	'H2'
'r_3144'	'H2'
'r_3145'	'H2'
'r_3146'	'H2'
'r_3147'	'H2'
'r_3148'	'H2'
'r_3149'	'H2'
'r_3150'	'H2'
'r_3151'	'H2'
'r_3152'	'H2'
'r_3153'	'H2'
'r_3154'	'H2'
'r_3155'	'H2'
'r_3156'	'H2'
'r_3157'	'H2'
'r_3158'	'H2'
'r_3159'	'H2'
'r_3160'	'H2'
'r_3161'	'H2'
'r_3162'	'H2'
'r_3163'	'H2'
'r_3164'	'H2'
'r_3165'	'H2'
'r_3166'	'H2'
'r_3167'	'H2'
'r_3168'	'H2'
'r_3169'	'H2'
'r_3170'	'H2'
'r_3171'	'H2'
'r_3172'	'H2'
'r_3173'	'H2'
'r_3174'	'H2'
'r_3175'	'H2'
'r_3176'	'H2'
'r_3177'	'H2'
'r_3178'	'H2'
'r_3179'	'H2'
'r_3180'	'H2'
'r_3181'	'H2'
'r_3182'	'H2'
'r_3183'	'H2'
'r_3184'	'H2'
'r_3185'	'H2'
'r_3186'	'H2'
'r_3187'	'H2'
'r_3188'	'H2'
'r_3189'	'H2'
'r_3190'	'H2'
'r_3191'	'H2'
'r_3192'	'H2'
'r_3193'	'H2'
'r_3194'	'H2'
'r_3195'	'H2'
'r_3196'	'H2'
'r_3197'	'H2'
'r_3198'	'H2'
'r_3199'	'H2'
'r_3200'	'H2'
'r_3201'	'H2'
'r_3202'	'H2'
'r_3203'	'H2'
'r_3204'	'H2'
'r_3205'	'H2'
'r_3206'	'H2'
'r_3207'	'H2'
'r_3208'	'H2'
'r_3209'	'H2'
'r_3210'	'H2'
'r_3211'	'H2'
'r_3212'	'H2'
'r_3213'	'H2'
'r_3214'	'H2'
'r_3215'	'H2'
'r_3216'	'H2'
'r_3217'	'H2'
'r_3218'	'H2'
'r_3219'	'H2'
'r_3220'	'H2'
'r_3221'	'H2'
'r_3222'	'H2'
'r_3223'	'H2'
'r_3224'	'H3'
'r_3225'	'H1'
'r_3226'	'H1'
'r_3227'	'H1'
'r_3228'	'H1'
'r_3229'	'H1'
'r_3230'	'H1'
'r_3231'	'H1'
'r_3232'	'H3'
'r_3233'	'H1'
'r_3234'	'H1'
'r_3235'	'H1'
'r_3236'	'H1'
'r_3237'	'H1'
'r_3238'	'H1'
'r_3239'	'H1'
'r_3240'	'H2'
'r_3241'	'H2'
'r_3242'	'H2'
'r_3243'	'H2'
'r_3244'	'H2'
'r_3245'	'H2'
'r_3246'	'H2'
'r_3247'	'H2'
'r_3248'	'H2'
'r_3249'	'H2'
'r_3250'	'H2'
'r_3251'	'H2'
'r_3264'	'H-2'
'r_3265'	'H-2'
'r_3266'	'H-2'
'r_3267'	'H-2'
'r_3296'	'H2'
'r_3316'	'H-1'
'r_3317'	'H-1'
'r_3318'	'O-1H-1'
'r_3319'	'O-1H-1'
'r_3320'	'H-1'
'r_3321'	'H-1'
'r_3322'	'O-1H-1'
'r_3323'	'O-1H-1'
'r_4042'	'O-1H-2'
'r_3348'	'H-2'
'r_3356'	'H-2'
'r_3364'	'H-2'
'r_3372'	'H-2'
'r_3380'	'H-2'
'r_3388'	'H-2'
'r_3396'	'H-2'
'r_3404'	'H-2'
'r_3412'	'H-2'
'r_3420'	'H-2'
'r_3428'	'H-2'
'r_3436'	'H-2'
'r_3444'	'H-2'
'r_3452'	'H-2'
'r_3460'	'H-2'
'r_3468'	'H-2'
'r_3476'	'H-2'
'r_3484'	'H-2'
'r_3492'	'H-2'
'r_3500'	'H-2'
'r_1449'	'C28.5703N0.089736O1.5911P0.089736H57.1406'
'r_1450'	'C28.9353N0.061683O1.2545P0.061683H57.8705'
'r_1451'	'C28.4743N0.073737O2.4311P0.073737H56.9486'
'r_1452'	'C28.8393N0.045683O2.0945P0.045683H57.6785'
'r_1453'	'C28.6663N0.10574O0.75111P0.10574H57.3325'
'r_1454'	'C29.0313N0.077682O0.41446P0.077682H58.0625'
'r_1455'	'C28.5703N0.089736O1.5911P0.089736H57.1406'
'r_1456'	'C28.9353N0.061683O1.2545P0.061683H57.8705'
'r_1457'	'C28.3783N0.057738O3.2711P0.057738H56.7566'
'r_1458'	'C28.7433N0.029684O2.9345P0.029684H57.4866'
'r_1479'	'C22.6583N-0.29853O-7.1724P-0.59706H46.2123'
'r_1480'	'C22.6867N-0.32658O-7.8738P-0.65317H46.3531'
'r_1481'	'C22.3704N-0.31453O-6.5404P-0.62906H45.6843'
'r_1482'	'C22.3987N-0.34258O-7.2417P-0.68516H45.8251'
'r_1483'	'C22.3704N-0.31453O-6.5404P-0.62906H45.6843'
'r_1484'	'C22.3987N-0.34258O-7.2417P-0.68516H45.8251'
'r_1485'	'C22.0824N-0.33053O-5.9084P-0.66106H45.1563'
'r_1486'	'C22.1107N-0.35858O-6.6097P-0.71716H45.2972'
'r_1487'	'C21.7944N-0.34653O-5.2764P-0.69305H44.6283'
'r_1488'	'C21.8227N-0.37458O-5.9777P-0.74916H44.7692'
'r_1509'	'C27.163N-0.072406O-0.39234P-0.072406H54.4708'
'r_1510'	'C27.3597N-0.10046O-0.86926P-0.10046H54.9202'
'r_1511'	'C26.971N-0.088405O0.36767P-0.088405H54.1188'
'r_1512'	'C27.1677N-0.11646O-0.10925P-0.11646H54.5682'
'r_1513'	'C27.355N-0.056407O-1.1524P-0.056407H54.8228'
'r_1514'	'C27.5516N-0.08446O-1.6293P-0.08446H55.2722'
'r_1515'	'C27.163N-0.072406O-0.39234P-0.072406H54.4708'
'r_1516'	'C27.3597N-0.10046O-0.86926P-0.10046H54.9202'
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'r_4202'	'N1H1R2'
'r_4219'	'O1'
'r_4235'	'H-1'
'r_4245'	'H-2'
'r_4250'	'H-1R1'
'r_4253'	'H-2R1'
'r_4267'	'H1'
'r_4268'	'H-1'
'r_4271'	'O8H16R1'
'r_4279'	'H4'
'r_4286'	'H-2'
'r_4303'	'H1'
'r_4304'	'H1'
'r_4313'	'H-1'
'r_4320'	'H-2R1'
'r_4321'	'H-2R1'
'r_4328'	'H2R-1'
'r_4442'	'C2N1S1H8'
'r_4453'	'H-2'
'r_4456'	'H-2'
'r_4459'	'H-2'
'r_4465'	'H-2'
'r_4467'	'H1'
'r_4494'	'C1O1H4'
'r_4495'	'H2'
'r_4496'	'C5N2O3H10'
'r_4497'	'C6O8H3'
'r_4498'	'C12O11H22'
'r_4499'	'C6O7H9'
'r_4500'	'C6O6H12'
'r_4501'	'C12O11H22'
'r_4502'	'C6O9P1H11'
'r_4503'	'C18O16H32'
'r_4504'	'C6O9P1H11'
'r_4505'	'C7O6H14'
'r_4506'	'C6N1O5H14'
'r_4507'	'C3O3H6'
'r_4508'	'C8N3O4H15'
'r_4509'	'C9N2O3H18'
'r_4510'	'C7N3O4H13'
'r_4511'	'C9N4O3H14'
'r_4512'	'C6N3O4H11'
'r_4513'	'C8N2O5H13'
'r_4514'	'C7N2O3S1H14'
'r_4515'	'C7N2O5H11'
'r_4516'	'C7N2O5H11'
'r_4517'	'C7N2O4H14'
'r_4518'	'C8N2O3S1H16'
'r_4519'	'C6N3O3H13'
'r_4520'	'C4N1O2H9'
'r_4521'	'C5N1O4P1H13'
'r_4522'	'C3O6P1H7'
'r_4523'	'C3O7P1H4'
'r_4524'	'C10N5O8P1H12'
'r_4525'	'C3N1O6P1H6'
'r_4526'	'C3N1O6P1H6'
'r_4527'	'O7P2H1'
'r_4528'	'O10P3'
'r_4529'	'C3O6P1H2'
'r_4530'	'C6N4O5P1H14'
'r_4531'	'C1N1O5P1H2'
'r_4532'	'C2N1O4P1H7'
'r_4533'	'C2N1O3S1P1H7'
'r_4534'	'C10N5O8P1H12'
'r_4535'	'C3O6P1H7'
'r_4536'	'C10N5O8P1H12'
'r_4537'	'C2O6P1H2'
'r_4538'	'C6O10P1H10'
'r_4539'	'C6O9P1H11'
'r_4540'	'C10N5O7P1H11'
'r_4541'	'C9N1O6P1H10'
'r_4542'	'C4N1O6P1H8'
'r_4543'	'C3O7P1H4'
'r_4544'	'C10N5O7P1H12'
'r_4545'	'C10N5O7P1H12'
'r_4546'	'C10N5O6P1H11'
'r_4547'	'C6O9P1H11'
'r_4548'	'C10N5O7P1H12'
'r_4549'	'C7N1O3S1H12'
'r_4550'	'C5N1O3S1H11'
'r_4551'	'C3N1O4S1H6'
'r_4552'	'C5N1O3S1H8'
'r_4553'	'C3N1O5S1H6'
'r_4554'	'C2O4S1H5'
'r_4555'	'C4O3H5'
'r_4556'	'C7N1O5H9'
'r_4557'	'C9N2O9P1H11'
'r_4558'	'C9N3O8P1H12'
'r_4559'	'C10N2O8P1H13'
'r_4560'	'C10N2O8P1H13'
'r_4561'	'C9N3O8P1H12'
'r_4562'	'C9N2O9P1H11'
'r_4563'	'C9N2O9P1H11'
'r_4564'	'C9N3O7P1H11'
'r_4565'	'C9N2O8P1H10'
'r_4567'	'O-1H-2'
'r_4568'	'O-1'
'r_4571'	'C-21N-7O-15S-1P-3H-34'
'r_4577'	'O-1'
'r_4593'	'Cl1'
'r_4594'	'Cu1'
'r_4595'	'Mn1'
'r_4596'	'Zn1'
'r_4597'	'Mg1'
'r_4600'	'Ca1'

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the master branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue

[edkerk]

@eiden309 is systematically correcting mass- and charge balancing reactions by correcting metabolite formulae and charges, and correcting reaction stoichiometries, primarily through manual curation.

[BenjaSanchez]

update: after merging #222, the remaining unbalanced reactions are:

model.rxns	Imbalance issue(s) to check	Charge difference	Elemental difference
r_0013	checkMetCharge	4	[]
r_0229	checkMetCharge	2	[]
r_0365	checkMetCharge	-1	[]
r_0438	checkMetChargeAndFormula	-0.633	H0.633
r_0439	checkMetChargeAndFormula	1.266	H-1.266
r_0532	checkMetCharge	-2	[]
r_1603	checkMetFormula	[]	H-2
r_2070	checkMetCharge	-2	[]
r_2071	checkMetCharge	-2	[]
r_4170	checkMetFormula	[]	R-1
r_4250	checkMetFormula	[]	R1
r_4253	checkMetFormula	[]	R1
r_4271	checkMetFormula	[]	R1
r_4320	checkMetChargeAndFormula	2	R1
r_4321	checkMetChargeAndFormula	-2	R1
r_4328	checkMetFormula	[]	R-1
r_4568	checkMetFormula	[]	O-1