Feat/stoichiometric consistency

Main improvements in this PR:

Fully resolves #99 and partly resolves #79. This PR adds chemical formula and charge to all metabolites missing this information and mass-balances most of the remaining reactions.

After this PR there is 31 reactions that are not mas or charge balances, but 16 of these are biomass / pseudo-reactions. The remaining 17 reactions are: ACTS16b: ddhkACPact_c + fmnh2_c + o2_c --> dhkACPact_c + fmn_c + h2o_c + 2.0 h_c; {'charge': 2.0} ACTS18: dhkdhqn_c + fmnh2_c + o2_c <=> fmn_c + h2o_c + hdhk_c; {'H': -2.0} AHMMPS: air_c + 2.0 h_c --> 4ahmmp_c + gcald_c + pi_c; {'charge': -2.0} MMSYNA: mmyC_c --> mmyA_c; {'O': 1.0} MMYSYN1: accoa_c + malACPmmy_c --> actACPmmy_c + co2_c + coa_c; {'charge': -1.0, 'H': 1.0} MMYSYN2: actACPmmy_c + mmyint1_c --> ACPmmy_c + mmyint2_c; {'O': -1.0} MMYSYN3: mmyint2_c --> mmyC_c; {'H': -7.0, 'O': -3.0} SCB11: 3oiC9ACP_c + dhap_c --> 2o3pp8m3onn_c + ACP_c; {'charge': 2.0, 'C': 1.0, 'H': 4.0} SCB14: h2o_c + mh5othfmdp_c --> afactor_c + pi_c; {'charge': -2.0, 'H': -2.0, 'O': 1.0} SCB15: afactor_c + h_c + nadph_c --> nadp_c + scb1_c; {'O': -1.0} SCB21a: 3odcoa_c + dhap_c --> 2o3pop3odn_c + coa_c; {'charge': 2.0, 'H': 2.0} SCB21b: 3oddecACP_c + dhap_c --> 2o3pop3odn_c + ACP_c; {'charge': 2.0, 'C': -2.0, 'H': -2.0} SCB24: 4o5othf3mdp_c + h2o_c --> 4hm3odhf2o_c + pi_c; {'charge': -2.0, 'H': -2.0} SCB31: 3oiC10ACP_c + dhap_c --> 2o3pp8m3onn_c + ACP_c; {'charge': 2.0, 'H': 2.0} SCB32: 2o3pp8m3onn_c --> 46mo5o25dhf3mdhp_c + h2o_c; {'C': 1.0, 'H': 2.0} SCB34: 465mo5othf3mdhp_c + h2o_c --> 4hm36modhf2o_c + pi_c; {'charge': -2.0, 'H': -2.0, 'O': 1.0} SCB35: 4hm36modhf2o_c + h_c + nadph_c --> nadp_c + scb3_c; {'O': -1.0}

The remaining reactions are mostly associated with the biosynthesis of ACT, methylenomycin or Gamma-butyrolactones, and I believe that this represents an actual lack of knowledg

I hereby confirm that I have:

[x] Tested my code with all requirements for running the model
[x] Selected devel as a target branch (top left drop-down menu)
[x] If needed, asked first in the Gitter chat room about this PR

Note: replace [ ] with [X] to check the box.

SysBioChalmers / Sco-GEM

Feat/stoichiometric consistency #148

Main improvements in this PR: