Reading metabolite conc bounds from: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/experimentalData/metaboliteConcentrations/HumanCofactorConcentrations.txt adp[c] 1e-07 0.0019 adp[m] 0.0026 0.0094 amp[c] 1e-07 0.0012 atp[c] 0.00129 0.0049 atp[m] 0.0028 0.0204 coa[c] 2.92e-05 0.0001168 coa[m] 0.0022 0.0039 na1[c] 1e-07 0.025 na1[e] 0.1326 0.1554 nad[c] 0.00010546 0.0007572 nad[m] 0.0005 0.0075 nadh[c] 9.2574e-07 0.00038294 nadh[m] 1e-07 0.0011 nadp[c] 1e-07 5.8284e-06 nadp[m] 1e-07 0.0015 nadph[c] 1e-07 0.00037523 nadph[m] 1e-07 0.0042 nh4[c] 0.0007 0.0009 pi[c] 0.001 0.0063 ppi[c] 0.0021 0.0076 udp[g] 1.4e-06 0.00014

There are mass imbalanced reactions, see /home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/vonBertalanffy/Recon3DModel_301_results/Recon3DModel_301_results_mass_imbalanced_reactions.txt There are mass balanced, but charge imbalanced reactions, see /home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/vonBertalanffy/Recon3DModel_301_results/Recon3DModel_301_results_charge_imbalanced_reactions.txt

removing: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/componentContribution/old removing: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/directionalityReport/old removing: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/groupContribution/old removing: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/inchi/old removing: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/molFiles/old removing: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/protons/old removing: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/trainingModel/old adding: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/componentContribution/new adding: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/groupContribution/new adding: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/inchi/new adding: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/molFiles/new adding: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/protons/new adding: /home/rfleming/work/sbgCloud/code/fork-cobratoolbox/src/analysis/thermo/trainingModel/new ChemAxon Marvin Beans is installed and working. linux-vdso.so.1 (0x00007ffe937e7000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f25ad526000) libopenbabel.so.5 => /usr/lib/libopenbabel.so.5 (0x00007f25ad2d6000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f25ad0bc000) libgcc_s.so.1 => /usr/local/bin/MATLAB/R2021a/sys/os/glnxa64/libgcc_s.so.1 (0x00007f25acea4000) /lib64/ld-linux-x86-64.so.2 (0x00007f25ad746000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f25ace9c000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f25ace80000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f25acd31000) libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f25accec000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f25accc9000) babel must depend on the system libstdc++.so.6 not the one from MATLAB Trying to edit the 'LD_LIBRARY_PATH' to make sure that it has the correct system path before the Matlab path! The solution will be arch dependent Successfully added 3914 values from TECRDB Successfully added 223 formation energies Successfully added 13 redox potentials mol2inchi: could not generate inchi for C00080 0 molecules converted 2 audit log messages createInChIStruct: no molecule identifier in C00080 mol2inchi: could not generate inchi for C00080 0 molecules converted 2 audit log messages mol2inchi: could not generate inchi for C00080 0 molecules converted 2 audit log messages mol2inchi: could not generate inchi for C00080 0 molecules converted 2 audit log messages mol2inchi: could not generate inchi for C00125 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C00125 mol2inchi: could not generate inchi for C00125 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00125 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00125 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00126 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C00126 mol2inchi: could not generate inchi for C00126 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00126 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00126 babel: Alias R was not chemically interpreted mol2inchi: no annotation in C00225 createInChIStruct: no molecule identifier in C00225 mol2inchi: no annotation in C00225 mol2inchi: no annotation in C00225 mol2inchi: no annotation in C00225 mol2inchi: could not generate inchi for C00229 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C00229 mol2inchi: could not generate inchi for C00229 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00229 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00229 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00342 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C00342 mol2inchi: could not generate inchi for C00342 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00342 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00342 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00343 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C00343 mol2inchi: could not generate inchi for C00343 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00343 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C00343 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01003 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C01003 mol2inchi: could not generate inchi for C01003 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01003 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01003 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01194 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C01194 mol2inchi: could not generate inchi for C01194 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01194 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01194 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01209 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C01209 mol2inchi: could not generate inchi for C01209 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01209 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01209 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01277 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C01277 mol2inchi: could not generate inchi for C01277 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01277 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01277 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01281 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C01281 mol2inchi: could not generate inchi for C01281 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01281 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01281 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01299 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C01299 mol2inchi: could not generate inchi for C01299 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01299 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01299 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01931 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C01931 mol2inchi: could not generate inchi for C01931 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01931 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C01931 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02163 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C02163 mol2inchi: could not generate inchi for C02163 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02163 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02163 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02553 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C02553 mol2inchi: could not generate inchi for C02553 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02553 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02553 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02554 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C02554 mol2inchi: could not generate inchi for C02554 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02554 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02554 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02780 0 molecules converted 2 audit log messages createInChIStruct: no molecule identifier in C02780 mol2inchi: could not generate inchi for C02780 0 molecules converted 2 audit log messages mol2inchi: could not generate inchi for C02780 0 molecules converted 2 audit log messages mol2inchi: could not generate inchi for C02780 0 molecules converted 2 audit log messages mol2inchi: could not generate inchi for C02839 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C02839 mol2inchi: could not generate inchi for C02839 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02839 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02839 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02988 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C02988 mol2inchi: could not generate inchi for C02988 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02988 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02988 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02992 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C02992 mol2inchi: could not generate inchi for C02992 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02992 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C02992 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03127 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C03127 mol2inchi: could not generate inchi for C03127 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03127 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03127 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03511 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C03511 mol2inchi: could not generate inchi for C03511 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03511 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03511 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03875 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C03875 mol2inchi: could not generate inchi for C03875 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03875 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03875 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03939 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C03939 mol2inchi: could not generate inchi for C03939 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03939 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C03939 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04246 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C04246 mol2inchi: could not generate inchi for C04246 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04246 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04246 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04618 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C04618 mol2inchi: could not generate inchi for C04618 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04618 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04618 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04688 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C04688 mol2inchi: could not generate inchi for C04688 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04688 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C04688 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06020 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C06020 mol2inchi: could not generate inchi for C06020 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06020 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06020 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06021 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C06021 mol2inchi: could not generate inchi for C06021 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06021 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06021 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06567 babel: Alias R was not chemically interpreted createInChIStruct: no molecule identifier in C06567 mol2inchi: could not generate inchi for C06567 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06567 babel: Alias R was not chemically interpreted mol2inchi: could not generate inchi for C06567 babel: Alias R was not chemically interpreted 672 = number of model metabolites 657 ... with mol files 15 ... without mol files 627 ... with nonstandard inchi 45 ... without nonstandard inchi 0 ... compositie inchi removed Estimating metabolite pKa values for training trainingModel... ...done. There are mass imbalanced reactions, see /home/rfleming/work/sbgCloud/code/fork-COBRA.tutorials/analysis/vonBertalanffy/Recon3DModel_301_results/trainingData_mass_imbalanced_reactions.txt Performing reverse Legendre transform

TECRDB_79 C01101 <=> C00231 TECRDB_244 C00041 <=> C00133 TECRDB_580 C00002 + C00065 + C01650 <=> C00013 + C00020 + C02553 TECRDB_698 C00003 + C00644 <=> C00004 + C00085 TECRDB_733 C01101 <=> C00231 TECRDB_815 C00002 + C00055 <=> C00008 + C00112 TECRDB_1090 C00001 + C00006 + C00311 <=> C00005 + C00026 + C00288 TECRDB_1272 C00001 + C06322 <=> C06749 TECRDB_2030 C00041 <=> C00133 TECRDB_2202 C00003 + C00579 <=> C00004 + C00248 TECRDB_2339 C00063 + C00103 <=> C00013 + C00501 TECRDB_2392 C01213 <=> C00683 TECRDB_2584 C00041 <=> C00133 TECRDB_2620 C00026 + C00041 <=> C00022 + C00025 TECRDB_2621 C00002 + C01107 <=> C00008 + C01143 TECRDB_2629 C00025 <=> C00217 TECRDB_2639 C00002 + C00104 <=> C00008 + C00081 TECRDB_2746 C00031 <=> C00095 TECRDB_2791 C00010 + C00042 + C00044 <=> C00009 + C00035 + C00091 TECRDB_2841 2 C00008 <=> C00002 + C00020 TECRDB_2894 C00041 <=> C00133 TECRDB_3608 C00031 <=> C00095 TECRDB_3640 C00047 <=> C00739 TECRDB_3803 C00636 <=> C00275 TECRDB_3808 C00075 + C00103 <=> C00013 + C00029 TECRDB_4052 C00041 <=> C00133 TECRDB_4271 C00935 <=> C00190 TECRDB_4375 C00123 <=> C01570 TECRDB_4377 C00009 + C00299 <=> C00106 + C00620 TECRDB_4398 C00026 + C00041 <=> C00022 + C00025 TECRDB_4536 C00031 <=> C00095 TECRDB_4537 C00031 <=> C00095 FORM_C00023 <=> C00023 FORM_C00034 <=> C00034 FORM_C00080 <=> C00080

9/10600 reactions with DrGtMin=DrGtMax~=0 4/10600 reactions with DrGtMin=DrGtMax=0 Qualitative internal reaction directionality: 8791 internal reconstruction reaction directions. 5208 forward reconstruction assignment. 4 reverse reconstruction assignment. 3579 reversible reconstruction assignment. Quantitative internal reaction directionality: 8791 internal reconstruction reaction directions. 8036 of which have a thermodynamic assignment. 751 of which have no thermodynamic assignment. 1636 forward thermodynamic only assignment. 1512 reverse thermodynamic only assignment. 4888 reversible thermodynamic only assignment. Qualitiative vs Quantitative: 2525 Reversible -> Reversible 347 Reversible -> Forward 583 Reversible -> Reverse 120 Reversible -> Uncertain 1286 Forward -> Forward 929 Forward -> Reverse 2362 Forward -> Reversible 631 Forward -> Uncertain 1 Reverse -> Reverse 3 Reverse -> Forward 1 Reverse -> Reversible 0 Reversible -> Uncertain Breakdown of relaxation of reaction directionality, Qualitiative vs Quantitative: 2362 qualitatively forward reactions that are quantitatively reversible (total). 1183 of which are quantitatively reversible by range of dGt0. P(\Delta_{r}G^{\primeo}<0) > 0.7 0 of which are quantitatively reversible by range of dGt0. 0.3< P(\Delta_{r}G^{\primeo}<0) < 0.7 1179 of which are quantitatively reversible by range of dGt0. P(\Delta_{r}G^{\primeo}<0) < 0.3 56 of which are quantitatively forward by fixed dGr0t, but reversible by concentration alone (zero fixed DrGt0). 0 of which are quantitatively reverse by dGr0t, but reversible by concentration (negative fixed DrGt0). 0 of which are quantitatively forward by dGr0t, but reversible by concentration (positve fixed DrGt0). 0 of which are quantitatively reverse by dGr0t, but reversible by concentration (uncertain negative DrGt0). 0 of which are quantitatively forward by dGr0t, but reversible by concentration (uncertain positive DrGt0).