{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# FullThermoPkg example" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "tags": [] }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "WARNING:cobrakbase.core.kbasefba.fbamodel_builder:unable to add sink for [cpd15302_c0]: not found\n" ] } ], "source": [ "# define the environment path \n", "import os\n", "local_cobrakbase_path = os.path.join('C:', 'Users', 'Andrew Freiburger','Documents','Argonne','cobrakbase')\n", "os.environ[\"HOME\"] = local_cobrakbase_path\n", "\n", "# import the models\n", "import cobrakbase\n", "token = 'WE6CHYRDTJSGOHFIDGPE7WYFT6PRPXJL'\n", "kbase_api = cobrakbase.KBaseAPI(token)\n", "\n", "#Put the path to ModelSEEDpy on your machine here\n", "# import sys\n", "# sys.path.append(\"/Users/chenry/code/ModelSEEDpy\")\n", "#import modelseedpy.fbapkg\n", "from modelseedpy import KBaseMediaPkg, FullThermoPkg\n", "from modelseedpy import FBAHelper\n" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true }, "tags": [] }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "WARNING:cobrakbase.core.kbasefba.fbamodel_builder:unable to add sink for [cpd15302_c0]: not found\n" ] }, { "data": { "text/html": [ "

Objective

1.0 bio1 = 26.513845730068834

Uptake

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MetaboliteReactionFluxC-NumberC-Flux
arabttr_e0EX_arabttr_e08.76400.00%
cpd00001_e0EX_cpd00001_e010000.00%
cpd00007_e0EX_cpd00007_e010000.00%
cpd00009_e0EX_cpd00009_e044.1100.00%
cpd00028_e0EX_cpd00028_e00.1238340.04%
cpd00030_e0EX_cpd00030_e00.123800.00%
cpd00034_e0EX_cpd00034_e00.123800.00%
cpd00039_e0EX_cpd00039_e08.84460.46%
cpd00047_e0EX_cpd00047_e030.9910.27%
cpd00063_e0EX_cpd00063_e00.123800.00%
cpd00065_e0EX_cpd00065_e0100119.64%
cpd00076_e0EX_cpd00076_e01001210.51%
cpd00084_e0EX_cpd00084_e02.60730.07%
cpd00104_e0EX_cpd00104_e00.1238100.01%
cpd00106_e0EX_cpd00106_e052.1241.83%
cpd00108_e0EX_cpd00108_e01.30260.07%
cpd00119_e0EX_cpd00119_e010065.26%
cpd00122_e0EX_cpd00122_e04.90480.34%
cpd00149_e0EX_cpd00149_e00.123800.00%
cpd00159_e0EX_cpd00159_e010032.63%
cpd00166_e0EX_cpd00166_e00.1238720.08%
cpd00179_e0EX_cpd00179_e082.65128.69%
cpd00182_e0EX_cpd00182_e0100108.76%
cpd00205_e0EX_cpd00205_e00.123800.00%
cpd00218_e0EX_cpd00218_e00.247560.01%
cpd00220_e0EX_cpd00220_e00.2475170.04%
cpd00221_e0EX_cpd00221_e010032.63%
cpd00224_e0EX_cpd00224_e010054.38%
cpd00254_e0EX_cpd00254_e00.123800.00%
cpd00263_e0EX_cpd00263_e00.123880.01%
cpd00280_e0EX_cpd00280_e02.60460.14%
cpd00305_e0EX_cpd00305_e00.1238120.01%
cpd00311_e0EX_cpd00311_e06.167100.54%
cpd00322_e0EX_cpd00322_e011.4460.60%
cpd00363_e0EX_cpd00363_e010021.75%
cpd00367_e0EX_cpd00367_e010097.88%
cpd00393_e0EX_cpd00393_e00.3713190.06%
cpd00396_e0EX_cpd00396_e01.30260.07%
cpd00644_e0EX_cpd00644_e00.247590.02%
cpd00654_e0EX_cpd00654_e095.4997.53%
cpd00971_e0EX_cpd00971_e00.123800.00%
cpd10515_e0EX_cpd10515_e00.247500.00%
cpd11591_e0EX_cpd11591_e097.7976.00%
cpd11640_e0EX_cpd11640_e010000.00%
cpd15500_e0EX_cpd15500_e00.1238510.06%
cpd15551_e0EX_cpd15551_e05.71270.35%
cpd15605_e0EX_cpd15605_e0100119.64%
cpd15606_e0EX_cpd15606_e0100119.64%
cps_bt_e0EX_cps_bt_e00.123800.00%
galam_e0EX_galam_e010000.00%
glyasn_e0EX_glyasn_e010000.00%
hspg_degr_11_e0EX_hspg_degr_11_e010000.00%
hspg_degr_6_e0EX_hspg_degr_6_e010000.00%
leuleu_e0EX_leuleu_e057.7900.00%
lps_bt_e0EX_lps_bt_e00.515700.00%
pe_cer1_bt_e0EX_pe_cer1_bt_e00.123800.00%
pect_e0EX_pect_e00.512800.00%
phearg_e0EX_phearg_e010000.00%
sphmyln_bt_e0EX_sphmyln_bt_e00.123800.00%

Secretion

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MetaboliteReactionFluxC-NumberC-Flux
arabinan101_e0EX_arabinan101_e0-1.30200.00%
argarg_e0EX_argarg_e0-46.1200.00%
cpd00011_e0EX_cpd00011_e0-10010.73%
cpd00013_e0EX_cpd00013_e0-10000.00%
cpd00020_e0EX_cpd00020_e0-10032.20%
cpd00027_e0EX_cpd00027_e0-10064.41%
cpd00029_e0EX_cpd00029_e0-10021.47%
cpd00033_e0EX_cpd00033_e0-10021.47%
cpd00035_e0EX_cpd00035_e0-10032.20%
cpd00036_e0EX_cpd00036_e0-10042.94%
cpd00041_e0EX_cpd00041_e0-10042.94%
cpd00053_e0EX_cpd00053_e0-10053.67%
cpd00054_e0EX_cpd00054_e0-10032.20%
cpd00060_e0EX_cpd00060_e0-93.753.44%
cpd00066_e0EX_cpd00066_e0-95.2196.30%
cpd00067_e0EX_cpd00067_e0-10000.00%
cpd00069_e0EX_cpd00069_e0-96.4496.38%
cpd00082_e0EX_cpd00082_e0-10064.41%
cpd00092_e0EX_cpd00092_e0-94.2542.77%
cpd00105_e0EX_cpd00105_e0-10053.67%
cpd00107_e0EX_cpd00107_e0-10064.41%
cpd00116_e0EX_cpd00116_e0-10010.73%
cpd00117_e0EX_cpd00117_e0-10032.20%
cpd00132_e0EX_cpd00132_e0-93.7842.76%
cpd00141_e0EX_cpd00141_e0-55.0231.21%
cpd00156_e0EX_cpd00156_e0-13.7750.51%
cpd00161_e0EX_cpd00161_e0-93.4642.75%
cpd00164_e0EX_cpd00164_e0-10064.41%
cpd00249_e0EX_cpd00249_e0-92.8496.14%
cpd00276_e0EX_cpd00276_e0-10064.41%
cpd00430_e0EX_cpd00430_e0-10085.88%
cpd00438_e0EX_cpd00438_e0-94.25106.93%
cpd15836_e0EX_cpd15836_e0-97.5496.45%
hspg_degr_12_e0EX_hspg_degr_12_e0-10000.00%
indlac_e0EX_indlac_e0-98.5400.00%
unsdigalur_e0EX_unsdigalur_e0-10000.00%
cpd11416_c0SK_cpd11416_c0-26.5100.00%
" ], "text/plain": [ "" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model = kbase_api.get_from_ws(\"E_iAH991V2\",40576)\n", "model.solver = 'glpk'\n", "kmp = KBaseMediaPkg(model)\n", "kmp.build_package(None)\n", "FBAHelper.set_objective_from_target_reaction(model,\"bio1\")\n", "sol=model.optimize()\n", "model.summary()\n" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "12ethd_e0 has no modelseed ID!\n", "12ethd_c0 has no modelseed ID!\n", "2ameph_c0 has no modelseed ID!\n", "pald_c0 has no modelseed ID!\n", "2fuclac_e0 has no modelseed ID!\n", "cpd11493_c0 has modelseed ID cpd11493 but does not have a valid deltaG!\n", "2mbutACP_c0 has no modelseed ID!\n", "2mmal_c0 has no modelseed ID!\n", "2mmale_c0 has no modelseed ID!\n", "e3mmal_c0 has no modelseed ID!\n", "3fuclac_e0 has no modelseed ID!\n", "3hgACPm_c0 has no modelseed ID!\n", "egACPm_c0 has no modelseed ID!\n", "3hpACPm_c0 has no modelseed ID!\n", "epACPm_c0 has no modelseed ID!\n", "cpd11482_c0 has modelseed ID cpd11482 but does not have a valid deltaG!\n", "cpd11475_c0 has modelseed ID cpd11475 but does not have a valid deltaG!\n", "10m3hundecACP_c0 has no modelseed ID!\n", "10mtundec2eACP_c0 has no modelseed ID!\n", "10m3hddcaACP_c0 has no modelseed ID!\n", "10mtddec2eACP_c0 has no modelseed ID!\n", "11m3hddcaACP_c0 has no modelseed ID!\n", "11mtddec2eACP_c0 has no modelseed ID!\n", "cpd11480_c0 has modelseed ID cpd11480 but does not have a valid deltaG!\n", "cpd11469_c0 has modelseed ID cpd11469 but does not have a valid deltaG!\n", "cpd15366_c0 has modelseed ID cpd15366 but does not have a valid deltaG!\n", "cpd15569_c0 has modelseed ID cpd15569 but does not have a valid deltaG!\n", "12m3htridecACP_c0 has no modelseed ID!\n", "12mttritec2eACP_c0 has no modelseed ID!\n", "12m3hmyrsACP_c0 has no modelseed ID!\n", "12mtmrs2eACP_c0 has no modelseed ID!\n", "13m3hmyrsACP_c0 has no modelseed ID!\n", "13mtmrs2eACP_c0 has no modelseed ID!\n", "cpd11484_c0 has modelseed ID cpd11484 but does not have a valid deltaG!\n", "cpd11467_c0 has modelseed ID cpd11467 but does not have a valid deltaG!\n", "cpd15368_c0 has modelseed ID cpd15368 but does not have a valid deltaG!\n", "cpd15570_c0 has modelseed ID cpd15570 but does not have a valid deltaG!\n", "14m3hpentdecACP_c0 has no modelseed ID!\n", "14mtpentdec2eACP_c0 has no modelseed ID!\n", "14m3hpalmACP_c0 has no modelseed ID!\n", "14mtpalm2eACP_c0 has no modelseed ID!\n", "15m3hpalmACP_c0 has no modelseed ID!\n", "15mtpalm2eACP_c0 has no modelseed ID!\n", "cpd11481_c0 has modelseed ID cpd11481 but does not have a valid deltaG!\n", "cpd11477_c0 has modelseed ID cpd11477 but does not have a valid deltaG!\n", "cpd15369_c0 has modelseed ID cpd15369 but does not have a valid deltaG!\n", "cpd15571_c0 has modelseed ID cpd15571 but does not have a valid deltaG!\n", "cpd15371_c0 has modelseed ID cpd15371 but does not have a valid deltaG!\n", "cpd15572_c0 has modelseed ID cpd15572 but does not have a valid deltaG!\n", "cpd15370_c0 has modelseed ID cpd15370 but does not have a valid deltaG!\n", "cpd15568_c0 has modelseed ID cpd15568 but does not have a valid deltaG!\n", "cpd11836_c0 has modelseed ID cpd11836 but does not have a valid deltaG!\n", "cpd11465_c0 has modelseed ID cpd11465 but does not have a valid deltaG!\n", "4m3hpentACP_c0 has no modelseed ID!\n", "4mtpent2eACP_c0 has no modelseed ID!\n", "4m3hhexACP_c0 has no modelseed ID!\n", "4mthex2eACP_c0 has no modelseed ID!\n", "5m3hhexACP_c0 has no modelseed ID!\n", "5mthex2eACP_c0 has no modelseed ID!\n", "cpd11479_c0 has modelseed ID cpd11479 but does not have a valid deltaG!\n", "cpd11473_c0 has modelseed ID cpd11473 but does not have a valid deltaG!\n", "6m3hheptACP_c0 has no modelseed ID!\n", "6mthept2eACP_c0 has no modelseed ID!\n", "6m3hocACP_c0 has no modelseed ID!\n", "6mtoct2eACP_c0 has no modelseed ID!\n", "7m3hocACP_c0 has no modelseed ID!\n", "7mtoct2eACP_c0 has no modelseed ID!\n", "cpd11483_c0 has modelseed ID cpd11483 but does not have a valid deltaG!\n", "cpd11471_c0 has modelseed ID cpd11471 but does not have a valid deltaG!\n", "8m3hdcaACP_c0 has no modelseed ID!\n", "8mtdec2eACP_c0 has no modelseed ID!\n", "8m3hnonACP_c0 has no modelseed ID!\n", "8mtnon2eACP_c0 has no modelseed ID!\n", "9m3hdcaACP_c0 has no modelseed ID!\n", "9mtdec2eACP_c0 has no modelseed ID!\n", "3ogACPm_c0 has no modelseed ID!\n", "3opACPm_c0 has no modelseed ID!\n", "cpd11487_c0 has modelseed ID cpd11487 but does not have a valid deltaG!\n", "10m3oundecACP_c0 has no modelseed ID!\n", "10m3oddcaACP_c0 has no modelseed ID!\n", "11m3oddcaACP_c0 has no modelseed ID!\n", "cpd11489_c0 has modelseed ID cpd11489 but does not have a valid deltaG!\n", "cpd15373_c0 has modelseed ID cpd15373 but does not have a valid deltaG!\n", "12m3otridecACP_c0 has no modelseed ID!\n", "12m3omyrsACP_c0 has no modelseed ID!\n", "13m3omyrsACP_c0 has no modelseed ID!\n", "cpd11491_c0 has modelseed ID cpd11491 but does not have a valid deltaG!\n", "cpd15374_c0 has modelseed ID cpd15374 but does not have a valid deltaG!\n", "14m3opentdecACP_c0 has no modelseed ID!\n", "14m3opalmACP_c0 has no modelseed ID!\n", "15m3opalmACP_c0 has no modelseed ID!\n", "cpd11485_c0 has modelseed ID cpd11485 but does not have a valid deltaG!\n", "cpd15375_c0 has modelseed ID cpd15375 but does not have a valid deltaG!\n", "cpd15377_c0 has modelseed ID cpd15377 but does not have a valid deltaG!\n", "cpd15376_c0 has modelseed ID cpd15376 but does not have a valid deltaG!\n", "cpd11488_c0 has modelseed ID cpd11488 but does not have a valid deltaG!\n", "4m3opentACP_c0 has no modelseed ID!\n", "4m3ohexACP_c0 has no modelseed ID!\n", "5m3ohexACP_c0 has no modelseed ID!\n", "cpd11486_c0 has modelseed ID cpd11486 but does not have a valid deltaG!\n", "6m3oheptACP_c0 has no modelseed ID!\n", "6m3oocACP_c0 has no modelseed ID!\n", "7m3oocACP_c0 has no modelseed ID!\n", "cpd11490_c0 has modelseed ID cpd11490 but does not have a valid deltaG!\n", "8m3odcaACP_c0 has no modelseed ID!\n", "8m3ononACP_c0 has no modelseed ID!\n", "9m3odcaACP_c0 has no modelseed ID!\n", "cpd11492_c0 has modelseed ID cpd11492 but does not have a valid deltaG!\n", "cpd11470_c0 has modelseed ID cpd11470 but does not have a valid deltaG!\n", "10mundecACP_c0 has no modelseed ID!\n", "10mddcaACP_c0 has no modelseed ID!\n", "11mddcaACP_c0 has no modelseed ID!\n", "cpd11474_c0 has modelseed ID cpd11474 but does not have a valid deltaG!\n", "cpd15416_c0 has modelseed ID cpd15416 but does not have a valid deltaG!\n", "12mtridecACP_c0 has no modelseed ID!\n", "12mmyrsACP_c0 has no modelseed ID!\n", "13mmyrsACP_c0 has no modelseed ID!\n", "cpd11468_c0 has modelseed ID cpd11468 but does not have a valid deltaG!\n", "cpd15415_c0 has modelseed ID cpd15415 but does not have a valid deltaG!\n", "cpd11466_c0 has modelseed ID cpd11466 but does not have a valid deltaG!\n", "cpd15294_c0 has modelseed ID cpd15294 but does not have a valid deltaG!\n", "cpd15277_c0 has modelseed ID cpd15277 but does not have a valid deltaG!\n", "cpd15239_c0 has modelseed ID cpd15239 but does not have a valid deltaG!\n", "2mpropACP_c0 has no modelseed ID!\n", "3mbutACP_c0 has no modelseed ID!\n", "4mpentACP_c0 has no modelseed ID!\n", "4mhexACP_c0 has no modelseed ID!\n", "5mhexACP_c0 has no modelseed ID!\n", "cpd11464_c0 has modelseed ID cpd11464 but does not have a valid deltaG!\n", "6mheptACP_c0 has no modelseed ID!\n", "6mocACP_c0 has no modelseed ID!\n", "7mocACP_c0 has no modelseed ID!\n", "cpd11472_c0 has modelseed ID cpd11472 but does not have a valid deltaG!\n", "8mdcaACP_c0 has no modelseed ID!\n", "8mnonACP_c0 has no modelseed ID!\n", "9mdcaACP_c0 has no modelseed ID!\n", "7ocholate_c0 has no modelseed ID!\n", "cpd00971_c0 has modelseed ID cpd00971 but does not have a valid deltaG!\n", "7ocholate_e0 has no modelseed ID!\n", "cpd00971_e0 has modelseed ID cpd00971 but does not have a valid deltaG!\n", "acgal6p_c0 has no modelseed ID!\n", "kdnp_c0 has no modelseed ID!\n", "cpd15522_c0 has modelseed ID cpd15522 but does not have a valid deltaG!\n", "cpd15327_c0 has modelseed ID cpd15327 but does not have a valid deltaG!\n", "cpd15524_c0 has modelseed ID cpd15524 but does not have a valid deltaG!\n", "cpd15526_c0 has modelseed ID cpd15526 but does not have a valid deltaG!\n", "1aipdecg3p_c0 has no modelseed ID!\n", "aipdcoa_c0 has no modelseed ID!\n", "paai15_c0 has no modelseed ID!\n", "aihpdcoa_c0 has no modelseed ID!\n", "1aihpdecg3p_c0 has no modelseed ID!\n", "paai17_c0 has no modelseed ID!\n", "itdcoa_c0 has no modelseed ID!\n", "1itdecg3p_c0 has no modelseed ID!\n", "pai14_c0 has no modelseed ID!\n", "ipdcoa_c0 has no modelseed ID!\n", "1ipdecg3p_c0 has no modelseed ID!\n", "pai15_c0 has no modelseed ID!\n", "ihdcoa_c0 has no modelseed ID!\n", "1ihdecg3p_c0 has no modelseed ID!\n", "pai16_c0 has no modelseed ID!\n", "ihpdcoa_c0 has no modelseed ID!\n", "1ihpdecg3p_c0 has no modelseed ID!\n", "pai17_c0 has no modelseed ID!\n", "cpd11494_c0 has modelseed ID cpd11494 but does not have a valid deltaG!\n", "cpd12370_c0 has modelseed ID cpd12370 but does not have a valid deltaG!\n", "cpd00421_c0 has modelseed ID cpd00421 but does not have a valid deltaG!\n", "cpd00166_e0 has modelseed ID cpd00166 but does not have a valid deltaG!\n", "cpd00166_c0 has modelseed ID cpd00166 but does not have a valid deltaG!\n", "galam6p_c0 has no modelseed ID!\n", "ncptrc_c0 has no modelseed ID!\n", "cpd15521_c0 has modelseed ID cpd15521 but does not have a valid deltaG!\n", "cpd15268_c0 has modelseed ID cpd15268 but does not have a valid deltaG!\n", "cpd15328_c0 has modelseed ID cpd15328 but does not have a valid deltaG!\n", "cpd11825_c0 has modelseed ID cpd11825 but does not have a valid deltaG!\n", "cpd15527_c0 has modelseed ID cpd15527 but does not have a valid deltaG!\n", "s2l2n2m2m_e0 has no modelseed ID!\n", "s2l2n2m2mn_e0 has no modelseed ID!\n", "chtbs_e0 has no modelseed ID!\n", "n2m2mn_e0 has no modelseed ID!\n", "m2mn_e0 has no modelseed ID!\n", "cpd11421_c0 has modelseed ID cpd11421 but does not have a valid deltaG!\n", "cpd11420_c0 has modelseed ID cpd11420 but does not have a valid deltaG!\n", "14mpalmACP_c0 has no modelseed ID!\n", "alaasp_c0 has no modelseed ID!\n", "alaasp_e0 has no modelseed ID!\n", "alaglu_c0 has no modelseed ID!\n", "alaglu_e0 has no modelseed ID!\n", "alagly_c0 has no modelseed ID!\n", "alagly_e0 has no modelseed ID!\n", "alathr_c0 has no modelseed ID!\n", "alathr_e0 has no modelseed ID!\n", "cpd03485_c0 has modelseed ID cpd03485 but does not have a valid deltaG!\n", "cpd15494_c0 has modelseed ID cpd15494 but does not have a valid deltaG!\n", "amannan140_e0 has no modelseed ID!\n", "2dmmql10_c0 has no modelseed ID!\n", "mql10_c0 has no modelseed ID!\n", "2dmmql11_c0 has no modelseed ID!\n", "mql11_c0 has no modelseed ID!\n", "2dmmql7_c0 has no modelseed ID!\n", "cpd11451_c0 has modelseed ID cpd11451 but does not have a valid deltaG!\n", "2dmmql9_c0 has no modelseed ID!\n", "mql9_c0 has no modelseed ID!\n", "strch1_e0 has no modelseed ID!\n", "strch2_e0 has no modelseed ID!\n", "amylose300_e0 has no modelseed ID!\n", "starch1200_e0 has no modelseed ID!\n", "pmACP_c0 has no modelseed ID!\n", "arabttr_e0 has no modelseed ID!\n", "arabinan101_e0 has no modelseed ID!\n", "arabinogal_e0 has no modelseed ID!\n", "argarg_c0 has no modelseed ID!\n", "argarg_e0 has no modelseed ID!\n", "Largn_c0 has no modelseed ID!\n", "hspg_degr_4_e0 has no modelseed ID!\n", "hspg_degr_5_e0 has no modelseed ID!\n", "hspg_degr_9_e0 has no modelseed ID!\n", "hspg_degr_10_e0 has no modelseed ID!\n", "hspg_degr_3_e0 has no modelseed ID!\n", "hspg_degr_8_e0 has no modelseed ID!\n", "mn_e0 has no modelseed ID!\n", "apoC_Lys_c0 has no modelseed ID!\n", "apoC_Lys_btn_c0 has no modelseed ID!\n", "cpd00063_e0 has modelseed ID cpd00063 but does not have a valid deltaG!\n", "cpd00063_c0 has modelseed ID cpd00063 but does not have a valid deltaG!\n", "cpd15836_c0 has modelseed ID cpd15836 but does not have a valid deltaG!\n", "cpd15836_e0 has modelseed ID cpd15836 but does not have a valid deltaG!\n", "cpd00635_e0 has modelseed ID cpd00635 but does not have a valid deltaG!\n", "cpd00635_c0 has modelseed ID cpd00635 but does not have a valid deltaG!\n", "cpd00110_c0 has modelseed ID cpd00110 but does not have a valid deltaG!\n", "cpd00109_c0 has modelseed ID cpd00109 but does not have a valid deltaG!\n", "cpd01012_c0 has modelseed ID cpd01012 but does not have a valid deltaG!\n", "cpd01012_e0 has modelseed ID cpd01012 but does not have a valid deltaG!\n", "cdpglc_c0 has no modelseed ID!\n", "cdpddg_c0 has no modelseed ID!\n", "cer1_bt_c0 has no modelseed ID!\n", "sphmyln_bt_c0 has no modelseed ID!\n", "pe_cer1_bt_c0 has no modelseed ID!\n", "kdn_c0 has no modelseed ID!\n", "ckdn_c0 has no modelseed ID!\n", "cpd15536_c0 has modelseed ID cpd15536 but does not have a valid deltaG!\n", "cpd15426_c0 has modelseed ID cpd15426 but does not have a valid deltaG!\n", "cpd15538_c0 has modelseed ID cpd15538 but does not have a valid deltaG!\n", "cpd15428_c0 has modelseed ID cpd15428 but does not have a valid deltaG!\n", "cpd15540_c0 has modelseed ID cpd15540 but does not have a valid deltaG!\n", "cpd15430_c0 has modelseed ID cpd15430 but does not have a valid deltaG!\n", "pgai15_c0 has no modelseed ID!\n", "clpnai15_c0 has no modelseed ID!\n", "pgai17_c0 has no modelseed ID!\n", "clpnai17_c0 has no modelseed ID!\n", "pgi14_c0 has no modelseed ID!\n", "clpni14_c0 has no modelseed ID!\n", "pgi15_c0 has no modelseed ID!\n", "clpni15_c0 has no modelseed ID!\n", "pgi16_c0 has no modelseed ID!\n", "clpni16_c0 has no modelseed ID!\n", "pgi17_c0 has no modelseed ID!\n", "clpni17_c0 has no modelseed ID!\n", "cpd00149_c0 has modelseed ID cpd00149 but does not have a valid deltaG!\n", "cpd00149_e0 has modelseed ID cpd00149 but does not have a valid deltaG!\n", "cps_bt_c0 has no modelseed ID!\n", "cps_bt_e0 has no modelseed ID!\n", "cspg_a_degr_e0 has no modelseed ID!\n", "acgalglcur_e0 has no modelseed ID!\n", "cspg_b_degr_e0 has no modelseed ID!\n", "acgalidour2s_e0 has no modelseed ID!\n", "cspg_c_degr_e0 has no modelseed ID!\n", "cspg_a_e0 has no modelseed ID!\n", "cspg_ab_rest_e0 has no modelseed ID!\n", "cspg_b_e0 has no modelseed ID!\n", "cspg_c_e0 has no modelseed ID!\n", "cspg_c_rest_e0 has no modelseed ID!\n", "cspmd_c0 has no modelseed ID!\n", "cpd00099_e0 has modelseed ID cpd00099 but does not have a valid deltaG!\n", "cpd00099_c0 has modelseed ID cpd00099 but does not have a valid deltaG!\n", "cpd00058_e0 has modelseed ID cpd00058 but does not have a valid deltaG!\n", "cpd00058_c0 has modelseed ID cpd00058 but does not have a valid deltaG!\n", "cpd15309_c0 has modelseed ID cpd15309 but does not have a valid deltaG!\n", "l2a6o_c0 has no modelseed ID!\n", "cpd15417_c0 has modelseed ID cpd15417 but does not have a valid deltaG!\n", "cpd15423_c0 has modelseed ID cpd15423 but does not have a valid deltaG!\n", "cpd15419_c0 has modelseed ID cpd15419 but does not have a valid deltaG!\n", "cpd15420_c0 has modelseed ID cpd15420 but does not have a valid deltaG!\n", "cdpdaipdecg_c0 has no modelseed ID!\n", "cdpdaihpdecg_c0 has no modelseed ID!\n", "cdpditdecg_c0 has no modelseed ID!\n", "cdpdipdecg_c0 has no modelseed ID!\n", "cdpdihdecg_c0 has no modelseed ID!\n", "cdpdihpdecg_c0 has no modelseed ID!\n", "cpd11658_e0 has modelseed ID cpd11658 but does not have a valid deltaG!\n", "dkdglcn_c0 has no modelseed ID!\n", "6hmhptpp_c0 has no modelseed ID!\n", "cpd15830_c0 has modelseed ID cpd15830 but does not have a valid deltaG!\n", "cpd15851_c0 has modelseed ID cpd15851 but does not have a valid deltaG!\n", "cpd15360_c0 has modelseed ID cpd15360 but does not have a valid deltaG!\n", "dt5hsu_e0 has no modelseed ID!\n", "dt5hsu_c0 has no modelseed ID!\n", "gACPm_c0 has no modelseed ID!\n", "pmACPm_c0 has no modelseed ID!\n", "14mpentdecACP_c0 has no modelseed ID!\n", "15mpalmACP_c0 has no modelseed ID!\n", "kdolipid4_bt_c0 has no modelseed ID!\n", "kdolipid4L_bt_c0 has no modelseed ID!\n", "2omfuc_e0 has no modelseed ID!\n", "2omxyl_e0 has no modelseed ID!\n", "3ddlhept_e0 has no modelseed ID!\n", "Ser_Thr_e0 has no modelseed ID!\n", "T_antigen_e0 has no modelseed ID!\n", "Tn_antigen_e0 has no modelseed ID!\n", "acerA_e0 has no modelseed ID!\n", "acgalidour_e0 has no modelseed ID!\n", "apio_D_e0 has no modelseed ID!\n", "core2_e0 has no modelseed ID!\n", "core3_e0 has no modelseed ID!\n", "core4_e0 has no modelseed ID!\n", "core5_e0 has no modelseed ID!\n", "core6_e0 has no modelseed ID!\n", "core7_e0 has no modelseed ID!\n", "core8_e0 has no modelseed ID!\n", "dsT_antigen_e0 has no modelseed ID!\n", "f1a_e0 has no modelseed ID!\n", "cpd03725_e0 has modelseed ID cpd03725 but does not have a valid deltaG!\n", "fucneulacnhx_e0 has no modelseed ID!\n", "galam_e0 has no modelseed ID!\n", "gam26s_e0 has no modelseed ID!\n", "gchola_e0 has no modelseed ID!\n", "glyasn_e0 has no modelseed ID!\n", "glyasp_e0 has no modelseed ID!\n", "glycogen1500_e0 has no modelseed ID!\n", "glyglu_e0 has no modelseed ID!\n", "cpd15604_e0 has modelseed ID cpd15604 but does not have a valid deltaG!\n", "cpd15605_e0 has modelseed ID cpd15605 but does not have a valid deltaG!\n", "glypro_e0 has no modelseed ID!\n", "cpd15606_e0 has modelseed ID cpd15606 but does not have a valid deltaG!\n", "gncore1_e0 has no modelseed ID!\n", "gncore2_e0 has no modelseed ID!\n", "ha_e0 has no modelseed ID!\n", "ha_deg1_e0 has no modelseed ID!\n", "ha_pre1_e0 has no modelseed ID!\n", "cpd00531_e0 has modelseed ID cpd00531 but does not have a valid deltaG!\n", "homogal_e0 has no modelseed ID!\n", "hspg_e0 has no modelseed ID!\n", "hspg_degr_1_e0 has no modelseed ID!\n", "hspg_degr_11_e0 has no modelseed ID!\n", "hspg_degr_12_e0 has no modelseed ID!\n", "hspg_degr_13_e0 has no modelseed ID!\n", "hspg_degr_14_e0 has no modelseed 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"levantttr_e0 has no modelseed ID!\n", "lmn2_e0 has no modelseed ID!\n", "lmn30_e0 has no modelseed ID!\n", "lps_bt_e0 has no modelseed ID!\n", "cpd15494_e0 has modelseed ID cpd15494 but does not have a valid deltaG!\n", "manb_e0 has no modelseed ID!\n", "manpt_e0 has no modelseed ID!\n", "mantr_e0 has no modelseed ID!\n", "manttr_e0 has no modelseed ID!\n", "mbenz_e0 has no modelseed ID!\n", "metala_e0 has no modelseed ID!\n", "cpd00030_e0 has modelseed ID cpd00030 but does not have a valid deltaG!\n", "mqn10_e0 has no modelseed ID!\n", "mqn11_e0 has no modelseed ID!\n", "mqn9_e0 has no modelseed ID!\n", "neulacnttr_e0 has no modelseed ID!\n", "oligofru4_e0 has no modelseed ID!\n", "cpd04097_e0 has modelseed ID cpd04097 but does not have a valid deltaG!\n", "pe_cer1_bt_e0 has no modelseed ID!\n", "pect_e0 has no modelseed ID!\n", "pecticgal_e0 has no modelseed ID!\n", "phearg_e0 has no modelseed ID!\n", "cpd00028_e0 has modelseed ID cpd00028 but does not have a valid deltaG!\n", "phppa_e0 has no modelseed ID!\n", "plac_e0 has no modelseed ID!\n", "pullulan1200_e0 has no modelseed ID!\n", "rhamnogalurI_e0 has no modelseed ID!\n", "rhamnogalurII_e0 has no modelseed ID!\n", "s2l2fn2m2masn_e0 has no modelseed ID!\n", "s2l2n2m2masn_e0 has no modelseed ID!\n", "sT_antigen_e0 has no modelseed ID!\n", "sTn_antigen_e0 has no modelseed ID!\n", "sphmyln_bt_e0 has no modelseed ID!\n", "stys_e0 has no modelseed ID!\n", "unsdigalur_e0 has no modelseed ID!\n", "cpd00034_e0 has modelseed ID cpd00034 but does not have a valid deltaG!\n", "cpd15237_c0 has modelseed ID cpd15237 but does not have a valid deltaG!\n", "cpd15238_c0 has modelseed ID cpd15238 but does not have a valid deltaG!\n", "cpd15269_c0 has modelseed ID cpd15269 but does not have a valid deltaG!\n", "cpd15274_c0 has modelseed ID cpd15274 but does not have a valid deltaG!\n", "cpd11438_c0 has modelseed ID cpd11438 but does not have a valid deltaG!\n", "cpd11433_c0 has modelseed ID cpd11433 but does not have a 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modelseed ID cpd00205 but does not have a valid deltaG!\n", "leugly_c0 has no modelseed ID!\n", "leuleu_c0 has no modelseed ID!\n", "lipidX_bt_c0 has no modelseed ID!\n", "u2ga_bt_c0 has no modelseed ID!\n", "lipidAds_bt_c0 has no modelseed ID!\n", "core_lps_bt_c0 has no modelseed ID!\n", "lps_bt_c0 has no modelseed ID!\n", "malcoam_c0 has no modelseed ID!\n", "mantr_c0 has no modelseed ID!\n", "mbenz_c0 has no modelseed ID!\n", "metala_c0 has no modelseed ID!\n", "cpd15498_c0 has modelseed ID cpd15498 but does not have a valid deltaG!\n", "cpd00030_c0 has modelseed ID cpd00030 but does not have a valid deltaG!\n", "lipidA_bt_c0 has no modelseed ID!\n", "nicrns_c0 has no modelseed ID!\n", "cpd02968_c0 has modelseed ID cpd02968 but does not have a valid deltaG!\n", "cpd04097_c0 has modelseed ID cpd04097 but does not have a valid deltaG!\n", "cpd15531_c0 has modelseed ID cpd15531 but does not have a valid deltaG!\n", "cpd15542_c0 has modelseed ID cpd15542 but does not have a valid deltaG!\n", "cpd15535_c0 has modelseed ID cpd15535 but does not have a valid deltaG!\n", "cpd15543_c0 has modelseed ID cpd15543 but does not have a valid deltaG!\n", "cpd15545_c0 has modelseed ID cpd15545 but does not have a valid deltaG!\n", "cpd15547_c0 has modelseed ID cpd15547 but does not have a valid deltaG!\n", "cpd15548_c0 has modelseed ID cpd15548 but does not have a valid deltaG!\n", "cpd15541_c0 has modelseed ID cpd15541 but does not have a valid deltaG!\n", "pgpai15_c0 has no modelseed ID!\n", "pgpai17_c0 has no modelseed ID!\n", "pgpi14_c0 has no modelseed ID!\n", "pgpi15_c0 has no modelseed ID!\n", "pgpi16_c0 has no modelseed ID!\n", "pgpi17_c0 has no modelseed ID!\n", "phearg_c0 has no modelseed ID!\n", "phppa_c0 has no modelseed ID!\n", "plac_c0 has no modelseed ID!\n", "cpd15654_c0 has modelseed ID cpd15654 but does not have a valid deltaG!\n", "cpd15552_c0 has modelseed ID cpd15552 but does not have a valid deltaG!\n", "cpd15528_c0 has modelseed ID cpd15528 but does 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Objective

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" ], "text/plain": [ "" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ftp = FullThermoPkg(model)\n", "modelseed_db_path = os.path.join('..', '..', '..', 'ModelSEEDDatabase') # /Users/chenry/code/ModelSEEDDatabase/\n", "ftp.build_package({\"modelseed_path\":modelseed_db_path})\n", "with open('FullThermo.lp', 'w') as out:\n", " out.write(str(model.solver))\n", "sol=model.optimize()\n", "#Next minimize active reactions\n", "model.summary()" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.12" } }, "nbformat": 4, "nbformat_minor": 4 }