def Initialize(self, db): from pygibbs.unified_group_contribution import UnifiedGroupContribution ugc = UnifiedGroupContribution(db) ugc.LoadGroups(FromDatabase=True) ugc.LoadObservations(FromDatabase=True) ugc.LoadGroupVectors(FromDatabase=True) ugc.LoadData(FromDatabase=True) ugc.init() self.groups_data = ugc.groups_data self.group_decomposer = ugc.group_decomposer result_dict = ugc._GetContributionData(ugc.S.copy(), ugc.cids, ugc.b.copy(), ugc.anchored) self.g_pgc = result_dict['group_contributions'] self.P_L_pgc = result_dict['pgc_conservations']
plt.figure(figsize=(6, 6), dpi=90) bins = np.arange(-30, 30, 2) plt.hist([err_feist_nist, err_ugcm_nist], bins=bins, histtype='bar', cumulative=False, normed=False) plt.xlabel('Error in kJ/mol') plt.ylabel('# of reactions') plt.legend(['value in iAF1260', 'UGCM estimation']) plt.savefig(FIG_FNAME + "_fig3.svg", fmt='.svg') db = SqliteDatabase('../res/gibbs.sqlite', 'w') ugc = UnifiedGroupContribution(db) ugc.LoadGroups(True) ugc.LoadObservations(True) ugc.LoadGroupVectors(True) ugc.LoadData(True) ugc.init() r_list = [] #r_list += [Reaction.FromFormula("C00036 + C00044 = C00011 + C00035 + C00074")] #r_list += [Reaction.FromFormula("C00003 + C00037 + C00101 = C00004 + C00011 + C00014 + C00080 + C00143")] # glycine synthase r_list += [Reaction.FromFormula("C00001 + C00002 + C00064 + C04376 => C00008 + C00009 + C00025 + C04640")] #r_list += [Reaction.FromFormula("C00001 + 2 C00002 + C00064 + C00288 <=> 2 C00008 + C00009 + C00025 + C00169")] kegg = Kegg.getInstance() S, cids = kegg.reaction_list_to_S(r_list) logging.getLogger('').setLevel(logging.DEBUG) dG0_prime = ugc.GetTransfromedReactionEnergies(S, cids, pH=pH, I=I, pMg=pMg, T=T) RT = R * T for i in xrange(len(r_list)):
bins=bins, histtype='bar', cumulative=False, normed=False) plt.xlabel('Error in kJ/mol') plt.ylabel('# of reactions') plt.legend(['value in iAF1260', 'UGCM estimation']) plt.savefig(FIG_FNAME + "_fig3.svg", fmt='.svg') db = SqliteDatabase('../res/gibbs.sqlite', 'w') ugc = UnifiedGroupContribution(db) ugc.LoadGroups(True) ugc.LoadObservations(True) ugc.LoadGroupVectors(True) ugc.LoadData(True) ugc.init() r_list = [] #r_list += [Reaction.FromFormula("C00036 + C00044 = C00011 + C00035 + C00074")] #r_list += [Reaction.FromFormula("C00003 + C00037 + C00101 = C00004 + C00011 + C00014 + C00080 + C00143")] # glycine synthase r_list += [ Reaction.FromFormula( "C00001 + C00002 + C00064 + C04376 => C00008 + C00009 + C00025 + C04640" ) ] #r_list += [Reaction.FromFormula("C00001 + 2 C00002 + C00064 + C00288 <=> 2 C00008 + C00009 + C00025 + C00169")] kegg = Kegg.getInstance() S, cids = kegg.reaction_list_to_S(r_list) logging.getLogger('').setLevel(logging.DEBUG)