def python_main(): sys.path.append('../python') from training_data import TrainingData from component_contribution import ComponentContribution from kegg_model import KeggModel reaction_strings = open(REACTION_FNAME, 'r').readlines() model = KeggModel.from_formulas(reaction_strings) td = TrainingData() cc = ComponentContribution(td) model.add_thermo(cc) dG0_prime, dG0_std = model.get_transformed_dG0(pH=7.5, I=0.2, T=298.15) sys.stdout.write('[' + ', '.join([str(x) for x in model.dG0.flat]) + '; ' + ', '.join([str(x) for x in dG0_prime.flat]) + ']')
params["contributions"] = [dG0_rc, dG0_gc] params["covariances"] = [V_rc, V_gc, V_inf] params["MSEs"] = [MSE_rc, MSE_gc, MSE_inf] params["projections"] = [P_R_rc, P_R_gc * G.T * P_N_rc, P_N_gc * G.T * P_N_rc, P_R_gc, P_N_rc, P_N_gc] params["inverses"] = [inv_S, inv_GS, inv_SWS, inv_GSWGS] # Calculate the total of the contributions and covariances cov_dG0 = V_rc * MSE_rc + V_gc * MSE_gc + V_inf * MSE_inf return dG0_cc, cov_dG0, params if __name__ == "__main__": from kegg_model import KeggModel reaction_strings = sys.stdin.readlines() td = TrainingData() cc = ComponentContribution(td) model = KeggModel.from_formulas(reaction_strings) model_dG0, model_cov_dG0 = cc.estimate_kegg_model(model) model_dG0_prime = model_dG0 + model.get_transform_ddG0(pH=7.5, I=0.2, T=298.15) sys.stdout.write( "[" + ", ".join([str(x) for x in model_dG0.flat]) + "; " + ", ".join([str(x) for x in model_dG0_prime.flat]) + "]" )
with open('../examples/vz/StoiMat.tsv', 'r') as tsv: tabinput = [line.strip().split('\t') for line in tsv] reactions = tabinput[0] reactions = reactions[1:] tabinput = tabinput[1:] S = np.zeros((len(tabinput), len(tabinput[0]) - 1)) cids = list() for i in range(len(tabinput)): cids.append(float(tabinput[i][0].replace('"', ''))) for j in range(len(tabinput[0]) - 1): S[i, j] = tabinput[i][j + 1] model = KeggModel(S, cids) model = model.check_S_balance() td = TrainingData() cc = ComponentContribution(td) model_dG0, model_cov_dG0 = cc.estimate_kegg_model(model) model_dG0_prime = model_dG0 + model.get_transform_ddG0(pH=7.5, I=0.2, T=298.15) dG0_std = np.sqrt(model_cov_dG0.diagonal()) out_file = '../examples/vz/output/cc_dG.tsv' outf = open(out_file, "w") outf.write("reaction\tdGr\tdGrSD\n") for i in range(len(reactions)): outf.write(reactions[i] + "\t" + str(float(model_dG0_prime[i])) + "\t" + str(float(dG0_std[0, i])) + "\n")
params['contributions'] = [dG0_rc, dG0_gc] params['covariances'] = [V_rc, V_gc, V_inf] params['MSEs'] = [MSE_rc, MSE_gc, MSE_inf] params['projections'] = [P_R_rc, P_R_gc * G.T * P_N_rc, P_N_gc * G.T * P_N_rc, P_R_gc, P_N_rc, P_N_gc] params['inverses'] = [inv_S, inv_GS, inv_SWS, inv_GSWGS] # Calculate the total of the contributions and covariances cov_dG0 = V_rc * MSE_rc + V_gc * MSE_gc + V_inf * MSE_inf return dG0_cc, cov_dG0, params if __name__ == '__main__': from kegg_model import KeggModel reaction_strings = sys.stdin.readlines() td = TrainingData() cc = ComponentContribution(td) model = KeggModel.from_formulas(reaction_strings) model_dG0, model_cov_dG0 = cc.estimate_kegg_model(model) model_dG0_prime = model_dG0 + model.get_transform_ddG0(pH=7.5, I=0.2, T=298.15) sys.stdout.write('[' + ', '.join([str(x) for x in model_dG0.flat]) + '; ' + ', '.join([str(x) for x in model_dG0_prime.flat]) + ']')
with open('../examples/vz/StoiMat.tsv','r') as tsv: tabinput = [line.strip().split('\t') for line in tsv] reactions = tabinput[0] reactions = reactions[1:] tabinput = tabinput[1:] S = np.zeros((len(tabinput), len(tabinput[0])-1)) cids = list() for i in range(len(tabinput)): cids.append(float(tabinput[i][0].replace('"',''))) for j in range(len(tabinput[0])-1): S[i,j] = tabinput[i][j+1] model = KeggModel(S, cids) model = model.check_S_balance() td = TrainingData() cc = ComponentContribution(td) model_dG0, model_cov_dG0 = cc.estimate_kegg_model(model) model_dG0_prime = model_dG0 + model.get_transform_ddG0(pH=7.5, I=0.2, T=298.15) dG0_std = np.sqrt(model_cov_dG0.diagonal()) out_file = '../examples/vz/output/cc_dG.tsv' outf = open(out_file, "w") outf.write("reaction\tdGr\tdGrSD\n") for i in range(len(reactions)): outf.write(reactions[i] + "\t" + str(float(model_dG0_prime[i])) + "\t" +str(float(dG0_std[0,i]))+ "\n") outf.close()