diff --git a/propka/output.py b/propka/output.py index 85f807e..be0e353 100644 --- a/propka/output.py +++ b/propka/output.py @@ -82,9 +82,9 @@ def write_pka(protein, parameters, filename=None, conformation='1A', str_ += get_summary_section(protein, conformation, parameters) str_ += "%s\n" % get_the_line() # printing Folding Profile - str_ += get_folding_profile_section(protein, conformation=conformation, - reference=reference, - window=[0., 14., 1.0]) + str_ += get_folding_profile_section( + protein, conformation=conformation, reference=reference, + window=[0., 14., 1.0]) # printing Protein Charge Profile str_ += get_charge_profile_section(protein, conformation=conformation) # now, writing the pka text to file @@ -116,8 +116,9 @@ def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.], else: str_ = " suggested Tm-profile for %s\n" % (protein.name) for (ph, tm_) in profile: - if ph >= window[0] and ph <= window[1] and (ph%window[2] < 0.01 \ - or ph%window[2] > 0.99*window[2]): + if (ph >= window[0] and ph <= window[1] + and (ph%window[2] < 0.01 + or ph%window[2] > 0.99*window[2])): str_ += "%6.2lf%10.2lf\n" % (ph, tm_) info(str_) @@ -163,15 +164,16 @@ def get_determinant_section(protein, conformation, parameters): # printing determinants for chain in protein.conformations[conformation].chains: for residue_type in parameters.write_out_order: - groups = [g for g in protein.conformations[conformation].groups \ + groups = [ + g for g in protein.conformations[conformation].groups if g.atom.chain_id == chain] for group in groups: if group.residue_type == residue_type: - str_ += "%s" \ - % group.get_determinant_string(parameters.remove_penalised_group) + str_ += "%s" % group.get_determinant_string( + parameters.remove_penalised_group) # Add a warning in case of coupled residues - if protein.conformations[conformation].non_covalently_coupled_groups \ - and not protein.options.display_coupled_residues: + if (protein.conformations[conformation].non_covalently_coupled_groups + and not protein.options.display_coupled_residues): str_ += 'Coupled residues (marked *) were detected.' str_ += 'Please rerun PropKa with the --display-coupled-residues \n' str_ += 'or -d option for detailed information.\n' @@ -193,8 +195,8 @@ def get_summary_section(protein, conformation, parameters): for residue_type in parameters.write_out_order: for group in protein.conformations[conformation].groups: if group.residue_type == residue_type: - str_ += "%s" \ - % group.get_summary_string(parameters.remove_penalised_group) + str_ += "%s" % group.get_summary_string( + parameters.remove_penalised_group) return str_ @@ -219,9 +221,10 @@ def get_folding_profile_section(protein, conformation='AVR', str_ += "\n" str_ += "Free energy of %9s (kcal/mol) as a function" % direction str_ += " of pH (using %s reference)\n" % reference - profile, [ph_opt, dg_opt], [dg_min, dg_max], [ph_min, ph_max] \ - = protein.get_folding_profile(conformation=conformation, - reference=reference, grid=[0., 14., 0.1]) + profile, [ph_opt, dg_opt], [dg_min, dg_max], [ph_min, ph_max] = ( + protein.get_folding_profile( + conformation=conformation, reference=reference, + grid=[0., 14., 0.1])) if profile is None: str_ += "Could not determine folding profile\n" else: @@ -234,7 +237,8 @@ def get_folding_profile_section(protein, conformation='AVR', str_ += "Could not determine pH optimum\n" else: str_ += "The pH of optimum stability is %4.1lf" % ph_opt - str_ += " for which the free energy is %6.1lf kcal/mol at 298K\n" % dg_opt + str_ += (" for which the free energy is %6.1lf kcal/mol at 298K\n" + % dg_opt) if dg_min is None or dg_max is None: str_ += "Could not determine pH values where the free energy" str_ += " is within 80 %s of minimum\n" % ("%") @@ -273,8 +277,7 @@ def get_charge_profile_section(protein, conformation='AVR', _=None): if pi_pro is None or pi_mod is None: str_ += "Could not determine the pI\n\n" else: - str_ += "The pI is %5.2lf (folded) and %5.2lf (unfolded)\n" % (pi_pro, - pi_mod) + str_ += ("The pI is %5.2lf (folded) and %5.2lf (unfolded)\n") return str_ @@ -311,23 +314,39 @@ def get_propka_header(): """ today = date.today() str_ = "propka3.1 %93s\n" % (today) - str_ += "-------------------------------------------------------------------------------------------------------\n" - str_ += "-- --\n" - str_ += "-- PROPKA: A PROTEIN PKA PREDICTOR --\n" - str_ += "-- --\n" - str_ += "-- VERSION 1.0, 04/25/2004, IOWA CITY --\n" - str_ += "-- BY HUI LI --\n" - str_ += "-- --\n" - str_ += "-- VERSION 2.0, 11/05/2007, IOWA CITY/COPENHAGEN --\n" - str_ += "-- BY DELPHINE C. BAS AND DAVID M. ROGERS --\n" - str_ += "-- --\n" - str_ += "-- VERSION 3.0, 01/06/2011, COPENHAGEN --\n" - str_ += "-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --\n" - str_ += "-- --\n" - str_ += "-- VERSION 3.1, 07/01/2011, COPENHAGEN --\n" - str_ += "-- BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON --\n" - str_ += "-------------------------------------------------------------------------------------------------------\n" - str_ += "\n" + str_ += ("---------------------------------------------------------------" + "----------------------------------------\n") + str_ += ("-- " + " --\n") + str_ += ("-- PROPKA: A PROTEIN PKA " + "PREDICTOR --\n") + str_ += ("-- " + " --\n") + str_ += ("-- VERSION 1.0, 04/25/2004, " + "IOWA CITY --\n") + str_ += ("-- BY HUI LI " + " --\n") + str_ += ("-- " + " --\n") + str_ += ("-- VERSION 2.0, 11/05/2007, IOWA " + "CITY/COPENHAGEN --\n") + str_ += ("-- BY DELPHINE C. BAS AND DAVID " + "M. ROGERS --\n") + str_ += ("-- " + " --\n") + str_ += ("-- VERSION 3.0, 01/06/2011, " + "COPENHAGEN --\n") + str_ += ("-- BY MATS H.M. OLSSON AND CHRESTEN " + "R. SONDERGARD --\n") + str_ += ("-- " + " --\n") + str_ += ("-- VERSION 3.1, 07/01/2011, " + "COPENHAGEN --\n") + str_ += ("-- BY CHRESTEN R. SONDERGARD AND " + "MATS H.M. OLSSON --\n") + str_ += ("---------------------------------------------------------------" + "----------------------------------------\n") + str_ += ("\n") return str_ @@ -338,27 +357,38 @@ def get_references_header(): string """ str_ = "" - str_ += "-------------------------------------------------------------------------------------------------------\n" - str_ += " References:\n" - str_ += "\n" - str_ += " Very Fast Empirical Prediction and Rationalization of Protein pKa Values\n" - str_ += " Hui Li, Andrew D. Robertson and Jan H. Jensen\n" - str_ += " PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)\n" - str_ += " \n" - str_ += " Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes\n" - str_ += " Delphine C. Bas, David M. Rogers and Jan H. Jensen\n" - str_ += " PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)\n" - str_ += " \n" - str_ += " PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions\n" - str_ += " Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen\n" - str_ += " Journal of Chemical Theory and Computation, 7(2):525-537 (2011)\n" - str_ += " \n" - str_ += " Improved Treatment of Ligands and Coupling Effects in Empirical Calculation\n" - str_ += " and Rationalization of pKa Values\n" - str_ += " Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen\n" - str_ += " Journal of Chemical Theory and Computation, (2011)\n" - str_ += " \n" - str_ += "-------------------------------------------------------------------------------------------------------\n" + str_ += ("---------------------------------------------------------------" + "----------------------------------------\n") + str_ += (" References:\n") + str_ += ("\n") + str_ += (" Very Fast Empirical Prediction and Rationalization of " + "Protein pKa Values\n") + str_ += (" Hui Li, Andrew D. Robertson and Jan H. Jensen\n") + str_ += (" PROTEINS: Structure, Function, and Bioinformatics 61:704-721" + " (2005)\n") + str_ += (" \n") + str_ += (" Very Fast Prediction and Rationalization of pKa Values for " + "Protein-Ligand Complexes\n") + str_ += (" Delphine C. Bas, David M. Rogers and Jan H. Jensen\n") + str_ += (" PROTEINS: Structure, Function, and Bioinformatics 73:765-" + "783 (2008)\n") + str_ += (" \n") + str_ += (" PROPKA3: Consistent Treatment of Internal and Surface " + "Residues in Empirical pKa predictions\n") + str_ += (" Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, " + "and Jan H. Jensen\n") + str_ += (" Journal of Chemical Theory and Computation, 7(2):525-537 " + "(2011)\n") + str_ += (" \n") + str_ += (" Improved Treatment of Ligands and Coupling Effects in " + "Empirical Calculation\n") + str_ += (" and Rationalization of pKa Values\n") + str_ += (" Chresten R. Sondergaard, Mats H.M. Olsson, Michal " + "Rostkowski, and Jan H. Jensen\n") + str_ += (" Journal of Chemical Theory and Computation, (2011)\n") + str_ += (" \n") + str_ += ("--------------------------------------------------------------" + "-----------------------------------------\n") return str_ @@ -381,10 +411,14 @@ def get_determinants_header(): string """ str_ = "" - str_ += "--------- ----- ------ --------------------- -------------- -------------- --------------\n" - str_ += " DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC \n" - str_ += " RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION \n" - str_ += "--------- ----- ------ --------- --------- -------------- -------------- --------------\n" + str_ += ("--------- ----- ------ --------------------- " + "-------------- -------------- --------------\n") + str_ += (" DESOLVATION EFFECTS " + "SIDECHAIN BACKBONE COULOMBIC \n") + str_ += (" RESIDUE pKa BURIED REGULAR RE " + "HYDROGEN BOND HYDROGEN BOND INTERACTION \n") + str_ += ("--------- ----- ------ --------- --------- " + "-------------- -------------- --------------\n") return str_ @@ -402,7 +436,7 @@ def get_summary_header(): def get_the_line(): - """Draw the line - Johnny Cash would have been proud - or actually Aerosmith! + """Draw the line-Johnny Cash would have been proud-or actually Aerosmith! NOTE - Johnny Cash walked the line.