omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

Clean up line breaks in output.py

Browse Source 
See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 20:00:10 -07:00
parent a27f054ac7
commit c796ba6b4d
1 changed files with 95 additions and 61 deletions
Download Patch File Download Diff File Expand all files Collapse all files

154
propka/output.py
View File

@@ -82,8 +82,8 @@ 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,
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)
@@ -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.