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Fix complicated string formatting.

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PEP8 be damned!  https://www.python.org/dev/peps/pep-0008/#a-foolish-consistency-is-the-hobgoblin-of-little-minds

Addresses https://github.com/jensengroup/propka-3.1/pull/40#discussion_r432302025
This commit is contained in:
Nathan Baker
2020-05-29 20:08:41 -07:00
parent 7bd12c725e
commit b54190ef27
1 changed files with 49 additions and 76 deletions
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125
propka/output.py
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@@ -319,40 +319,26 @@ def get_propka_header():
string
"""
today = date.today()
str_ = "propka3.1 {0:>93s}\n".format(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_ = "propka3.1 {0!s:>93s}\n".format(today)
str_ += """
-------------------------------------------------------------------------------
-- --
-- PROPKA: A PROTEIN PKA PREDICTOR --
-- --
-- VERSION 1.0, 04/25/2004, IOWA CITY --
-- BY HUI LI --
-- --
-- VERSION 2.0, 11/05/2007, IOWA CITY/COPENHAGEN --
-- BY DELPHINE C. BAS AND DAVID M. ROGERS --
-- --
-- VERSION 3.0, 01/06/2011, COPENHAGEN --
-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --
-- --
-- VERSION 3.1, 07/01/2011, COPENHAGEN --
-- BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON --
-- --
-------------------------------------------------------------------------------
"""
return str_
@@ -362,39 +348,29 @@ def get_references_header():
Returns:
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_ = """
-------------------------------------------------------------------------------
References:
Very Fast Empirical Prediction and Rationalization of Protein pKa Values.
Hui Li, Andrew D. Robertson and Jan H. Jensen. PROTEINS: Structure, Function,
and Bioinformatics. 61:704-721 (2005)
Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand
Complexes. Delphine C. Bas, David M. Rogers and Jan H. Jensen. PROTEINS:
Structure, Function, and Bioinformatics 73:765-783 (2008)
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical
pKa predictions. Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski,
and Jan H. Jensen. Journal of Chemical Theory and Computation, 7(2):525-537
(2011)
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation
and Rationalization of pKa Values. Chresten R. Sondergaard, Mats H.M. Olsson,
Michal Rostkowski, and Jan H. Jensen. Journal of Chemical Theory and
Computation, (2011)
-------------------------------------------------------------------------------
"""
return str_
@@ -416,15 +392,12 @@ def get_determinants_header():
Returns:
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_ = """
--------- ----- ------ --------------------- -------------- -------------- --------------
DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC
RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION
--------- ----- ------ --------- --------- -------------- -------------- --------------
"""
return str_