Merge branch 'nathan/strings' into nathan/delint
This commit is contained in:
Nathan Baker
8
propka/__main__.py
Normal file
8
propka/__main__.py
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@@ -0,0 +1,8 @@
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"""Allow the PROPKA package to be run as a program.
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For example, `python -m propka`
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"""
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from .run import main
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if __name__ == "__main__":
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main()
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@@ -279,10 +279,10 @@ def build_parser(parser=None):
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return parser
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def loadOptions(args):
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"""Load the arguments parser with options.
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NOTE - verbosity is set as soon as this function is invoked.
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def loadOptions(args=None):
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"""
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Load the arguments parser with options. Note that verbosity is set as soon
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as this function is invoked.
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Arguments:
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args: list of arguments
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@@ -292,11 +292,8 @@ def loadOptions(args):
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# loading the parser
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parser = build_parser()
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# parsing and returning options and arguments
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if len(args) == 0:
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# command line
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options = parser.parse_args()
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else:
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options = parser.parse_args(args)
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options = parser.parse_args(args)
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# adding specified filenames to arguments
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options.filenames.append(options.input_pdb)
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# Convert titrate_only string to a list of (chain, resnum) items:
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136
propka/output.py
136
propka/output.py
@@ -203,10 +203,9 @@ def get_summary_section(protein, conformation, parameters):
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return str_
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def get_folding_profile_section(protein, conformation='AVR',
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direction="folding", reference="neutral",
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window=[0., 14., 1.0], _=False,
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__=None):
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def get_folding_profile_section(
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protein, conformation='AVR', direction="folding", reference="neutral",
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window=[0., 14., 1.0], _=False, __=None):
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"""Returns string with the folding profile section of the results.
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Args:
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@@ -245,9 +244,9 @@ def get_folding_profile_section(protein, conformation='AVR',
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dg_opt))
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if dg_min is None or dg_max is None:
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str_ += "Could not determine pH values where the free energy"
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str_ += " is within 80 %% of minimum\n"
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str_ += " is within 80 % of minimum\n"
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else:
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str_ += "The free energy is within 80 %% of maximum"
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str_ += "The free energy is within 80 % of maximum"
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str_ += " at pH {0:>4.1f} to {1:>4.1f}\n".format(dg_min, dg_max)
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if ph_min is None or ph_max is None:
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str_ += "Could not determine the pH-range where the free"
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@@ -319,40 +318,26 @@ def get_propka_header():
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string
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"""
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today = date.today()
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str_ = "propka3.1 {0:>93s}\n".format(today)
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str_ += ("---------------------------------------------------------------"
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"----------------------------------------\n")
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str_ += ("-- "
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" --\n")
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str_ += ("-- PROPKA: A PROTEIN PKA "
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"PREDICTOR --\n")
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str_ += ("-- "
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" --\n")
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str_ += ("-- VERSION 1.0, 04/25/2004, "
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"IOWA CITY --\n")
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str_ += ("-- BY HUI LI "
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" --\n")
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str_ += ("-- "
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" --\n")
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str_ += ("-- VERSION 2.0, 11/05/2007, IOWA "
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"CITY/COPENHAGEN --\n")
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str_ += ("-- BY DELPHINE C. BAS AND DAVID "
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"M. ROGERS --\n")
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str_ += ("-- "
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" --\n")
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str_ += ("-- VERSION 3.0, 01/06/2011, "
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"COPENHAGEN --\n")
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str_ += ("-- BY MATS H.M. OLSSON AND CHRESTEN "
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"R. SONDERGARD --\n")
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str_ += ("-- "
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" --\n")
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str_ += ("-- VERSION 3.1, 07/01/2011, "
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"COPENHAGEN --\n")
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str_ += ("-- BY CHRESTEN R. SONDERGARD AND "
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"MATS H.M. OLSSON --\n")
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str_ += ("---------------------------------------------------------------"
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"----------------------------------------\n")
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str_ += ("\n")
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str_ = "propka3.1 {0!s:>93s}\n".format(today)
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str_ += """
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-------------------------------------------------------------------------------
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-- --
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-- PROPKA: A PROTEIN PKA PREDICTOR --
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-- --
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-- VERSION 1.0, 04/25/2004, IOWA CITY --
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-- BY HUI LI --
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-- --
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-- VERSION 2.0, 11/05/2007, IOWA CITY/COPENHAGEN --
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-- BY DELPHINE C. BAS AND DAVID M. ROGERS --
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-- --
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-- VERSION 3.0, 01/06/2011, COPENHAGEN --
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-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --
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-- --
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-- VERSION 3.1, 07/01/2011, COPENHAGEN --
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-- BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON --
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-- --
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-------------------------------------------------------------------------------
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"""
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return str_
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@@ -362,39 +347,29 @@ def get_references_header():
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Returns:
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string
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"""
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str_ = ""
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str_ += ("---------------------------------------------------------------"
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"----------------------------------------\n")
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str_ += (" References:\n")
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str_ += ("\n")
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str_ += (" Very Fast Empirical Prediction and Rationalization of "
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"Protein pKa Values\n")
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str_ += (" Hui Li, Andrew D. Robertson and Jan H. Jensen\n")
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str_ += (" PROTEINS: Structure, Function, and Bioinformatics 61:704-721"
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" (2005)\n")
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str_ += (" \n")
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str_ += (" Very Fast Prediction and Rationalization of pKa Values for "
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"Protein-Ligand Complexes\n")
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str_ += (" Delphine C. Bas, David M. Rogers and Jan H. Jensen\n")
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str_ += (" PROTEINS: Structure, Function, and Bioinformatics 73:765-"
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"783 (2008)\n")
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str_ += (" \n")
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str_ += (" PROPKA3: Consistent Treatment of Internal and Surface "
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"Residues in Empirical pKa predictions\n")
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str_ += (" Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, "
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"and Jan H. Jensen\n")
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str_ += (" Journal of Chemical Theory and Computation, 7(2):525-537 "
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"(2011)\n")
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str_ += (" \n")
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str_ += (" Improved Treatment of Ligands and Coupling Effects in "
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"Empirical Calculation\n")
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str_ += (" and Rationalization of pKa Values\n")
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str_ += (" Chresten R. Sondergaard, Mats H.M. Olsson, Michal "
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"Rostkowski, and Jan H. Jensen\n")
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str_ += (" Journal of Chemical Theory and Computation, (2011)\n")
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str_ += (" \n")
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str_ += ("--------------------------------------------------------------"
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"-----------------------------------------\n")
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str_ = """
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-------------------------------------------------------------------------------
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References:
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Very Fast Empirical Prediction and Rationalization of Protein pKa Values.
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Hui Li, Andrew D. Robertson and Jan H. Jensen. PROTEINS: Structure, Function,
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and Bioinformatics. 61:704-721 (2005)
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Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand
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Complexes. Delphine C. Bas, David M. Rogers and Jan H. Jensen. PROTEINS:
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Structure, Function, and Bioinformatics 73:765-783 (2008)
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PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical
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pKa predictions. Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski,
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and Jan H. Jensen. Journal of Chemical Theory and Computation, 7(2):525-537
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(2011)
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Improved Treatment of Ligands and Coupling Effects in Empirical Calculation
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and Rationalization of pKa Values. Chresten R. Sondergaard, Mats H.M. Olsson,
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Michal Rostkowski, and Jan H. Jensen. Journal of Chemical Theory and
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Computation, (2011)
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-------------------------------------------------------------------------------
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"""
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return str_
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@@ -416,15 +391,12 @@ def get_determinants_header():
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Returns:
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string
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"""
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str_ = ""
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str_ += ("--------- ----- ------ --------------------- "
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"-------------- -------------- --------------\n")
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str_ += (" DESOLVATION EFFECTS "
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"SIDECHAIN BACKBONE COULOMBIC \n")
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str_ += (" RESIDUE pKa BURIED REGULAR RE "
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"HYDROGEN BOND HYDROGEN BOND INTERACTION \n")
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str_ += ("--------- ----- ------ --------- --------- "
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"-------------- -------------- --------------\n")
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str_ = """
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--------- ----- ------ --------------------- -------------- -------------- --------------
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DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC
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RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION
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--------- ----- ------ --------- --------- -------------- -------------- --------------
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"""
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return str_
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