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Merge remote-tracking branch 'upstream/master' into nathan/strings

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Nathan Baker
2020-05-29 20:06:57 -07:00
parent 87347a7d60 5916a80d56
commit 7bd12c725e
3 changed files with 16 additions and 11 deletions
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4
README.md
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@@ -9,9 +9,9 @@ For proteins without ligands both version should produce the same result.
The method is described in the following papers, which you should cite The method is described in the following papers, which you should cite
in publications: in publications:
* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295. * Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295. doi:[10.1021/ct200133y](https://doi.org/10.1021/ct200133y)
* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537. * Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537. doi:[10.1021/ct100578z](https://doi.org/10.1021/ct100578z)
See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server, See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server,
using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial). using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial).

8
propka/__main__.py Normal file
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@@ -0,0 +1,8 @@
"""Allow the PROPKA package to be run as a program.
For example, `python -m propka`
"""
from .run import main
if __name__ == "__main__":
main()

13
propka/lib.py
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@@ -279,10 +279,10 @@ def build_parser(parser=None):
return parser return parser
def loadOptions(args): def loadOptions(args=None):
"""Load the arguments parser with options. """
Load the arguments parser with options. Note that verbosity is set as soon
NOTE - verbosity is set as soon as this function is invoked. as this function is invoked.
Arguments: Arguments:
args: list of arguments args: list of arguments
@@ -292,11 +292,8 @@ def loadOptions(args):
# loading the parser # loading the parser
parser = build_parser() parser = build_parser()
# parsing and returning options and arguments # parsing and returning options and arguments
if len(args) == 0:
# command line
options = parser.parse_args()
else:
options = parser.parse_args(args) options = parser.parse_args(args)
# adding specified filenames to arguments # adding specified filenames to arguments
options.filenames.append(options.input_pdb) options.filenames.append(options.input_pdb)
# Convert titrate_only string to a list of (chain, resnum) items: # Convert titrate_only string to a list of (chain, resnum) items: