Settings

Most submodules have a settings.py file. These contain a listing of annotated variables and values.

The SettingsManager is called by the main program (__main__) to read in configuration files.

Note

Settings should be retrieved directly from the corresponding settings modules and not copied locally in the code. This ensures that settings read in from the configuration files are properly loaded by modules.

mollib/core/settings.py

#: The default pH of new molecules
default_pH = 7.0

#: The default pKs of ionizable amino-acids. [Ref]_
#:
#: Some amino-acids have degenerate ionizeable atoms; these are listed and
#: separated by '-' characters. The different pKs for each ionization is
#: listed in the subsequent items in the tuple.
#:
#:  .. [Ref] G. R. Grimsley, J. M. Scholtz, C. N. Pace, Protein Sci. 18, 247-51
#:           (2009).
pKs = {'ASP': {'OD1-OD2': (-1.0, 3.5)},
       'GLU': {'OE1-OE2': (-1.0, 4.2)},
       'HIS': {'ND1-NE2': (6.6, 14.0)},
       'CYS': {'SG': (6.8,)},
       'TYR': {'OH': (10.3,)},
       'LYS': {'NZ': (10.5, 14.0, 14.0)},
       'last': {'O-OXT': (-1.0, 3.3)},
       'first': {'N': (7.7, 14.0, 14.0),}
     }

#: Path for the datasets
dataset_path = 'data/'

#: Path for model input molecule identifiers
model_molecule_identifiers = ('high_res.txt',
                              #'high_res_short.txt',
                              )

#: Path for the Ramachandran statistics datasets
ramachandran_dataset_path = 'data/ramachandranstatistics/'

#: Path for the Hbond statistics datasets
hbond_dataset_path = 'data/hbondstatistics/'

#: The cutoff Energy (in kT) to report good, warning and bad energies.
energy_cutoff_good = 3.4  # Within 96.6% of observed values
energy_cutoff_warning = 5.4  # Within 99.5% of observed values
energy_cutoff_bad = 20.0  # Only observed < 0.5% of the time.

#: urls to download PDB files
pdb_urls = ('https://files.rcsb.org/download/',)

#: Only load the first model, by default
pdb_first_model = True