def createPropkaOptions(pH, verbose=False):
"""
Create a propka options object for running propka.
"""
#build propka options
propkaOpts = ExtraOptions()
propkaOpts.pH = pH
propkaOpts.reference = "neutral"
propkaOpts.chains = None
propkaOpts.thermophiles = None
propkaOpts.alignment = None
propkaOpts.mutations = None
propkaOpts.verbose = verbose
propkaOpts.protonation = "old-school"
propkaOpts.window = (0.0, 14.0, 1.0)
propkaOpts.grid = (0.0, 14.0, 0.1)
propkaOpts.mutator = None
propkaOpts.mutator_options = None
propkaOpts.display_coupled_residues = None
propkaOpts.print_iterations = None
propkaOpts.version_label = "Nov30"
#These adds a few bits to propkaOpts
from propka30.Source import lib
lib.interpretMutator(propkaOpts)
#With the current defaults used here this does not do anything.
#However if we start adding the propka options we'll need to do this.
lib.setDefaultAlignmentFiles(propkaOpts)
return propkaOpts
def createPropkaOptions(pH, verbose=False, reference="neutral"):
"""
Create a propka options object for running propka.
"""
# build propka options
propkaOpts = ExtraOptions()
propkaOpts.pH = pH
propkaOpts.reference = reference
propkaOpts.chains = None
propkaOpts.thermophiles = None
propkaOpts.alignment = None
propkaOpts.mutations = None
propkaOpts.verbose = verbose
propkaOpts.protonation = "old-school"
propkaOpts.window = (0.0, 14.0, 1.0)
propkaOpts.grid = (0.0, 14.0, 0.1)
propkaOpts.mutator = None
propkaOpts.mutator_options = None
propkaOpts.display_coupled_residues = None
propkaOpts.print_iterations = None
propkaOpts.version_label = "Nov30"
# These adds a few bits to propkaOpts
from propka30.Source import lib
lib.interpretMutator(propkaOpts)
# With the current defaults used here this does not do anything.
# However if we start adding the propka options we'll need to do this.
lib.setDefaultAlignmentFiles(propkaOpts)
return propkaOpts