4.2.2. propka.lib

4.2.2.1. Set-up of a PROPKA calculation

Implements many of the main functions used to call PROPKA.

Functions

build_parser([parser])	Build an argument parser for PROPKA.
configuration_compare(conf)	TODO - figure out what this function does.
debug(*args)	Log a message to debug.
generate_combinations(interactions)	Generate combinations of interactions.
get_sorted_configurations(configuration_keys)	Extract and sort configurations.
info(*args)	Log a message to info.
loadOptions([args])	Load the arguments parser with options.
make_combination(combis, interaction)	Make a specific set of combinations.
make_grid(min_, max_, step)	Make a grid across the specified tange.
make_molecule(atom, atoms)	Make a molecule from atoms.
make_tidy_atom_label(name, element)	Returns a ‘tidier’ atom label for printing to the new PDB file.
parse_res_string(res_str)	Parse a residue string.
protein_precheck(conformations, names)	Check protein for correct number of atoms, etc.
resid_from_atom(atom)	Return string with atom residue information.
split_atoms_into_molecules(atoms)	Maps atoms into molecules.
warning(*args)	Log a message to warning.

propka.lib.build_parser(parser=None)

Build an argument parser for PROPKA.

Parameters

parser – existing parser. If this is not None, then the PROPKA parser will be created as a subparser to this existing parser. Otherwise, a new parser will be created.

Returns

ArgumentParser object.

propka.lib.configuration_compare(conf)

TODO - figure out what this function does.

propka.lib.debug(*args)

Log a message to debug.

Level defaults to DEBUG unless overridden.

Parameters

args – argument list

propka.lib.generate_combinations(interactions)

Generate combinations of interactions.

Parameters

interactions – list of interactions

Returns

list of combinations

propka.lib.get_sorted_configurations(configuration_keys)

Extract and sort configurations.

Parameters

configuration_keys – list of configuration keys

Returns

list of configurations

propka.lib.info(*args)

Log a message to info.

Level defaults to INFO unless overridden.

Parameters

args – argument list

propka.lib.loadOptions(args=None)

Load the arguments parser with options. Note that verbosity is set as soon as this function is invoked.

Parameters

args – list of arguments

Returns

argparse namespace

propka.lib.make_combination(combis, interaction)

Make a specific set of combinations.

Parameters

• combis – list of combinations

• interaction – interaction to add to combinations

Returns

list of combinations

propka.lib.make_grid(min_, max_, step)

Make a grid across the specified tange.

TODO - figure out if this duplicates existing generators like range or numpy function.

Parameters

• min – minimum value of grid

• max – maximum value of grid

• step – grid step size

propka.lib.make_molecule(atom, atoms)

Make a molecule from atoms.

Parameters

• atom – one of the atoms

• atoms – a list of the remaining atoms

Returns

list of atoms

propka.lib.make_tidy_atom_label(name, element)

Returns a ‘tidier’ atom label for printing to the new PDB file.

Parameters

• name – atom name

• element – atom element

Returns

string

propka.lib.parse_res_string(res_str)

Parse a residue string.

Parameters

res_string – residue string in format “chain:resnum[inscode]”

Returns

a tuple of (chain, resnum, inscode).

Raises

ValueError if the input string is invalid. –

propka.lib.protein_precheck(conformations, names)

Check protein for correct number of atoms, etc.

Parameters

names – conformation names to check

propka.lib.resid_from_atom(atom)

Return string with atom residue information.

Parameters

atom – atom to generate string for

Returns

string

propka.lib.split_atoms_into_molecules(atoms)

Maps atoms into molecules.

Parameters

atoms – list of atoms

Returns

list of molecules

propka.lib.warning(*args)

Log a message to warning.

Level defaults to WARNING unless overridden.

Parameters

args – argument list