propka.lib

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.
generate_combinations(interactions)	Generate combinations of interactions.
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_list(titrate_only)
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.

Classes

Options()

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.

Changed in version 3.4.0: Argument –generate-propka-input has been removed as writing PROPKA input files is no longer supported.

propka.lib.generate_combinations(interactions: Iterable[T]) → List[List[T]]

Generate combinations of interactions.

Parameters:

interactions – list of interactions

Returns:

list of combinations

propka.lib.loadOptions(args=None) → Options

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: List[List[T]], interaction: T) → List[List[T]]

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_: Number, max_: Number, step: Number) → Iterator[Number]

Make a grid across the specified tange.

Like range() for integers or numpy.arange() for floats, except that max_ is not excluded from the range.

Parameters:

• min – minimum value of grid

• max – maximum value of grid

• step – grid step size

propka.lib.make_molecule(atom: Atom, atoms: List[Atom])

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: str) → Tuple[str, int, 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: Dict[str, ConformationContainer], names: Iterable[str])

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: List[Atom])

Maps atoms into molecules.

Parameters:

atoms – list of atoms

Returns:

list of molecules