propka.output

Output

Output routines.

Functions

get_bond_order(atom1, atom2)	Get the order of a bond between two atoms.
get_charge_profile_section(protein[, ...])	Returns string with the charge profile section of the results.
get_determinant_section(protein, ...)	Returns string with determinant section of results.
get_determinants_header()	Create the Determinant header.
get_folding_profile_section(protein[, ...])	Returns string with the folding profile section of the results.
get_propka_header()	Create the header.
get_references_header()	Create the 'references' part of output file.
get_summary_header()	Create the summary header.
get_summary_section(protein, conformation, ...)	Returns string with summary section of the results.
get_the_line()	Draw the line-Johnny Cash would have been proud-or actually Aerosmith!
get_warning_header()	Create the 'warning' part of the output file.
make_interaction_map(name, list_, interaction)	Print out an interaction map named 'name' of the groups in 'list' based on the function 'interaction'
open_file_for_writing(input_file)	Open file or file-like stream for writing.
print_header()	Print header section of output.
print_pka_section(protein, conformation, ...)	Prints out pKa section of results.
print_result(protein, conformation, parameters)	Prints all resulting output from determinants and down.
write_mol2_for_atoms(atoms, filename)	Write out MOL2 file for atoms.
write_pdb_for_atoms(atoms, filename[, ...])	Write out PDB file for atoms.
write_pdb_for_conformation(conformation, ...)	Write PDB conformation to a file.
write_pka(protein, parameters[, filename, ...])	Write the pKa-file based on the given protein.

propka.output.get_bond_order(atom1, atom2)

Get the order of a bond between two atoms.

Parameters:

• atom1 – first atom in bond

• atom2 – second atom in bond

Returns:

string with bond type

propka.output.get_charge_profile_section(protein: MolecularContainer, conformation: str = 'AVR')

Returns string with the charge profile section of the results.

Parameters:

• protein – protein object

• conformation – specific conformation

• _ – options object

Returns:

string

propka.output.get_determinant_section(protein: MolecularContainer, conformation: str, parameters: Parameters)

Returns string with determinant section of results.

Parameters:

• protein – protein object

• conformation – specific conformation

• parameters – parameters

Returns:

string

propka.output.get_determinants_header()

Create the Determinant header.

Returns:

string

propka.output.get_folding_profile_section(protein: MolecularContainer, conformation: str = 'AVR', direction: str = 'folding', reference: str = 'neutral', window: Tuple[float, float, float] = (0.0, 14.0, 1.0))

Returns string with the folding profile section of the results.

Parameters:

• protein – protein object

• conformation – specific conformation

• direction – ‘folding’ or other

• reference – reference state

• window – pH window [min, max, step]

Returns:

string

propka.output.get_propka_header()

Create the header.

Returns:

string

propka.output.get_references_header()

Create the ‘references’ part of output file.

Returns:

string

propka.output.get_summary_header()

Create the summary header.

Returns:

string

propka.output.get_summary_section(protein: MolecularContainer, conformation: str, parameters: Parameters)

Returns string with summary section of the results.

Parameters:

• protein – protein object

• conformation – specific conformation

• parameters – parameters

Returns:

string

propka.output.get_the_line()

Draw the line-Johnny Cash would have been proud-or actually Aerosmith!

NOTE - Johnny Cash walked the line.

Returns:

string

propka.output.get_warning_header()

Create the ‘warning’ part of the output file.

TODO - this function is essentially a no-op.

Returns:

string

propka.output.make_interaction_map(name, list_, interaction)

Print out an interaction map named ‘name’ of the groups in ‘list’ based on the function ‘interaction’

Parameters:

• list – list of groups

• interaction – some sort of function

Returns:

string

propka.output.open_file_for_writing(input_file: IO[str] | PathLike | str) → IO[str]

Open file or file-like stream for writing.

TODO - convert this to a context manager.

Parameters:

• input_file – path to file or file-like object. If file-like object,

• mode. (then will attempt to get file) –

propka.output.print_header()

Print header section of output.

propka.output.print_pka_section(protein: MolecularContainer, conformation: str, parameters: Parameters)

Prints out pKa section of results.

Parameters:

• protein – protein object

• conformation – specific conformation

• parameters – parameters

propka.output.print_result(protein: MolecularContainer, conformation: str, parameters: Parameters)

Prints all resulting output from determinants and down.

Parameters:

• protein – protein object

• conformation – specific conformation

• parameters – parameters

propka.output.write_mol2_for_atoms(atoms, filename)

Write out MOL2 file for atoms.

Parameters:

• atoms – list of atoms

• filename – name of file

propka.output.write_pdb_for_atoms(atoms: List[Atom], filename: PathLike | str, make_conect_section=False)

Write out PDB file for atoms.

Parameters:

• atoms – list of atoms

• filename – name of file

• make_conect_section – generate a CONECT PDB section

propka.output.write_pdb_for_conformation(conformation: ConformationContainer, filename: PathLike | str)

Write PDB conformation to a file.

Parameters:

• conformation – conformation container

• filename – filename for output

propka.output.write_pka(protein: MolecularContainer, parameters: Parameters, filename: PathLike | str | None = None, conformation: str = '1A', reference: str = 'neutral', *, verbose: bool = True)

Write the pKa-file based on the given protein.

Parameters:

• protein – protein object

• filename – output file name

• conformation – specific conformation

• reference – reference state

• verbose – Boolean flag for verbosity