4.2.3. propka.output¶

4.2.3.1. 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.
`print_tm_profile`(protein[, reference, …])	Print Tm profile.
`write_file`(filename, lines)	Writes a new file.
`write_jackal_scap_file`([mutation_data, …])	Write a scap file for, i.e., generating a mutated protein
`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_pdb_for_protein`(protein[, pdbfile, …])	Write a residue to the new PDB file.
`write_pka`(protein, parameters[, filename, …])	Write the pKa-file based on the given protein.
`write_propka`(molecular_container, filename)	Write PROPKA input file for molecular container.
`write_scwrl_sequence_file`(sequence[, …])	Write a scwrl sequence file for, e.g., generating a mutated protein

propka.output.get_bond_order(atom1, atom2)[source]¶

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, conformation='AVR', _=None)[source]¶

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, conformation, parameters)[source]¶

Returns string with determinant section of results.

Parameters

protein – protein object
conformation – specific conformation
parameters – parameters

Returns

string

propka.output.get_determinants_header()[source]¶

Create the Determinant header.

Returns: string

propka.output.get_folding_profile_section(protein, conformation='AVR', direction='folding', reference='neutral', window=[0.0, 14.0, 1.0], _=False, __=None)[source]¶

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]
_ – Boolean for verbose output
__ – options object

Returns

string

propka.output.get_propka_header()[source]¶

Create the header.

Returns: string

propka.output.get_references_header()[source]¶

Create the ‘references’ part of output file.

Returns: string

propka.output.get_summary_header()[source]¶

Create the summary header.

Returns: string

propka.output.get_summary_section(protein, conformation, parameters)[source]¶

Returns string with summary section of the results.

Parameters

protein – protein object
conformation – specific conformation
parameters – parameters

Returns

string

propka.output.get_the_line()[source]¶

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()[source]¶

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)[source]¶

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)[source]¶

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

propka.output.print_header()[source]¶: Print header section of output.

propka.output.print_pka_section(protein, conformation, parameters)[source]¶

Prints out pKa section of results.

Parameters

protein – protein object
conformation – specific conformation
parameters – parameters

propka.output.print_result(protein, conformation, parameters)[source]¶

Prints all resulting output from determinants and down.

Parameters

protein – protein object
conformation – specific conformation
parameters – parameters

propka.output.print_tm_profile(protein, reference='neutral', window=[0.0, 14.0, 1.0], __=[0.0, 0.0], tms=None, ref=None, _=False, options=None)[source]¶

Print Tm profile.

I think Tm refers to the denaturation temperature.

Parameters

protein – protein object
reference – reference state
window – pH window [min, max, step]
__ – temperature range [min, max]
tms – TODO - figure this out
ref – TODO - figure this out (probably reference state?)
_ – Boolean for verbosity
options – options object

propka.output.write_file(filename, lines)[source]¶

Writes a new file.

Parameters

filename – name of file
lines – lines to write to file

propka.output.write_jackal_scap_file(mutation_data=None, filename='1xxx_scap.list', _=None)[source]¶

Write a scap file for, i.e., generating a mutated protein

TODO - figure out what this is

propka.output.write_mol2_for_atoms(atoms, filename)[source]¶

Write out MOL2 file for atoms.

Parameters

atoms – list of atoms
filename – name of file

propka.output.write_pdb_for_atoms(atoms, filename, make_conect_section=False)[source]¶

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, filename)[source]¶

Write PDB conformation to a file.

Parameters

conformation – conformation container
filename – filename for output

propka.output.write_pdb_for_protein(protein, pdbfile=None, filename=None, include_hydrogens=False, _=None)[source]¶

Write a residue to the new PDB file.

Parameters

protein – protein object
pdbfile – PDB file
filename – file to write to
include_hydrogens – Boolean indicating whether to include hydrogens
options – options object

propka.output.write_pka(protein, parameters, filename=None, conformation='1A', reference='neutral', _='folding', verbose=False, __=None)[source]¶

Write the pKa-file based on the given protein.

Parameters

protein – protein object
filename – output file name
conformation – TODO - figure this out
reference – reference state
_ – “folding” or other
verbose – Boolean flag for verbosity
__ – options object

propka.output.write_propka(molecular_container, filename)[source]¶

Write PROPKA input file for molecular container.

Parameters

molecular_container – molecular container
filename – output file name

propka.output.write_scwrl_sequence_file(sequence, filename='x-ray.seq', _=None)[source]¶

Write a scwrl sequence file for, e.g., generating a mutated protein

TODO - figure out what this is