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.

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_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_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