propka.output
Output
Output routines.
Functions
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Get the order of a bond between two atoms. |
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Returns string with the charge profile section of the results. |
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Returns string with determinant section of results. |
Create the Determinant header. |
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Returns string with the folding profile section of the results. |
Create the header. |
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Create the 'references' part of output file. |
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Create the summary header. |
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Returns string with summary section of the results. |
Draw the line-Johnny Cash would have been proud-or actually Aerosmith! |
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Create the 'warning' part of the output file. |
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Print out an interaction map named 'name' of the groups in 'list' based on the function 'interaction' |
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Open file or file-like stream for writing. |
Print header section of output. |
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Prints out pKa section of results. |
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Prints all resulting output from determinants and down. |
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Print Tm profile. |
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Writes a new file. |
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Write a scap file for, i.e., generating a mutated protein |
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Write out MOL2 file for atoms. |
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Write out PDB file for atoms. |
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Write PDB conformation to a file. |
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Write a residue to the new PDB file. |
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Write the pKa-file based on the given protein. |
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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: MolecularContainer, conformation: str, parameters: Parameters)[source]
Returns string with determinant section of results.
- Parameters
protein – protein object
conformation – specific conformation
parameters – parameters
- Returns
string
- propka.output.get_folding_profile_section(protein: MolecularContainer, 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_references_header()[source]
Create the ‘references’ part of output file.
- Returns
string
- propka.output.get_summary_section(protein: MolecularContainer, conformation: str, parameters: 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: Union[IO[str], PathLike, str]) IO[str] [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,
mode. (then will attempt to get file) –
- propka.output.print_pka_section(protein: MolecularContainer, conformation: str, parameters: Parameters)[source]
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)[source]
Prints all resulting output from determinants and down.
- Parameters
protein – protein object
conformation – specific conformation
parameters – parameters
- propka.output.print_tm_profile(protein: NoReturn, 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: List[Atom], filename: Union[PathLike, str], 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: ConformationContainer, filename: Union[PathLike, str])[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: MolecularContainer, parameters: Parameters, filename: Optional[Union[PathLike, str]] = 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