biotite.application.dssp.DsspApp

class biotite.application.dssp.DsspApp(atom_array, bin_path='mkdssp')[source]

Bases: biotite.application.localapp.LocalApp

Annotate the secondary structure of a protein structure using the DSSP software.

Internally this creates a Popen instance, which handles the execution.

DSSP differentiates between 8 different types of secondary structure elements:

  • C: loop, coil or irregular

  • H: \({\alpha}\)-helix

  • B: \({\beta}\)-bridge

  • E: extended strand, participation in \({\beta}\)-ladder

  • G: 3 10-helix

  • I: \({\pi}\)-helix

  • T: hydrogen bonded turn

  • S: bend

Parameters
atom_arrayAtomArray

The atom array to be annotated.

bin_pathstr, optional

Path of the DDSP binary.

Examples

>>> app = DsspApp(atom_array)
>>> app.start()
>>> app.join()
>>> print(app.get_sse())
['C' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'T' 'T' 'G' 'G' 'G' 'G' 'T' 'C' 'C' 'C'
 'C' 'C']
run(self)[source]

Commence the application run. Called in start().

PROTECTED: Override when inheriting.

evaluate(self)[source]

Evaluate application results. Called in join().

PROTECTED: Override when inheriting.

get_sse(self)[source]

Get the resulting secondary structure assignment.

Returns
ssendarray, dtype=”U1”

An array containing DSSP secondary structure symbols corresponding to the residues in the input atom array.

static annotate_sse(atom_array, bin_path='mkdssp')[source]

Perform a secondary structure assignment to an atom array.

This is a convenience function, that wraps the DsspApp execution.

Parameters
atom_arrayAtomArray

The atom array to be annotated.

bin_pathstr, optional

Path of the DDSP binary.

Returns
ssendarray, dtype=”U1”

An array containing DSSP secondary structure symbols corresponding to the residues in the input atom array.

add_additional_options(self, options)

Add additional options for the command line program. These options are put before the arguments automatically determined by the respective LocalApp subclass.

This method is focused on advanced users, who have knowledge on the available options of the command line program and the options already used by the LocalApp subclasses. Ignoring the already used options may result in conflicting CLI arguments and potential unexpected results. It is recommended to use this method only, when the respective LocalApp subclass does not provide a method to set the desired option.

Parameters
optionslist of str

A list of strings representing the command line options.

Notes

In order to see which options the command line execution used, try the get_command() method.

Examples

>>> seq1 = ProteinSequence("BIQTITE")
>>> seq2 = ProteinSequence("TITANITE")
>>> seq3 = ProteinSequence("BISMITE")
>>> seq4 = ProteinSequence("IQLITE")
>>> # Run application without additional arguments
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.start()
>>> app.join()
>>> print(app.get_command())
clustalo --in ...fa --out ...fa --output-order=tree-order --seqtype Protein --guidetree-out ...tree
>>> # Run application with additional argument
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.add_additional_options(["--full"])
>>> app.start()
>>> app.join()
>>> print(app.get_command())
clustalo --full --in ...fa --out ...fa --output-order=tree-order --seqtype Protein --guidetree-out ...tree
cancel(self)

Cancel the application when in RUNNING or FINISHED state.

clean_up(self)

Do clean up work after the application terminates.

PROTECTED: Optionally override when inheriting.

get_app_state(self)

Get the current app state.

Returns
app_stateAppState

The current app state.

get_command(self)

Get the executed command.

Cannot be called until the application has been started.

Returns
commandstr

The executed command.

Examples

>>> seq1 = ProteinSequence("BIQTITE")
>>> seq2 = ProteinSequence("TITANITE")
>>> seq3 = ProteinSequence("BISMITE")
>>> seq4 = ProteinSequence("IQLITE")
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.start()
>>> print(app.get_command())
clustalo --in ...fa --out ...fa --output-order=tree-order --seqtype Protein --guidetree-out ...tree
get_exit_code(self)

Get the exit code of the process.

PROTECTED: Do not call from outside.

Returns
codeint

The exit code.

get_process(self)

Get the Popen instance.

PROTECTED: Do not call from outside.

Returns
processPopen

The Popen instance

get_stderr(self)

Get the STDERR pipe content of the process.

PROTECTED: Do not call from outside.

Returns
stdoutstr

The standard error.

get_stdout(self)

Get the STDOUT pipe content of the process.

PROTECTED: Do not call from outside.

Returns
stdoutstr

The standard outpout.

is_finished(self)

Check if the application has finished.

PROTECTED: Override when inheriting.

Returns
finishedbool

True of the application has finished, false otherwise

join(self, timeout=None)

Conclude the application run and set its state to JOINED. This can only be done from the RUNNING or FINISHED state.

If the application is FINISHED the joining process happens immediately, if otherwise the application is RUNNING, this method waits until the application is FINISHED.

Parameters
timeoutfloat, optional

If this parameter is specified, the Application only waits for finishing until this value (in seconds) runs out. After this time is exceeded a TimeoutError is raised and the application is cancelled.

Raises
TimeoutError

If the joining process exceeds the timeout value.

set_arguments(self, arguments)

Set command line arguments for the application run.

PROTECTED: Do not call from outside.

Parameters
argumentslist of str

A list of strings representing the command line options.

set_exec_dir(self, exec_dir)

Set the directory where the application should be executed. If not set, it will be executed in the working directory at the time the application was created.

PROTECTED: Do not call from outside.

Parameters
exec_dirstr

The execution directory.

start(self)

Start the application run and set its state to RUNNING. This can only be done from the CREATED state.

wait_interval(self)

The time interval of is_finished() calls in the joining process.

PROTECTED: Override when inheriting.

Returns
intervalfloat

Time (in seconds) between calls of is_finished() in join()