schrodinger.ui.sequencealignment.jobs module

Job handling functions for multiple sequence viewer.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.ui.sequencealignment.jobs.stderr_msg(header, msg)[source]

When no display is available, we can re-route dialog popups to stderr

schrodinger.ui.sequencealignment.jobs.getSchrodingerPath()[source]

Returns a path to Schrodinger directory.

Return type

string

Returns

Schrodinger path or None if the path is not found.

schrodinger.ui.sequencealignment.jobs.checkJobIsRunning()[source]

Checks if there is another job currently running.

schrodinger.ui.sequencealignment.jobs.processPendingEvents()[source]

Processess pending events from Qt and Maestro.

schrodinger.ui.sequencealignment.jobs.killJob(job_id)[source]

Kills a specified job using jobcontrol.

schrodinger.ui.sequencealignment.jobs.run_job_via_jobcontrol(command_list, log_file_name, dialog_title='Job Progress', initial_text='', progress_dialog=None, quiet=False, no_jobid=False, monitor_job=True, settings='')[source]

Runs a job using Job class of jobcontrol module.

Note

Eventually, we will migrate all jobs to use this function.

Parameters

command (str) – Command to be executed.

Return type

int

Returns

0 on successfull execution, error code otherwise

schrodinger.ui.sequencealignment.jobs.run_job(command, use_windows_shell=True, quiet=False, progress_dialog=None, no_jobid=False)[source]

Executes the specified command and waits until it returns. It processess pending Qt events, so the main program is not blocked.

Parameters

command (list) – Command list to be executed.

Return type

bool

Returns

True on successfull execution, False otherwise

schrodinger.ui.sequencealignment.jobs.run_clustal(widget, sequence_group, ss_constraints=False, merge_groups=False, progress_dialog=None, global_alignment=True, quick_alignment=True, ignore_selection=False, viewer=None)[source]

Runs Clustal alignment job and incorporates the results.

Parameters

sequence_group (SequenceGroup) – target sequence group

schrodinger.ui.sequencealignment.jobs.run_pfam(sequence_group, progress_dialog=None, job_settings='')[source]

Runs a Pfam job and incorporates the results.

Parameters

sequence_group (SequenceGroup) – target sequence group

schrodinger.ui.sequencealignment.jobs.removeTmpJobDir(tmpdir, keep=[])[source]

Empties the temporary job directory and removes it. Be careful with this function.

Parameters

keep (list of strings) – Optional list of files that should not be deleted.

schrodinger.ui.sequencealignment.jobs.run_ssp(sequence_group, progress_dialog=None, job_settings='')[source]

Runs a secondary structure prediction job and incorporates the results.

Parameters

sequence_group (SequenceGroup) – target sequence group

schrodinger.ui.sequencealignment.jobs.incorporatePDB(sequence_group, pdb_file_name, chain_id=None, maestro_include=False, new_list=None, viewer=None)[source]
schrodinger.ui.sequencealignment.jobs.fetch_pdb(sequence_group, entry_id, maestro_include=False, maestro_incorporate=True, progress_dialog=None, progress=None, remote_query_dialog=None, viewer=None)[source]

Fetches a PDB file from from a thirdparty directory or from online repository if thirdpary is not available.

Parameters

  • sequence_group (SequenceGroup) – target sequence group.

  • entry_id (str) – PDB entry ID (4- or 5-letter code)

Return type

string

Returns

Return status, can be “ok”, “error”, “cancelled” or “invalid”

schrodinger.ui.sequencealignment.jobs.fetch_entrez(sequence_group, entry_id, progress_dialog=None, remote_query_dialog=None)[source]

Fetches a protein sequence entry from Entrez repository.

Parameters

  • sequence_group (SequenceGroup) – target sequence group.

  • entry_id (str) – Entrez entry ID

Return type

bool

Returns

True on success, False otherwise.

schrodinger.ui.sequencealignment.jobs.make_blast_table_tooltip(full_name, seq1, seq2)[source]
schrodinger.ui.sequencealignment.jobs.blast_get_default_settings()[source]

Returns a list of default BLAST settings.

Temporarily changes preferences for “ALLOW_WEB_BLAST” to the user’s preference when running a BLAST search, then resets back to the original preference when the search is over.

Parameters

remotely (bool or NoneType) – Whether the user has requested a remote search or None to leave global preference unchanged

schrodinger.ui.sequencealignment.jobs.blast_run(sequence_group, settings=None, progress_dialog=None, results_dialog=None, quiet=False, remote_query_dialog=None, job_settings='')[source]

Runs a Blast search. Appends the results to the sequence group.

Parameters

  • sequence_group (SequenceGroup) – target sequence group.

  • nodialog (bool) – Do not display settings dialog.

Return type

string

Returns

status, can be “ok”, “failed”, or “cancelled”

schrodinger.ui.sequencealignment.jobs.run_align_structures(sequence_group, progress_dialog=None, viewer=None, job_settings='')[source]

This function aligns all or selected structures in current sequence group using external “ska” program. The alignment is then incorporated into MSV and structures are reoriented in Maestro workspace according to the alignment.

schrodinger.ui.sequencealignment.jobs.pdb_align_structure_to_sequence(sequence, structure, ssa=None)[source]

Aligns PDB structure to SEQRES sequence.