schrodinger.application.msv.jobs.clustal module

class schrodinger.application.msv.jobs.clustal.ClustalJob(aln, second_aln=None, profile_mode='profile', matrix=None, gapopen=None, gapext=None, quicktree=False, output_fname=None)

Bases: PyQt5.QtCore.QObject

Class to run a clustal job:

Cvar:progressMade: A signal emitted with the number of lines output by the clustal job.

cancel()

progressMade

run()

Run the clustal job.

Raises:RuntimeError if no clustal executable can be found Returns:Output alignment and tree string. The sequences are output in the same order as input. Sequence attributes are preserved. The tree is in Newick format. This function returns (None,None) if the job is canceled. Return type:tuple of (ProteinAlignment, str) or (None,None)

schrodinger.application.msv.jobs.clustal.getClustalPath()

Returns a path to ClustalW executable.

This function attempts to find clustalw2 excutable in following locations:

1. Maestro bin directory based on MAESTRO_EXEC env var.
2. Maestro bin directory based on $SCHRODINGER/maestro-v*/bin/* path.
3. User-defined location (CLUSTALW2 env var).

Return type:str Returns:path to ClustalW executable file, or None if the executable could not be located.