schrodinger.application.desmond.process_fep_traj module

schrodinger.application.desmond.process_fep_traj.get_ligands_asl(sid: schrodinger.utils.sea.Map) → Tuple[Optional[str], Optional[str]]

Returns the asl of both ligands :param sid: contents of the SID file :type sid: sea.Map

:rtype (str, str)

schrodinger.application.desmond.process_fep_traj.representative_frames(sid: schrodinger.utils.sea.Map) → Tuple[Optional[int], Optional[int]]

Given an FEP’s SID file, extract the contact data for both endpoints, then for each endpoint, calculate a similarity matrix based on the protein- ligand contacts. After clustering the matrix, return the representative frame number for each endpoint.

Representative frame is the centroid of the largest cluster. :param sid: contents of the SID file :type sid: sea.Map

Return type:(int | None, int | None)

schrodinger.application.desmond.process_fep_traj.extract_representative_structure(frame_id: Optional[str], lambda_name: str) → str

Given a representative frame number, extract that frame from the trajectory, save this into a maestro file, and return the filename. We also cleanup some properties desmond-specific properties from the mae file.

Returns:filename of the maestro

schrodinger.application.desmond.process_fep_traj.post_process_trj(jobname, n_win=12, ref_ct_fname=None)

For each endpoint trajectory – generate a reduced trajectory using ‘parch’ and then extracts the representative structure from this trajectory. :param jobname: name of the production/labda_hopping stage :type jobname: str

Parameters:

• n_win (int) – number of lambda windows used in FEP
• ref_ct_fname (str) – filename of the reference structure for alignment

Returns:

a list with filenames that should be copied back to analysis stage directory

Return type:

list of str