Package schrodinger :: Package application :: Package desmond :: Module process_fep_traj

Module process_fep_traj

Functions

_get_perturbation_type(sid)

get_ligands_asl(sid)
Returns the asl of both ligands

get_protein_asl(sid)
Returns the asl of both proteins (for PRM jobs)

(int | None, int | None)

representative_frames(sid)
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.

list of str or an empty list

generate_reduced_trajectory(cms_fn, trj_dir, out_fn, dew_asl, lambda_val, ref_st_fn=None, ref_asl=None, protein_fep=False, nwaters=200)
Generate a 'reduced' trajectory, where the ligands are solvated by 200 water molecules and the system is aligned on the first frame.

extract_representative_structure(frame_id, lambda_name)
Given a representative frame number, extract that frame from the trajectory, save this into a maestro file, and return the filename.

list of str

post_process_trj(jobname, n_win=12, ref_st_fn=None)
For each endpoint trajectory -- generate a reduced trajectory using 'parch' and then extracts the representative structure from this trajectory.

Variables

[hide private]

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

get_ligands_asl(sid)

Returns the asl of both ligands

Parameters:

sid (sea.Map
@rtype (str, str)
) - contents of the SID file

get_protein_asl(sid)

Returns the asl of both proteins (for PRM jobs)

Parameters:

sid (sea.Map
@rtype (str | None, str | None)
) - contents of the SID file

representative_frames(sid)

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.

Parameters:

sid (sea.Map) - contents of the SID file

Returns: (int | None, int | None)

generate_reduced_trajectory(cms_fn, trj_dir, out_fn, dew_asl, lambda_val, ref_st_fn=None, ref_asl=None, protein_fep=False, nwaters=200)

Generate a 'reduced' trajectory, where the ligands are solvated by 200 water molecules and the system is aligned on the first frame.

TODO: proved an input protein conformation such that all parched trajectories are aligned to a common structure

Parameters:

cms_fn - filename of the cms file
trj_dir - dirname of the trajectory directory
out_fn - the basename of output cms/trj
dew_asl - asl of the ligand around which the waters will be kept
lambda_val - lambda endpont -- 0 or 1
ref_asl - system to be aligned on provided asl
protein_fep - if the FEP calculation was a protein calculation

Returns: list of str or an empty list

a list of generated files/directories to copy over to the analysis stage dir.

extract_representative_structure(frame_id, lambda_name)

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

post_process_trj(jobname, n_win=12, ref_st_fn=None)

For each endpoint trajectory -- generate a reduced trajectory using 'parch' and then extracts the representative structure from this trajectory.

Parameters:

jobname (str) - name of the production/labda_hopping stage
n_win (int) - number of lambda windows used in FEP
ref_st_fn (str) - filename of the reference structure for alignment

Returns: list of str

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