schrodinger.application.peptide_workflow.utils module

Contains utility functions associated with running PeptideWorkflow. - Sorting - Renaming - Deduplicating structures

schrodinger.application.peptide_workflow.utils.sort_and_update_names(cache_list)

Sort the clustered results and write to the output.

Parameters:

cache_list ([Peptide]) – the clustered cached peptides in the run

Return type:

list[Structure]

Returns:

list of structures

schrodinger.application.peptide_workflow.utils.move_to_binding_site(st, grid_recept)

Place the peptide 1 Å from the grid center, in the direction pointing away from the center of the receptor :param st: structure to be moved :type st: structure.Structure :param st: the receptor from a Glide grid :type st: structure.Structure

schrodinger.application.peptide_workflow.utils.constrain_to_gridbox(st, grid_recept, margin=0.5)

Translate a structure the minimum distance needed to fit in a Glide grid.

The structure’s orientation and internal coordinates are preserved. If it already fits inside the outer grid box, its coordinates are unchanged.

Parameters:

  • st (Structure) – Structure to constrain.

  • grid_recept (Structure) – Receptor structure read from a Glide grid.

  • margin (float) – Minimum distance between every atom and the box boundary, in Angstroms.

Returns:

Whether the structure was translated.

Return type:

bool

Raises:

ValueError – If the structure cannot fit inside the outer box.

schrodinger.application.peptide_workflow.utils.remove_duplicate_peptide_poses(poses, cluster_method, num_poses=100)

Function that removes duplicate poses from a list of poses for a given ligand. A duplicate pose is any pose that has an RMSD < pose_rmsd to any previous pose after alignment, (thus, the output is order-dependent; for example, the first pose is always accepted). The original list of poses is not modified.

Parameters:

  • poses (list of [pose.Structure] objects) – A list of sorted docked poses for a ligand

  • cluster_method (BasicCluster) – method to cluster the poses

  • num_poses (int) – Max number of output poses per peptide

Return type:

list

Returns:

list of final output poses

schrodinger.application.peptide_workflow.utils.rename_poses(unique_poses)

Rename poses in order starting from 1 and return them as a list.

Parameters:

unique_poses (list(sts)) – unique st poses

Return type:

list[Structure]

Returns:

list of structures