schrodinger.application.glide_ws.db_queries module

Functions/Methods for facilitating common queries for the WScore Ligand Database.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.glide_ws.db_queries.Pose(id, ligand_id)

Bases: tuple

id

Alias for field number 0

ligand_id

Alias for field number 1

class schrodinger.application.glide_ws.db_queries.Property(name, id, range_type)

Bases: tuple

id

Alias for field number 1

name

Alias for field number 0

range_type

Alias for field number 2

schrodinger.application.glide_ws.db_queries.parse_cmd_arguments(cmd_args=None)

schrodinger.application.glide_ws.db_queries.poses_by_ligand_title(conn, lig_title)

Generator that yields all of the poses as Pose objects in the WScore DB associated with a single ligand title.

schrodinger.application.glide_ws.db_queries.poses_by_job_id(conn, job_id)

Generator that yields all the poses as Pose objects in the WScore DB associated with a single job record.

schrodinger.application.glide_ws.db_queries.structures_by_pose_id(conn, pose_id)

Generator that yields all of the structures in the WScore DB associated with a single pose_id.

schrodinger.application.glide_ws.db_queries.term_data_by_prop_id(conn, prop_id)

Get all values for a given property stored in the WScore DB

schrodinger.application.glide_ws.db_queries.properties_from_properties_table(conn)

Returns a list of Property namedtuples which includes all of the properties in the WScore DB.

schrodinger.application.glide_ws.db_queries.generate_term_summary_string(conn, prop_name, prop_id, value_list, range_type, nbins)

For a single scoring term, returns a string summarizing the range of values found in the WScore DB.

schrodinger.application.glide_ws.db_queries.get_ligand_summary_rows(conn, lig_title, properties, add_scoring_terms)

For a single ligand title, return a list of rows containing summary information for each of the poses associated with this ligand title.”

schrodinger.application.glide_ws.db_queries.generate_summary_rows_for_ligands(conn, lig_titles, add_scoring_terms)

Return a complete list of summary rows for a set of ligand titles

schrodinger.application.glide_ws.db_queries.write_lines(write_func, lines)

schrodinger.application.glide_ws.db_queries.row_to_string(row)

schrodinger.application.glide_ws.db_queries.output_ligand_summary_info(conn, lig_titles, csv_file, report_file, add_scoring_terms=False)

Output ligand summary information to a csv_file, a report_file, and/or stdout.

schrodinger.application.glide_ws.db_queries.output_summary_for_scoring_terms(conn, report_file, nbins=5)

Prepare frequency tables for each of the scoring terms in the database and output them to either the report_file or to stdout.

schrodinger.application.glide_ws.db_queries.export_poses(conn, pose_id, writer)

schrodinger.application.glide_ws.db_queries.export_ligand_poses(conn, lig_title, writer)

schrodinger.application.glide_ws.db_queries.export_job_poses(conn, job_id, writer)

schrodinger.application.glide_ws.db_queries.export_poses_to_file(conn, output_file, lig_titles, job_ids)