schrodinger.application.livedesign.export_controller module

class schrodinger.application.livedesign.export_controller.ExportType(value)

Bases: enum.Enum

An enumeration.

SDF = 'SDF'

MAESTRO = 'MAESTRO'

MAESTRO_SDF = 'MAESTRO_SDF'

CUSTOM = 'Custom'

schrodinger.application.livedesign.export_controller.ignore_cleanup_window(funct)

Decorator to temporarily disable the “Project cleanup in progress” window. This can decorate a class method or function.

class schrodinger.application.livedesign.export_controller.BaseDataMapWriter(output_file_path)

Bases: object

Custom TSV mapping file writer base class. Subclasses must define a HEADER class variable that contains the header text for each column in the output .tsv file.

Variables

HEADER (list(str)) – a list of header values for the data file written by this class. Must be defined in subclasses.

HEADER = []

__init__(output_file_path)

Parameters

output_file_path (str) – output file name with path

appendRow(row)

Append a row to the TSV file. :param row: a list of strings to add to the TSV file as a new row :type row: list(str)

close()

Close the file handle associated with the TSV writer.

class schrodinger.application.livedesign.export_controller.DataMapWriter(output_file_path)

Bases: schrodinger.application.livedesign.export_controller.BaseDataMapWriter

Meant to be used for writing .tsv files for use as input with the LDClient method start_export_assay_and_pose_data(). Should only be used if the LD version is 8.6 or earlier.

HEADER = ['Corporate ID', 'Model Name', 'Target Key', 'Ligand Key']

__init__(output_file_path)

Parameters

output_file_path (str) – output file name with path

appendRow(row)

Append a row to the TSV file. :param row: a list of strings to add to the TSV file as a new row :type row: list(str)

close()

Close the file handle associated with the TSV writer.

class schrodinger.application.livedesign.export_controller.DataMapWriter87(output_file_path)

Bases: schrodinger.application.livedesign.export_controller.BaseDataMapWriter

Meant to be used for writing .tsv files for use as input with the LDClient method load_assay_and_pose_data(). Should only be used if the LD version is 8.7 or later.

HEADER = ['s_ld_export_compound_id', 'entity_id', 'model_name', 'ligand_zip_file_path', 'target_zip_file_path']

__init__(output_file_path)

Parameters

output_file_path (str) – output file name with path

appendRow(row)

Append a row to the TSV file. :param row: a list of strings to add to the TSV file as a new row :type row: list(str)

close()

Close the file handle associated with the TSV writer.

class schrodinger.application.livedesign.export_controller.ExportController(ld_client, maestro_data, export_data_list, match_existing_compounds_by=None)

Bases: object

A class to prepare data for export to LD.

Variables

TEMP_FILE_PFX (str) – the prefix for all temporary file names produced by this class

TEMP_FILE_PFX = 'mae_exp'

__init__(ld_client, maestro_data, export_data_list, match_existing_compounds_by=None)

Parameters

• ld_client (client.LDClient) – LDClient instance to communicate with server

• maestro_data (maestro_data_types.BaseMaestroData) – Maestro data to export to LD

• export_data_list (list(panel_components.ExportData)) – list of things to export to LiveDesign

• match_existing_compounds_by (str) – property data name to copy over under the Corporate ID structure property so LD can match existing compounds by ID instead of structure.

exportBatched(batch_size=50)

Export data to LD in batches.

Parameters

batch_size (int) – Number of structures to export per batch

Returns

list of batched data for export

Return type

list(ExportBatch)

exportData(rl_map, export_3d)

Write the specified structures to an appropriate file type (.prjzip or .sdf) and produce other data (.tsv mapping file and SMARTS map) necessary for successful export. Return an ExportBatch object that contains this information.

Parameters

• rl_map (data_classes.ReceptorLigandMap) – the receptor-ligand map containing the structures to be exported

• export_3d (bool) – whether to prepare and return 3D data for export

Returns

all data necessary for exporting the supplied receptor-ligand map to LiveDesign

Return type

ExportBatch

property export_3d_requested

Returns

whether 3D export was requested

Return type

bool

addTemporaryProperties(rl_map)

Context manager for temporarily adding a copy of the title and corporate ID (if requested) to the structures in the project table, so that they will be present in the created prjzip file (used for 3D exports).

Parameters

rl_map (data_classes.ReceptorLigandMap) – the receptor-ligand map containing the structures to be exported

createMaeZip(rl_map)

Export each unique ligand and receptor in the receptor ligand map as an individual .mae file, then collect these into a .zip archive.

Parameters

rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

Returns

file path of the .zip archive

Return type

str

createSDFFile(rl_map, ligands_only)

Produce a .sdf file with each unique ligand in a receptor-ligand map, or optionally, the receptors as well.

Parameters

• rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

• ligands_only (bool) – whether to include only ligands from the receptor- ligand map in the .sdf file

Returns

the path to the new .sdf file

Return type

str

createDataMapFile(rl_map)

Generate the map file for the provided receptor-ligand map, which is necessary for upload to LiveDesign. If applicable, also generate a dict that maps each ligand’s dummy corporate ID to the SMARTS string of its corresponding companion ligand. This is necessary for uploads that require the 3D column to show a structure different from the rest of the row.

The map file is a tab-delimited .tsv file with four columns, something like

Corporate ID Model Name Target Key Ligand Key d60c83da-6dd8-4c9b-a3d9-5c34ff985c40 x 4 5 85a4557e-6b86-4860-92a6-5d8b6e5f91e2 x 6 7 e39011d0-2878-41be-9601-c75f31f369b0 x 8 9

The corporate ID values will either be a dummy string which has no use or a UUID string which will be replaced during the export process. The model name is selected by the user in the GUI. The target and ligand keys are either dummy values (2D export) or the entry ID used to identify structures within the .prjzip file (3D export).

Parameters

rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

Returns

a 2-tuple containing the name of the data mapping file and a companion SMARTS dictionary (empty if not applicable to this system)

Return type

tuple(str, dict(str, str))

appendAdditionalViewInformation()

Adding view info. of the structures to a file, will be used in LD for displaying the structures.

createAdditionalViewInformation()

Creates additional view information for LD. The info. needs to be in the right order.

Returns

View info.

Return type

str

createPrjzip(**kwargs)

This is the actual functionality encapsulating the decorated method.

ensurePrjzipCreationComplete(proj_file_name)

Since the maestro command to create a project returns before the prjzip has been built, we need to wait for the file to be successfully finished.

Parameters

proj_file_name (str) – The project file to wait on.

class schrodinger.application.livedesign.export_controller.ExportBatch(map_file_path, sdf_file_path=None, three_d_file_path=None, export_type=None, idx_lig_id_map=None)

Bases: object

Data class composed of all the data necessary to export a single batch to LiveDesign.

Variables

• map_file_path – the path to the file containing the mapping data; this file should be a .tsv

• sdf_file_path (str) – the path to the file containing non-3D structure data (this should be a .sdf file). This variable and/or three_d_file_path must be initialized.

• three_d_file_path (str) – the path to the file containing 3D structure data (this should be a .prjzip or .zip file containing .mae files). This variable and/or sdf_file_path must be initialized.

• export_type (ExportType) – the data type for this batch

Varype map_file_path

str

Parameters

idx_lig_id_map (dict(int, str)) – a dictionary mapping export batch indices to ligand IDs

__init__(map_file_path, sdf_file_path=None, three_d_file_path=None, export_type=None, idx_lig_id_map=None)

Initialize self. See help(type(self)) for accurate signature.