FEP+ to LiveDesign Export Panel

FEP+ to LiveDesign Export Panel Features

• Export to LiveReport options
  • Existing LiveReport
  • New LiveReport
• Map Maestro properties to LiveDesign properties section
  • Mappings link
  • Entity registration status options
  • Select Maestro properties: n selected link and menu
  • Properties table
• Match existing compounds by options and menu
• Choose data accessibility options
• Use pose name option and button
• Structures to export text
• Job name text box
• Restore settings from last export option
• Next button
• Cancel button

Export to LiveReport options

Choose the means of specifying the LiveReport to export to. The choice determines the controls that are displayed immediately below.

Existing LiveReport option

Select the option to export to an existing LiveReport by specifying the Project and LiveReport or by pasting a URL or ID.

• Project option—Choose the LiveDesign project you want to export the data to. The dropdown menu lists the projects that are available on the LiveDesign server you connected to. From the LiveReport dropdown menu, select a LiveReport from the Project selected.

• Paste LiveReport URL or ID text box and button—export to the LiveReport specified by a URL or by a report ID (number). Paste or type the URL or the ID in the text box. You can choose recently used LiveReport URLs or IDs from the dropdown menu that appears when you click the text box. Click the Load button to the right of the text box to load the information specified by the URL or ID. The project and LiveReport associated with the URL or ID are reported below.

New LiveReport option

Select the option to export to a new LiveReport by specifying the Project, name, and template to use.

• Project, Name, and Template fields—Choose the LiveDesign project you want to export the data to. The dropdown menu lists the projects that are available on the LiveDesign server you connected to. In the Name field, enter a name for the new LiveReport. You can also select a template (or blank template) to use from the Template dropdown.

Map Maestro properties to LiveDesign properties section

Mapping link

Save and load maps of Maestro properties to LiveDesign fields. The maps are used to populate the columns in the Map Maestro properties to LiveDesign properties table. Saving maps and reloading them avoids having to specify the mapping of each Maestro property to the corresponding LiveDesign column every time you perform an export.

Clicking on the Mapping dropdown shows a list of existing mapping names to select from.

Clicking on the "..." to the right of the Mapping dropdown opens the Export Mappings Manager Dialog Box, where you can Create New, Edit, and Delete mappings, as well as to Import or Export mappings.

Clicking on the Clear link will deselect the mapping name from the Mapping dropdown and deselect any Maestro properties for export.

Entity registration status option (for Generic Entity export only)

Select the entity registration status, either All new entities (default) or All registered in LiveDesign. If the All new entities option is selected, then all entities that do not exist in LiveDesign will be dropped from the export. If the All registered in LiveDesign option is selected, then all new generic entities will be dropped from the export.

Note: For Generic Entity export, if the file format is .cms, a zip file containing the .cms and the associated trajectory data will be exported. If the trajectory is not available, only the .cms will be exported.

Select Maestro properties: n selected link and menu

Click the n selected link to open a menu and choose the Maestro properties that you want to export. Only the properties that you choose to export will be exported. n is updated to show how many properties you have selected. Note: A warning icon will appear if a mapping is created with a property which is unavailable in the Project Table. You can still continue, but these unavailable properties will not be exported.

The properties are shown in a tree. You can search for the properties you want by typing in the search bar. The list is filtered as you type. To remove the filter, delete the text.

By default, several properties under FEP+ will be checked. In addition to properties generated by various applications, there are several other properties you can upload:

• 3D structures, under 3D Data. You can export the original ligand structures (3D Data item) and the representative structures for perturbations from each ligand (Representative Snapshots (3D) item). The representative structures can only be exported if you also export the original structure. For a given ligand, representative structures are exported for each connection ("edge") from that ligand to other ligands. The original structure and the representative structures are exported to the same column in LiveDesign, which is named 3D and cannot be changed in this panel. Representative structures for covalently bound ligands may be exported as entire complexes.
• The perturbation map (.fmp) file, under FEP map. The file is uploaded, and a link to this file is shown for every ligand it contains, in the specified endpoint column. The file can be downloaded from LiveDesign, allowing you to use it again in FEP+. If you upload the file again with the same model name, the file is replaced for each exported ligand, either globally or for the chosen LiveReport.
• The date of upload, under Other.
• Notes, under the Other options. These are entered in a dialog box, which you open by clicking Options in the table row. The notes are added to the LiveReport for each ligand, in a freeform column.
• Additional properties include: Core Smarts, FEP Type, FMP Filename, Web Services ID, Receptor Title, FEP User (Uploader), Schrödinger version, and Host.

Properties table

This table lists the Maestro properties that have been chosen for export, and allows you to map them to a LiveDesign column folder and property. The table has three columns.

• Maestro Property—Name of the Maestro properties that were selected in the Maestro properties list.
• LiveDesign Column—Name of the model or assay column folder in LiveDesign that you want to add the data to. Opens the LiveDesign Column Pane.
• LiveDesign Property—Name of the column in the LiveDesign report that will display the Maestro property. Opens the LiveDesign Property Pane.
• Options—Set options for the selected Maestro property. Click in the column to open a dialog box for setting the options, e.g. selecting the affinity units. Note that options for the predicted affinity are also applied to the predicted error, and are set from the predicted affinity cell: the predicted error cell is disabled, and shows a copy of the predicted affinity cell.

Match existing compounds by options and menu

Match existing compounds in the LiveReport by the property chosen from the following options:

• Structure—Match the compound by its 2D structure.
• Corporate ID—Match the compound by the corporate ID stored in a specified Maestro property. A Select column button is displayed. Click this button to open a property selector so you can select the Maestro property that contains the desired corporate ID. Note: If you select more than one entry with the same Corporate ID, only the first instance will be exported.

Choose data accessibility options

Choose where the exported data can be accessed in LiveDesign from the following options:

• Unpublished—Export the data so that it is only accessible for the selected LiveReport.
• Published—Export the data so that it is accessible from any LiveReport within the selected project.

Use pose name option and button

Choose a name template used for naming the exported poses. After checking the option, text displaying the current name template appears below. Click the Define button to set up the name template. Opens the Pose Name Specification dialog box, in which you can specify a short prefix to be used for all poses (Custom text box), then check the Include structure property option to select a structure property for the rest of the name (Select button). The prefix should be short as there is not much space in LiveDesign for the name. It should include any characters to separate it from the structure property, such as space or underscore. The structure property can be a string or a numerical value, such as a binding free energy. If a property is not given, the pose names will all be the same.

Structures to export text

This text gives a summary of the structures that will be exported. The number of total entries is displayed.

Job name text box

Specify a name for the export task.

Restore settings from last export option

This option is disabled by default. Select this option to clear the table and restore the settings used in the last export.

Next button

Display a summary of the export and its destination in LiveDesign for confirmation, then start the export. The job is run asynchronously, so you can continue with other work while it runs. When the export finishes, a dialog opens with a link to the uploaded LiveReport.

Note: If the user does not have Administrator permissions for a project involving generic entities and clicks Run, an error message will appear stating that only Admins and Project Admins have permission to export generic entities.

Cancel button

Go back to the FEP+ panel, and close this panel.. This allows you to choose a different set of structures and add their properties to LiveDesign.