2024-06-14 Release Note
The update for Hyper Lab on June 14, 2024, has been completed.
Hyper Lab Version : 2024.06.14
Changelogs
1. Change in Molecule Addition Method
The method of adding molecules through drawing or file upload has been updated.
Previously, after clicking a button, users would choose how to add molecules and data from a running screen. Now, after clicking the [Molecules/Data] button, users select the method of adding molecules and data directly from a displayed list, and then the appropriate interface for the chosen method is launched.
2. Improved File Upload Feature
The file upload functionality has been enhanced to allow not only the addition of molecular structures but also the selection and addition of data within the file directly into the fields of the Bench.
(1) File Upload Screen
In the Bench, by clicking on the [Molecules/Data] button and then [Upload file], the initial screen allows you to upload a file to add data, similar to the previous method.
File Upload Procedure:
Select the file you wish to upload.
Only files with the extensions SDF, CSV, TSV, CDXML can be uploaded.
Files with CSV and TSV formats cannot be uploaded with other types of files simultaneously.
If the total size of the files to be uploaded exceeds 50MB, the files cannot be uploaded.
Review the added files, then proceed with the file upload by clicking the [Add] or [Next] button at the bottom of the screen.
The [Add] and [Next] buttons may appear differently depending on the format of the uploaded file.
Optionally, you can perform selected calculations such as Hyper ADME/T or Hyper Binding concurrently with the addition by checking the corresponding buttons at the bottom of the screen.
The availability of these calculations depends on token possession within the Lab space and the presence of an active protein.
File Type-Specific Upload Procedures:
SDF, CDXML Files:
When uploading SDF or CDXML files, clicking the [Add] button at the bottom adds the molecules from the file to the Bench.
CSV, TSV Files:
Only one CSV or TSV file can be uploaded at a time (no simultaneous uploads with other files).
After adding a CSV or TSV file to the list, click the [Next] button at the bottom of the screen to proceed to the next page.
(2) CSV, TSV File Upload - Add as a New Molecule:
After uploading a CSV or TSV file and clicking [Next], you can choose between adding the data as ‘Add as a new molecule' or 'Merge to exisitng data’.
During the upload of CSV and TSV files, the following features can be utilized:
[Upload File Preview]
This feature allows you to verify that the file has been correctly recognized before uploading.
Files are displayed in a preview format, showing only the headers and the top 5 rows, which you can scroll through horizontally to ensure all columns are correctly recognized.
[Selecting molecule name and structure]
This section is crucial for adding new molecules as it allows you to identify and add molecule names and structures.
You must select these columns from the uploaded file.
Molecule name: Specify the column data to be added to the 'Name' field when a new molecule is added to the Bench.
Through the list in this area, you can select which column in the file should be designated as the ' Name' data.
If there is a column named 'Name' in the file, it is automatically recommended for matching.
Molecule structure: Specify the column that contains the Smiles data for representing the molecule structure in the Bench.
If there is a column named 'Structure' or 'Smiles', it is automatically recommended for matching.
[Selecting custom fields to match with columns]
After specifying the molecule name and structure, you can choose whether to add the remaining column data from the uploaded file to the Bench. This section allows you to select additional data from the uploaded file to be included with new molecules.
Columns of the file to upload: All recognized columns from the file are displayed. These can be added as data to the custom fields in Hyper Lab.
Custom Field: Choose the custom field where the column data will be added when incorporating it into the Bench.
The fields available for selection from the list are custom fields that have already been created in the current Bench. When data is added to an existing custom field, it is added to the Bench using the data type specified for that custom field.
Fields selected from the list cannot be duplicated across different columns, ensuring that each column is matched to a unique custom field.
Hyper Lab's default data fields cannot overwrite or add new data from the columns of the uploaded file.
If the uploaded file contains columns with names that match existing field names in Hyper Lab, an automatic recommendation for matching is made.
Add as a new field: When adding as a new molecule, the column's data can be created as a new custom field in the Bench. You will need to select the data type Text, Number, Tag) for displaying the column's data in this new field.
This is a field set as a merge key: The columns designated as molecule name and structure cannot be matched to new or other fields.
To match these columns to other fields, you must remove their assignment as molecule name or structure.
Data Type: When adding column data as a new field, specifying the data type is mandatory. You can add the data as Text, Number, or Tag.
[Update]
After all columns have been assigned to custom fields and data types have been selected, click the [Update] button to add the molecules.
(3) CSV, TSV File Upload - Merge to exisitng data
The merge to exisitng data feature allows for new data to be overlaid onto molecules already present in the Bench or for filling in empty values.
[Upload File Preview]
This feature allows you to verify that the file has been correctly recognized before uploading.
Files are displayed in a preview format, showing only the headers and the top 5 rows, which you can scroll through horizontally to ensure all columns are correctly recognized.
[Selecting molecule name and structure]
This section is crucial for adding new molecules as it allows you to identify and add molecule names and structures.
You must select these columns from the uploaded file.
Molecule name: Specify the column data to be added to the 'Name' field when a new molecule is added to the Bench.
Through the list in this area, you can select which column in the file should be designated as the ' Name' data.
If there is a column named 'Name' in the file, it is automatically recommended for matching.
Molecule structure: Specify the column that contains the Smiles data for representing the molecule structure in the Bench.
If there is a column named 'Structure' or 'Smiles', it is automatically recommended for matching.
[Selecting custom fields to match with columns]
After specifying the molecule name and structure, you can choose whether to add the remaining column data from the uploaded file to the Bench. This section allows you to select additional data from the uploaded file to be included with new molecules.
Columns of the file to upload: All recognized columns from the file are displayed. These can be added as data to the custom fields in Hyper Lab.
Update custom field: This section allows you to select the custom field in the Bench where you want to add data from the columns of the uploaded file. You can specify how to update each column’s data in the following ways:
Don’t use it: Do not update the data of this column in the existing molecule data fields.
Select custom field: Update the data within an existing custom field in the Bench with the data from the column.
The custom fields available for selection from the list are those already created by the user in the current Bench. When data is added to an existing custom field, it is incorporated according to the data type designated for that field and displayed in the Bench.
A custom field selected from the list cannot be matched with multiple columns; each custom field can only be linked to one column.
The default data fields provided by Hyper Lab cannot be overwritten with new data from the columns of uploaded files, nor can new data be added to them.
Add as a new field: When adding as a new molecule, the column's data can be created as a new custom field in the Bench. You will need to select the data type Text, Number, Tag) for displaying the column's data in this new field.
This is a field set as a merge key: The columns designated as molecule name and structure cannot be matched to new or other fields.
To match these columns to other fields, you must remove their assignment as molecule name or structure.
Update Method: Choose how to update the data into the selected custom fields from the columns of the uploaded shoe:
Keep existing: Do not add new data from the file’s columns; keep the data currently stored in the custom field.
Replace if empty: Update only the molecules in the selected custom field that have empty values with new data from the file’s column data.
Replace All: Update by overwriting all the data in the selected custom field with the column data from the uploaded file.
Data Type: When adding column data as a new field, specifying the data type is mandatory. You can add the data as Text, Number, or Tag.
[Add non-matching data as new molecules]
After updating existing molecules, any molecules in the uploaded file that do not match the existing data can be added as new molecules. If this option is unchecked, non-matching molecules will not be added as new molecules.
[Update]
After all columns have been assigned to custom fields and data types have been selected, click the [Update] button to add the molecules.
2. Improved Row/Column Adjustment Feature in Bench Tables
The functionality to adjust the height of rows and the width of columns in the Bench has been newly added and enhanced.
(1) Improved Bench Column Width Adjustment Feature
The previous method of displaying data with ellipses when the width of a column was narrowed has been improved. Text-type data is now left-aligned, and if the column width is reduced, the text will wrap to fit the height of the current row.
(2) New feature added for adjusting row height in Bench
The functionality to adjust the fixed row heights within the Bench table to desired heights has been added. If you adjust the height of a specific row by dragging, the adjusted height will be uniformly applied to all rows in the table.
3. Improved Filter Function for Number Type Data
The filtering functionality for number type data has been enhanced from a traditional conditional format to a more adjustable slider-based interface. The minimum and maximum values of the slider are set based on the lowest and highest values of the respective data field within the Bench.
4. Improvement of the Hyper Design Creation Status (AI) Data Field
The data in the ‘Hyper designed (AI)’ field, which previously included the [AI] tag for molecules generated by Hyper Design, has been updated. Instead of the [AI] tag, the following tags will now be displayed:
Replace: Indicates molecules generated through Hyper Design Replace calculations.
Add: Indicates molecules generated through Hyper Design Add calculations.
5. Improved Navigation to Detail View
The method of accessing detailed views by selecting a molecule and using the menu displayed at the bottom has been improved. Now, by simply hovering over the molecule name data, a [Go to details] icon will appear, making it easier to quickly access detailed information.
6. Addition of Distance Measurement Method between Ligands in 3D Viewer
The functionality of the right-click in the 3D Viewer has been changed from activating the magnifying feature to measuring distances between atoms and proteins.
The method for measuring distance is as follows:
Right-click the mouse at the starting point of the measurement.
While in this mode, right-click the mouse at the endpoint of the measurement.
Right-click the mouse again at the endpoint, and the distance between these points will be displayed as a green dotted line.
Bug fix
Bug fixes and stability improvements have been made.
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