Actions

Convert to Structure by ID from Database

With these options, you can specify the database and conversion settings for the following actions:

• Import from Database by IDs

• Resolve IDs into Structures

The figure below shows the available database and conversion settings.

Database Setting

By using these options, you can specify the database, table, and column from which you would like to import data.

Connection Name

All available databases are listed in the Select Entity dialog.

Entity Name

This field is automatically filled when a connection selected.

Entity Type

This field is automatically filled when a connection selected.

ID Column Name

Use the combo box to specify the name of the ID column.

Structure Column Name

Use the combo box to specify the name of the structure column.

Molecule Format

If you know the format of the structures to be imported, you can specify it by using the drop-down list. This speeds up the import process.

By default, the format is not specified.

Conversions

Convert Selection Only

Use this option to specify whether the Selection only box is automatically checked or not.

The possible values for this option are as follows:

• TRUE

• FALSE

• DEFAULT

The default value is DEFAULT, which is equal to FALSE.

Convert to Structure by ID from Compound Registration

With these options, you can specify the connection and parameter settings for the Resolve CompReg IDs into Structures action.

The figure below shows the available connection and parameter settings.

Connection

URL

Specify the URL of the CompReg database.

User Name

Specify the user name which can be used for login.

Password

Specify the password that is associated with the user name.

Parameter

Compound ID Type

Use this option to specify the compound ID type. The specified type must match the ID types on your sheet.

The following types are available:

• Lnb

• LN

• CN

• PCN

• LotId

• StructId

The default type is Lnb.

Convert HELM to Structure or Structure to HELM by Biomolecule Toolkit

With these options, you can specify the database and conversion settings for the following actions:

• ConvertHelmToStructureAction

• ConvertStructureToHelmAction

in Conversions

The figure below shows the available database and conversion settings.

Connection

URL

Specify the URL of the HELM to Structure - Structure to HELM service, http and secure https can be handled as well.

User Name

Specify the user name which can be used for login.

Password

Specify the password that is associated with the user name.

Parameters

Compound ID Type

Use this option to specify the default output display of peptide structures after the conversion.

The following types are available:

• Enable Explicit Hydrogens

• Expand Branching Amino Acids

• Expand Non-natural Amino Acids

The default type is False to all 3 options. The detailed description of these parameters are in the documentation of the Biomolecule Toolkit.

Convert from Structure

The figure below shows the available convert from structure options.

Placement

Placement

By using this option, you can specify whether the results of the conversion process replace the structures or not.

The available values are as follows:

• Replace

• InsertRight

The default value is Replace.

Convert to Structure

The figure below shows the available convert to structure options.

Cell Size

Resize to Default

By using this option, you can specify whether cells are resized to default before the process or not.

The available values for this option are as follows:

• TRUE

• FALSE

The default value is FALSE.

Placement

Placement

By using this option, you can specify whether the results of the conversion process replace the texts or not.

The available values are as follows:

• Replace

• InsertRight

The default value is Replace.

Statistics

Display Statistics

By using this option, you can specify the statistics display behavior.

The following values are available.

• On

• Off

• Warnings

The default value is Warnings. In this case, only issues are displayed, but no conversion report is generated.