Actions

    Convert to Structure by ID from Database

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

    The figure below shows the available database and conversion settings.

    images/download/attachments/1806980/Convert_to_Structure_by_ID_from_Options.png

    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.

    images/download/attachments/1806980/Convert_to_Structure_by_ID_from_Compound_Registration_Options.png

    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.

    images/download/attachments/1806980/image2020-10-8_17-10-23.png

    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.

    images/download/attachments/1806980/Convert_from_Structure_Options.png

    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.

    images/download/attachments/1806980/Convert_to_Structure_Options.png

    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.