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3.5.1 Options for Updates and New Projects

The Tools->Options for Updates and New Projects menu selection in ChemTree is only available from the opening screen prior to opening a project or starting a new project. The script server settings are only available under this menu selection. All the other option settings are the same as those available under the Current Project’s Options, but while options selected under Current Project’s Options are applied only to the currently-open project, the Options for Updates and New Projects allow you to set up default parameters for ChemTree that persist from one invocation of the program to another. New projects will inherit these options.

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Selecting Tools->Options for Updates and New Projects brings up a dialog with four tabs. The first two control the Tree and Node View parameters. The last two tabs control ChemTree’s Appearance and script server settings.

3.5.2 Current Project’s Options

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When a project is open and you select Tools->Current Project’s Options (Fig. 3.16), your settings only affect the open project.

Selecting Tools->Current Project’s Options in a project brings up a dialog with three tabs. The first two control the Tree and Node View parameters. The last tab controls ChemTree’s Appearance settings.

NOTE: To change the script server settings, please exit the current project and use Tools->Options for Updates and New Projects to access the script server setting tab.

3.5.3 Project Option Settings Available

3.5.3.1 Tree Options

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The Tools->Options for Updates and New Projects->Tree tab (Fig. 3.17) and the Tools->Current Project’s Options->Tree tab can also be accessed from within the tree settings window. Note that modifying options under Current Project’s Options sets a default for all trees in the current project, whereas modifying options from the tree settings modifies the options for that particular tree. (Modifying tree options under Options for Updates and New Projects sets defaults for project-wide tree option defaults.)

The Section (7.2) Setting Options for Tree Analysis discusses the various tree option settings in detail.

3.5.3.2 Node View Options

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This tab on the dialog allows you to control what calculated values will appear in the tree nodes. To add one of these values to the node display, click the associated check box. You can use this to avoid clutter and see just the values you wish. Again the project-wide option set from the main window can be overridden within any specific tree.

NOTE: The last check box, which only appears when setting either Options for Updates and New Projects or Current Project’s Options, determines whether you want to allow yourself to delete (not tree nodes, but) navigator nodes within new projects or within the current project.

3.5.3.3 Appearance

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Depending on your license, there may be features in ChemTree you are not authorized to use. You can choose how these features are displayed in menus using the Hide disabled menu options check box. If this box is checked, menu items representing unlicensed features are not displayed. If this box is unchecked, unlicensed features will be shown, but they will be disabled.

If you are running ChemTree under Linux, you will also be able to specify your preferred browser for displaying ChemTree help (accessed by pressing F1). Multiple browsers may be specified, and will be tried in order until a working location is found, or the list of browsers is exhausted. To add a browser to the list, first enter the path to the browser you would like to add, or select Browse to browse for it. Then click Add to add that location to the list of browser locations. The order in which the browsers are tried can be changed by using the Up and Down buttons to move browsers up and down in the list.

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3.5.3.4 Other

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This tab is used to set up communications with a script server. A script server is a feature of ChemTree that provides a central location for publishing scripts that all users can access. The first two parameters will probably be supplied by your system administrator and will depend on where the server has been installed. The Timeout for Connection to Server specifies how long ChemTree will continue to attempt making a connection before reporting an error. The Frequency to Update Menu Listings determines the time interval for synchronizing with the script server. This means that when new scripts are published to the server they will not appear in you local menu system until the next time you synchronize. The Test Server Connection button is a quick way to verify that your settings are correct and the server is running. A message will be displayed indicating whether the server is running or not.

The final button Install Python in Windows Registry applies only to Windows users. This button will make changes to your registry so that any additional Python packages you install will be available from the Python that is distributed with ChemTree.

3.5.4 View Project Log - Sorted by Node

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3.5.5 View Project Log - Chronological

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3.5.6 Run Script

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You may chose this option at any time to invoke python scripts. With this method, you can run scripts that can be run from the ChemTree menus, or scripts that could be run from the command line. More information on scripting can be found in chapter 5.3.

Activating the Tools->Run Script menu option will display a dialog prompting for the location of the script that you would like to run. You can then enter the path to the desired script manually, or use the browse button to browse to it. Once the location of the script is filled in, click Run Script to start the script.

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3.5.7 Run Python Shell

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To access the interactive scripting feature of ChemTree open the shell window from the Tools menu. The full functionality of ChemTree is accessible through the ghi object that will already be available to you. See 5 for a complete list of script objects and methods. If you are unfamiliar with Python, a good starting place is . The Python Quick Reference web site and the Dive Into Python online book are other noteworthy resources you may find on the web. From the shell you can also type help() to use the built-in documentation and help(ghi) to list the documentaton for the ghi module.

The Python Shell Window has a tool bar with a couple useful buttons listed below from left to right:
∙ Clear Shell - Erase the command history and clear the text on the shell.
∙ Open a Script - Run a script from which each line will be executed in the shell.
∙ Save as Script - Save the command history (not the output of the commands) as a script.

It may be useful when developing a script to experiment interactively in the ChemTree shell. Once a solution has been reached, the Save as Script button can be used to save the current history into a text file which can later be edited to make finishing touches.

3.5.8 Update ChemTree

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You can program ChemTree to automatically check for updates. The default is once every two weeks.

Clicking the menus selections Tools->Update ChemTree or pressing keys Alt+T and then U will launch a manual check for a ChemTree update. The updating process uses the Internet to access the Golden Helix web site and check for an update.

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Similar to when you first installed ChemTree, you can optionally adjust settings by clicking the Proxy Settings button. The settings that you successfully used to install the software the first time are retrieved and used when checking for updates. If these have changed, for example because your proxy server has changed, you may need to adjust these settings.

If a ChemTree update is found, it is downloaded to a temporary folder, and then you are prompted to proceed with installation. If you have the most recent version, the following dialog appears.

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