8/18/2018 Introducing MOE

Introducing MOE
● Overview of MOE
○ MOE's Multi-Tasking Environment
○ MOE's Batch and Web Modes
○ MOE's Multi-Processor Mode (SMP)
○ Customize MOE with SVL
○ Sample Programs
○ Journal of the Chemical Computing Group
○ SVL Exchange
● Manuals and Manual Conventions
○ Table of Contents
○ Keyboard Commands
○ MOE Windows
○ Menu Commands
○ SVL and Shell Commands
○ Examples
○ Additional Information
● MOE Graphical User Interface (GUI) Basics
○ Command Line Interface (CLI)
○ Prompts
○ Menus
■ Keyboard Accelerators (Hot Keys)
○ Bubble Help
○ Window Objects
○ File Selection Box
■ Single File Selection
■ Multiple File Selection

Overview of MOE
MOE, Chemical Computing Group's Molecular Operating Environment, is an interactive, windows-based chemical computing and
molecular modeling tool with a broad base of scientific applications:

Biologics Alanine / Disulfide / Resistance / Residue Scan, Sequence Design, Patch

Analyzer, Properties, Rotamer Explorer, Antibody Modeler

Bioinformatics Structure and Family Databases, Fold/Homologue Identification, Kinase Search,

Alignment, Superposition, Consensus

Protein Modeling Homology Modeling, Residue Mutation, Mechanics, Dynamics, Analysis, Protein
pKa

Ligand-Based Drug Design Ligand Explorer, Medicinal Chemistry Transformations, BREED: 3D Ligand
Generator, Scaffold Replacement, Fragment Analysis, Solvation, Pharmacophore
Discovery, Conformational Analysis, Protomers and Tautomers

Structure-Based Drug Design Solvent Analysis, Surfaces and Maps, Docking, Protein-Ligand Interactions and
Fingerprints, 3D Protonation State Assignment, Protomers and Tautomers

Cheminformatics Descriptors, Similarity and Diversity, Conformation Databases, 3D Search,

Pharmacophore Queries/Elucidation/Linkers, 2D Depiction, Structure-Activity
Analysis, RECAP Analysis, SD Pipeline Commands

High Throughput Discovery Combinatorial Library Design, HTS Analysis, Binary QSAR

Molecular Modeling and Forcefields, Electrostatics, Mechanics, Dynamics, Diffraction, 3D Molecule

Simulations Builders, Molecular Surfaces

Methodology Development Prototyping, Integrating, Distributed Computing

and Deployment

MOE/web SD Filter, Structure Activity Report, Homology Search, Small Molecule

Properties, Database Browser, SOAP Server

MOE provides a comprehensive and interactive visualization interface that permits multiple views of a molecular system:

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● MOE Window. This is MOE's primary interface window, which opens on startup. Molecular systems are displayed in a variety of
styles and can be selected and manipulated here. The MOE Window is the primary launch point for virtually all MOE
applications.

● Sequence Editor. This window displays a chain and residue representation of molecular systems that is well-suited for
biopolymer applications.

● System Manager. This window lists the molecular objects loaded in MOE and controls their visiblity, active state, and look.

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● Atom Manager. This window displays properties of molecular objects loaded in MOE.

● Database Viewer. A viewer for the display MOE databases and for the management of large collections of molecules or the
many conformations of a single molecule.

The MOE interface can be either menu-driven or command-line based, or a combination of both. The SVL Commands window
displays the output generated by SVL commands and MOE applications. MOE also includes an assortment of management windows
that control such features as geometric constraints, debugging, module loading, and task control.
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MOE is a cross-platform application that has been designed to operate on desktop equipment without limiting either the size of the
molecule under study or the kind of calculation that can be performed. Special purpose graphics workstations or terminals are not
required to run MOE effectively. To see a full list of supported platforms, refer to Installing and Running MOE and MOE/batch.

MOE also provides access to shell commands and to external software programs such as NAMD, GOLD, MOPAC, POV-Ray, and
PSILO, among others, as well as a variety of relational databases.

MOE's Multi-Tasking Environment

MOE is multi-tasking, making it possible to have multiple commands active at once. For example, you can monitor the potential
energy of a molecular system visually by coloring the atoms according to calculated forces, concurrently with the actual potential
energy minimization task itself. Any number of applications can be open and run simultaneously.

MOE's Batch and Web Modes

MOE can be run as a batch process. The application is called MOE/batch, and provides all of the features of MOE, including multi-
tasking, but without any graphical interfaces.

MOE applications can be invoked in MOE/batch either directly from the MOE/batch command line or from within SVL scripts or
programs to run as batch jobs. SVL scripts and programs can be used to automate workflow, and are convenient for performing
repetitive tasks or for modifying options. The following applications will generate custom SVL batch files from the parameters
provided in the graphical user interface (GUI):

Docking Ligand-receptor docking.

Dynamics Molecular dynamics simulation.

MedChem Transformations Rule-based ligand transformation.

BREED Ligand generation from existing ligands by genetic crossover.

Scaffold Replacement Ligand generation by replacement of a portion of the compound, preserving the
remaining chemical groups.

MOE/batch is used when web access to MOE is desired. MOE/web is a gateway between a web browser and the batch version of
MOE. Its purpose is to allow distributed access via networked computers to custom SVL programs or MOE built-in applications. The
MOE distribution includes a number of MOE/web applications.

For more information on MOE/batch, please see Installing and Running MOE and MOE/batch. For more information on MOE/web,
please see Installing and Running MOE/web.

MOE's Multi-Processor Mode (SMP)

MOE/cluster (MOE/smp) (Scalable Multi-Processor) is an enhancement to MOE and MOE/batch, allowing several MOE processes
to cooperate on large-scale distributed computing jobs. A single MOE session can harness the power of a heterogeneous collection
of computers, including laptops, workstations, and multi-processor supercomputers, each running a different operating system,
including various flavors of both UNIX and Windows.

The following computation-intensive applications in MOE are designed to run in parallel if MOE/cluster (MOE/smp) is enabled:

Conformation Import Small molecule conformation generation.

Database Partial Charges Compute partial charges for entries of a molecular database.

Docking Ligand-receptor docking.

Flexible Alignment Flexible alignment of small molecules.

Homology Modeling Protein homology modeling.

Model-Evaluate Evaluation of pharmacophore queries, QSAR models, fingerprint models, and composite
models for entries of a molecular database.

Potential Energy Potential energy evaluation.

Combinatorial Library Combinatorial library enumeration and estimation of activity of R-group and scaffold
molecules in a virtual combinatorial library.

To find out more about MOE/cluster (MOE/smp), please see Installing and Running MOE/smp.

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Customize MOE with SVL

MOE's open architecture combined with a built-in high level programming language SVL, the Scientific Vector Language, provides a
high degree of flexibility. Using MOE and SVL, new ideas and methods can be explored and implemented in a matter of hours.
Applications written in SVL automatically port to all platforms on which MOE runs.

For information on how to use custom MOE SVL files or how to customize the MOE menus, please see Configuring and Customizing
MOE. For information on customizing the default visualization settings, please see Visualization Setup.

Sample Programs
The MOE package includes a variety of sample SVL programs, which are located in the $MOE/sample directory and demonstrate
practical uses of SVL programming. These samples are examples of non-trivial applications that have been coded in SVL.

Journal of the Chemical Computing Group

The Chemical Computing Group web site contains the Journal of the CCG, a collection of articles describing specific applications and
algorithms in MOE. New articles are generally published with new releases of MOE, and highlight selected features of scientific and
general interest.

SVL Exchange
The SVL Exchange is a repository of programs and code samples written in SVL by users and developers of MOE. The SVL Exchange
is a valuable resource for users seeking specialized applications, utilities, or customizations for MOE.

Manuals and Manual Conventions

The MOE manuals comprise the following volumes:

● MOE Manual. Manual pages describing the MOE interface and MOE applications.
● SVL Function Reference. SVL function reference pages.
● Tutorials. Application tutorial pages.
● Programming Manuals. Scientific Vector Language (SVL) Manual and tutorials, and the C API Manual and Function Reference.
To obtain the C API package, please contact the Chemical Computing Group support department.

The MOE manuals can be launched in a browser from the MOE | Help menu:

MOE | Help Description

Contents Table of Contents

Panel Index Links to application manual pages

Function Index Links to SVL function reference pages

Mouse Mouse Reference panel

Tutorials Menu of tutorial pages

Release Notes Summary of what is new in the current release

In the manuals, it is assumed that you are using a three-button mouse. For information on using a two-button mouse, please see
Using the Mouse.

Table of Contents
The table of contents can be displayed in Short or Long form. In Long mode, all links on the table of contents page are shown. In
Short mode, only the section headings are displayed. Clicking a section heading or icon will show the links to the pages in that
section. Tutorial links are given by the school children icons.

A keyword search is available from the main table of contents. Type in the words of interest in the textfield located at the top of the
page and press Search. A list of relevant pages will be displayed.

To return to the MOE Table of Contents at any time, click on CCG logo in the upper right corner or scroll down to the bottom of the
manual page you are viewing and use the link titled MOE Table of Contents.

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Keyboard Commands
The manual uses the following conventions for keystrokes:

Key Description

Shift The Shift key, sometimes in combination with the mouse.

Shift+

Ctrl The Ctrl key, sometimes in combination with the mouse or another key.
Ctrl+

Alt The Alt key, sometimes in combination with the mouse or another key. Click here for workarounds if the
Alt+ system is missing this key.

Enter The Enter or Return key, used to enter information in textfields.

MOE Windows
This is how the primary windows of MOE are referenced in the Manual:

Window Description

MOE The MOE Window, which is primary interface window of graphical MOE, containing the 3D rendering area.

DBV A Database Viewer, used for examining the contents of MOE databases. More than one can be open at any given time.

SE The Sequence Editor, which provides a sequence-only view of molecules currently loaded in MOE.

SVL The SVL Commands window, in which output from applications is displayed, and where SVL commands can be entered.

TED The SVL Text Editor. This is a general text editor, with special support for SVL files.

Here are some components of the main windows:

Name Description

MOE | Footer The footer area of the MOE Window.

MOE | RHS The Right Hand Side button bar of the MOE Window.

CLI The Command Line Interface, a textfield where SVL commands can be entered. Certain applications
will temporarily replace the CLI with a prompter.

Settings The MOE, Sequence Editor, and Database Viewer windows each have a Settings menu accessible
from their menu bar and represented by a gear icon.

The SVL Commands window, the Sequence Editor, and any open Database Viewers can be raised using the eponymous buttons in
the MOE menu bar. These buttons are referenced as MOE | SVL, MOE | SEQ, and MOE | DBV, respectively. The DBV button
opens a menu listing the currently open viewers and is greyed if there are none open.

Menu Commands
Throughout the manual, menu items and window options are referred to using a shorthand notation:

Window | Menu | Submenu | Menu Item

For example:

MOE | Compute | Pharmacophore | Query Editor

Panel options are similarly specified:

Panel | Menu Title: Menu Item

or
Panel | Button Title: Button Name

For example, in the Pharmacophore Query Editor:

Query Rendering: Custom

Create: Feature

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Here is a list of the standard popup menus in MOE:

Menu Description Click right mouse button...

MOE | Popup MOE Window 3D rendering area popup. In the 3D rendering area.

MOE | Footer | Trackball Popup The View menu. On the MOE Window footer trackball.

DBV | Field Popup The Database Viewer Field Popup menu. In a field title (column heading) in the
Database Viewer.

DBV | Entry Popup The Database Viewer Entry Popup menu. On a entry number in the Database
Viewer.

DBV | Cell Popup The Database Viewer Cell Popup menu. On a cell containing numeric or
character data in the Database Viewer.

DBV | Molecule Cell Popup The Database Viewer Molecule Cell Popup menu. On a cell in a molecule field of the
Database Viewer.

DBV | Plot Popup The Database Viewer Plot Popup menu. In the plot area of the Database Viewer.

SE | Tag Popup The Sequence Editor Tag Popup menu. On the Tag Header or a tag name in the
Sequence Editor while holding <Ctrl>.

SE | Chain Popup The Sequence Editor Chain Popup menu. On the Chain Header or a chain number
in the Sequence Editor while holding
<Ctrl>.

SE | Residue Popup The Sequence Editor Residue Popup menu. In the residue drawing area of the
Sequence Editor while holding <Ctrl>.

SE | Residue Column Popup The Sequence Editor Residue Column Popup menu. In the Sequence Editor alignment ruler.

TED | Popup The SVL Text Editor popup menu. The popup menu In the SVL Text Editor writing area.
submenus are duplicates of the SVL Text Editor
menus.

SVL | Popup The SVL Commands window popup menu. In the SVL Commands window display
area.

The System Manager, MOE | RHS | System, is used to manage molecular systems in MOE.

The MOE | RHS | Themes menu is used to access both built-in and custom themes, as well as copying pictures to the
clipboard or saving them to files in a variety of possible formats.

SVL and Shell Commands

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SVL commands entered at the CLI are indicated by the svl> prompt. The return value, if any, is displayed on the following line
(without the prompt). E.g.

svl> igen 5
[1,2,3,4,5]

Shell commands are indicated by a % prompt. E.g.

% moebatch

Examples
Examples are highlighted in the text of the chapter. For example:

Example
An example of an example.

In the table of contents at the top of each manual page, the links to examples are similarly highlighted:

● Section 1
● Example 1
● Section 2
● Example 2

Additional Information
Additional information, for example, in-depth details on a particular subject, is sometimes provided in a text box.

Additional Information
An example of how supplementary details may be displayed.

MOE Graphical User Interface (GUI) Basics

This section gives a brief description of the basic objects used by MOE's graphical user interface (GUI).

Command Line Interface (CLI)

The Command Line Interface, or CLI, is used to invoke commands and SVL routines as well as to enter SVL statements and
expressions.

In fact, all MOE menu and command actions are mapped to SVL routines, and can be initiated directly from the CLI. For more
information, see the SVL Commands window.

Prompts
When certain commands are selected, the CLI changes to a prompt area. For instance, choosing
MOE | Edit | Measure | Distances in the MOE Window changes the CLI to an atom editing prompt as shown in the figure below:

In addition to the MOE Window, both the Sequence Editor and the Database Viewer make use of prompts in the CLI. Pressing Esc or
the red 'X' removes the prompt and returns the CLI to its normal state.

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In MOE 2012.10, prompts do not stack. When two prompts are raised in succession, the invoking the second prompt will cause the
first one to be canceled. If, during prompting, you wish to enter an SVL command, use the SVL Commands window, or another CLI
in the system (e.g. in the Sequence Editor); while one CLI is occupied by a prompt, other CLIs function as usual.

Finally, it is possible to add a CLI widget to any panel or window in MOE. For more information on widgets see the SVL Window
Toolkit.

Menus

Menu Bars

A menu bar appearing at the top of each MOE window displays the pull-down menus associated with the window. The look of menu
bars may differ slightly from platform to platform.

Pull-Down Menus

To open a pull-down menu, click on its name or type in its mnemonic. Mnemonics are key combinations used to open and navigate
pull-down menus without using the mouse. Each menu has one of its letters underlined; pressing this key in conjunction with the
Alt key is referred to as the mnemonic. For example, you can open the File menu by pressing Alt+F. This has the same effect as
clicking on File in the menu bar. Once open, the up and down arrow keys and mnemonics (in this case, solely the underlined letter
suffices) may be used to traverse the menu. The left and right arrow keys can be used to open successive menus in the menu bar.

To close a menu, press Esc or click away from the menu. The rest of the application is unresponsive to events until the menu is
serviced. Menus are automatically closed when windows are resized, repositioned, or hidden.

Menu Entries or Commands

Menu entries (also called commands) can be selected by:

● Clicking on the menu entry and releasing the mouse button. You can also perform the same operation in a single click-drag-
release operation.

● Pressing Return after having traversed (using arrow keys) an open menu.

● Typing the mnemonic of a menu item in an open menu.

● Typing the keyboard accelerator (described below).

Menu entries are greyed when a menu is context-sensitive and the action corresponding to the command would have no effect or is
not permitted.

Certain menu commands provide accelerators, or hot keys, for quick access. Accelerators appear to the right of their
corresponding menu command, and are usually of the form Ctrl+key. An accelerator can be used anywhere in a window,
but only while the window in question is active (i.e. has the focus). The following hot keys are noteworthy:

Shortcut Description

Ctrl+C Copy
Ctrl+V Paste
Ctrl+X Cut (text only, e.g. CLI, SVL Text Editor)

Ctrl+Z, Cmd+Z Undo

Ctrl+Shift+Z, Redo
Cmd+Shift+Z Redo
Ctrl+Y, Cmd+Y

Ctrl+R Raise all MOE Windows.

Del Delete the currently selected molecular objects.

Space Open the Command Line Interface (CLI) in the MOE Window/Sequence
Ctrl+Space Editor/Database Viewer.
Open the SVL Commands window.

An arrow indicates a pull-right menu.

... The trailing ellipsis indicates that a dialog box or a prompter in the CLI area will appear after selecting that command.
The prompter prompts for information which the command requires; for example, MOE | Edit | Measure prompts for
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atoms to use for the meters.

A toggle box (also called checkbox) shows the activation state of an attribute. A black indicator is used to show that the
attribute is enabled. To toggle, click on the box or press Return.

Popup Menus

Popup menus are used in many MOE windows and panels. To display a popup, position the cursor over the area and press the
mouse popup button.

Bubble Help
Bubble help appears when the cursor is placed over an interface control and held motionless for a moment. A small popup gives a
short description of the object in question. Bubble help disappears when the mouse is moved again.

If you are not seeing bubble help, it may be because it has been turned off. To configure bubble help, use the Miscellaneous page of
the Configuration Options panel ( MOE | Settings | Miscellaneous).

Window Objects

Checkbox

A checkbox is a toggle. When enabled, the box is drawn with a black square. Click on either
the graphical check box or on its label to toggle its state.

Color

The color chooser widget allows for selecting from a standard palette or for specifying a
custom color. When opened, the color chooser shows a bank of preset standard colors along
with recently-used colors.

Pressing the arrow button pulls down the custom color selector. A custom color can be chosen
either by dragging the crosshair over the color chart

and then adjusting the luminosity (intensity) by dragging the luminosity pointer,

or by specifying the color numerically in the RGB (Red-Green-Blue) or HSL (Hue-Saturation-

Luminosity) text fields at the bottom. The values can be given in either decimal or
hexadecimal format (in the latter case they must be prefixed by 0x) and are clipped to the
range [0..255] ([0..0xFF]). To use hexadecimal format, the Display Hex option must be on.

Certain applications have transparency enabled in the color widget. Transparency values are in
the range [0..255], where 0 is opaque.

The custom color is shown in the New box, which updates dynamically, and can be compared
with the Current color, displayed immediately below.

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Pressing OK puts the new color into effect and adds it to the front of the Recent Colors bank.
Cancel will leave the color chart in the current state, but will not put the new color into effect.

Listbox

A listbox displays a set of strings in single- or multi-column mode. The list entries can be
selecting using the mouse. Scrollbars are used to navigate long lists; the scroll mouse can also
be used to scroll through a list. If a list has a header and each list entry comprises a number
of fields, the header may provide a heading for each field. Clicking on a field heading results in
the list being sorted according to that field.

In MOE, there are single-select lists and multi-select lists:

a. Single-select lists allow the selection of a single entry at a time. In other words, clicking
on a new item automatically deselects the currently selected item. Depending on the list,
double-clicking on the selected item might perform an action.

b. Multi-select lists allow the simultaneous selection of several items in the list. Multi-
select lists are used for operations, such as choosing QuaSAR descriptors, that allow the
user to select more than one item.

There are two types of multi-select lists:

In the first type (referred to as multi-select style 1):

● To select one or more items, click on them. This is known as additive selection.
● To deselect an item, click on it again. This toggles its selection state.
● To select a range of entries, click on the first item then press Shift as you click on
the second.
● To clear the selection, press Ctrl and click anywhere in the list.

In the second type (referred to as multi-select style 2):

● To select an item, click on it. However, this will deselect any other selected items.
● To toggle the selection state of an item (or select non-consecutive items), press
Ctrl-click.
● To select a range of items, press Shift-click.

A List popup menu is displayed by placing the cursor over the list area or header and pressing
the mouse popup button. The List popup includes:

● Clear Selection
● Select All
● Invert Selection
● Scroll to First Selected
● Scroll to Last Selected
● Reset Sort Order
● Copy to Clipboard

Material

The material chooser widget allows for selecting from a standard palette or for specifying
custom material properties. When opened, the pull-down shows a bank of preset standard
materials along with sliders for customization. The widget has different options:

● Front and Back. In this mode, the widget maintains separate material properties for the
front and back faces of a graphic object. This is useful when rendering open graphical
objects such as surfaces. When this mode is disabled, the widget specifies properties for a
single material.

● Transparency. With this option, the widget can be used to modify the transparency of
the graphic object.

In all cases, the widget can be used to set the shading, gloss, and brightness material
properties. A custom material setting is saved by pressing Save and is recalled using the
Saved button from the material palette. The Reset button resets the widget to its value when
the pull-down was opened.

Option Menu

An option menu allows you to select an item from a list, with the selected item appearing in
the field. Clicking on the field opens the drop-down list of items (a down arrow in the field

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indicates that a drop-down list is attached). Select an item by clicking on it, or by using the
arrow keys and pressing Return.

Pushbutton

A pushbutton initiates an action. A trailing ellipsis (...) in the button label indicates that a
dialog box, a window, or a prompter in the CLI will appear.

Radio Button

Radio buttons present a set of mutually exclusive options. To select an option, simply click on
it. At all times, a single button is in the pressed state.

Scrollbar

Scrollbars appear when window contents exceed the size of the window.

To scroll through the display, drag the scroll box (sometimes also called the thumb). It reflects
the current position of the box in the scrollbar. Pressing the Ctrl key as you drag the scroll
box slows down the scrolling action, giving you more precise control as you scroll the display.
(On Windows systems, the scroll wheel may also be used to scroll.)

Click the scroll arrows to move the scroll box by single increments in either direction.

Press and hold the arrow buttons to scroll the list continuously.

Click in the scrollbar (anywhere other than on the scroll box) to scroll one page at a time. You
can also move the scroll box to an absolute location by clicking the middle mouse button
anywhere in the scrollbar.

Position the cursor over the scrollbar and press the mouse popup button to obtain a popup
menu of relevant commands.

Slider

Drag the slider with the left mouse button, or move it to an absolute location by clicking the
middle mouse button anywhere on the slider. The position of the slider box determines the
numeric value.

Some sliders are associated with a text field. In this case, the value of the slider may be given
by entering values in the text field and pressing Return. This type of window object is
sometimes referred to as a scale.

Spin Button

Spin buttons are used for numeric data entry. You can type a value directly in the text field or
you can click the increment and decrement arrow buttons to modify the value by a fixed
amount.

Text Field

Text fields accept both text and numeric data entry.

Numeric fields may specify minimum and maximum values to prevent the entry of invalid
data, and may forbid the entry of non-numeric data.

The mouse can be used to select text. Click and drag to select. Double-clicking selects an
entire word. Double-clicking at the end of an entry (trailing white space) selects the entire
contents of the text field.

On X-based systems, the middle mouse button will paste the current selection at the location
of the mouse click.

The following key actions exist in a text field:

Cut to clipboard Shift+Del

Copy to clipboard Ctrl+Ins

Paste from clipboard Shift+Ins

Move cursor to beginning of field Home

Move cursor to end of field End

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Move cursor left/right Left/right arrow keys

Highlight while moving cursor Shift+ arrow keys

Move to next text field Tab

A text field may have a short cut list associated with it. In this case a small down arrow is
displayed to the right of the field. When the arrow is clicked on with the left mouse button a
pulldown menu is displayed with items to choose from. The selected item will replace the
current text in the text field.

On Windows based systems, if the mouse has a wheel, wheel movement will cycle through the
shortcut list. Note that if the text in the text field does not match any of the shortcut items
then the wheel will have no effect.

A file selection text field looks and acts like a regular text field, however, it has an added
feature of file name completion when you press the Tab key. The filename will complete up to
the point of ambiguity.

Trackball

The trackball performs 3D transformations, for example, for changing the positions of 3D
objects, or for manipulating the view. Dragging the mouse over the widget while pressing the
left mouse button results in rotation. Clicking close to one of the edges of the trackball widget
will restrict rotations to be about either the X or Y axes.

If <Shift> is held down at the same time, X-Y translation results. If <Ctrl> is held down, then
zooming (translation along the Z axis) results.

If a small box appears in one of the corners of the widget, clicking it will put the widget into
"translation mode", where dragging left produces X-Y translations instead of rotations and is
equivalent to holding down the <Shift> key. Pressing the box again releases the widget from
this mode. The box is marked with either an 'R' or a 'T' to indicate the current mode.

Wheel (or Dial)

To adjust a wheel, drag the wheel right or left (using the left mouse button). Pressing Ctrl as
you drag increases the precision of the movement. Some wheels have a reset button to return
to a preset value (gray box to the right).

File Selection Box

The file selection box (FSB) is used to specify one or more files or directories. There are two versions of the FSB, a single file
selection and a multiple file selection, differing only in the presence, in the latter case, of a second list in which selected files are
accumulated. In this section, the single FSB will be described in detail; the differences to the multi-select FSB are presented at the
end.

Single File Selection

The single file selection FSB comprises a files list, above which are navigational controls and a directory path area, and below which
are a filename textfield and filter pulldown.

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Navigation. Browsing the file tree can be accomplished in different ways:

● Arrows. The forward and back buttons navigate the history of visited directories. The FSB is
opened in the current working directory. Pressing the back (left) arrow will visit the directory last visited in
the most recent previously-opened FSB.

● Favorites. The top row of the Favorites menu contains shortcuts for $MOE, $HOME, the working folder
(also referred to as the current working directory (CWD)), and $DESKTOP. The second row contains drive
letters, if any. The rest of the menu is populated by recently visited directories.
Favorites
● Directory Path. The currently-listed directory is detailed in the directory path area. To ascend the
directory tree, press the appropriate component of the directory path. Pressing an arrow in the directory
path drops down a menu of all subdirectories of the parent directory. If the subdirectories are sufficiently Directory Path
numerous, the menu is paged.

● Directory Path Textfield. Clicking in the empty area of the directory path field opens the directory path textfield into which a
directory path can be typed. Pressing Enter, or, equivalently, the green checkmark, changes to the specified directory and
closes the textfield. The red X quits the textfield display, as does pressing Esc.

● CWD. Sets the current working directory to the currently browsed folder. The current working directory, as returned by the
SVL cd function, is the directory which is read from and written to by default, when no file path information is specified.

File Selection. Selecting a file can be accomplished as follows:

● Files List. Clicking in the list will select a file. The name will appear in the filename textfield below; the textfield is
automatically sync'ed to the file list selection. When there is a file selected, pressing OK causes the FSB to trigger (return its
value). Double-clicking in the list has the same effect.

● File textfield. Entering the name of a file causes that file to be selected. Pressing Return causes the FSB to trigger. Filename
completion is activated with the Tab key.

Filters. The Filter menu to the right of the File textfield may contain common filter groups by name (e.g. Sequence Files), and
has a textfield into which a name pattern may be entered. The filter is applied to the displayed directory listing, and all files
matching the search pattern are displayed. The non-matching files are hidden.

Sorting. The files list may be sorted by name, type, size, or date by pressing the header field titles. Successive presses to the
same field header will toggle between ascending and descending sort order.

FSB Popup. Right-clicking in the FSB raises a popup menu containing the following items:

Folders If enabled, folders (directory names) will be displayed in the list.

Dot-names If enabled, files and folders with names beginning with a dot ('.') will be displayed in th
Hidden If enabled, hidden files will be displayed in the list.

Rename Rename selected file or folder.

Delete Permanently delete the selected file or folder. A confirmation dialog will appear.
New Folder Create a new folder in the displayed directory.

Set Working Folder Set the working folder (also referred to as the current working directory, CWD) to the c
directory.

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Clear Selection Deselect all files/folders.

Select All Select all files/folders.

Invert Selection Deselect all currently selected list items and select all currently unselected list items.
Scroll to First Scroll the list display to show the first selected list item.
Selection

Scroll to Last Scroll the list display to show the last selected list item.
Selection

Reset Sort Order Restore the list order to its initial state.

Multiple File Selection

Some applications allow several files to be processed at the same time. In these cases, a multiple file
selection box is offered. The multiple file selection box allows you to create a list of files to be used. Files can be added and
removed from the list before returning from the selection box.

The multiple file selection box functions in the same manner as the single file selection box with the exception that when a file is
chosen it is placed in the list. Once the list is complete, press OK to return the list of files.

MOE Table of Contents

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