Bundle Example: Add a Command

This tutorial builds on the material from Bundle Example: Hello World.

This example describes how to create a ChimeraX bundle that defines two new commands, tutorial cofm and tutorial highlight. The steps in implementing the bundle are:

  1. Create a bundle_info.xml containing information about the bundle,

  2. Create a Python package that interfaces with ChimeraX and implements the command functionality, and

  3. Install and test the bundle in ChimeraX.

The final step builds a Python wheel that ChimeraX uses to install the bundle. So if the bundle passes testing, it is immediately available for sharing with other users.

Before deciding on the name and syntax of your own command, you should peruse the command style guide.

Source Code Organization

The source code for this example may be downloaded as a zip-format file containing a folder named tut_cmd. Alternatively, one can start with an empty folder and create source files based on the samples below. The source folder may be arbitrarily named, as it is only used during installation; however, avoiding whitespace characters in the folder name bypasses the need to type quote characters in some steps.

Sample Files

The files in the tut_cmd folder are:

  • tut_cmd - bundle folder

    • bundle_info.xml - bundle information read by ChimeraX

    • src - source code to Python package for bundle

      • __init__.py - package initializer and interface to ChimeraX

      • cmd.py - source code to implement two tutorial commands

      • docs/user/commands/tutorial.html - help file for the tutorial commands

The file contents are shown below.

bundle_info.xml

bundle_info.xml is an eXtensible Markup Language format file whose tags are listed in Bundle Information XML Tags. While there are many tags defined, only a few are needed for bundles written completely in Python. The bundle_info.xml in this example is similar to the one from the hello world example with changes highlighted. For explanations of the unhighlighted lines, please see Bundle Example: Hello World.

The BundleInfo, Synopsis and Description tags are changed to reflect the new bundle name and documentation (lines 8-10 and 17-25). The DataFiles tag is added to include documentation files (lines 33-35). The only other change is replacing the ChimeraXClassifier tags to declare the two commands in this bundle (lines 49-52).

Note that the two command, tutorial cofm (Center OF Mass) and tutorial highlight, are multi-word commands that share the same initial word. Most bundles that provide multiple commands should add multi-word commands that share the same “umbrella” name, e.g., tutorial in this example. All names in the command may be shortened, so tut high is an accepted alternative to tutorial highlight, which minimizes the typing burden on the user. Note also that the ChimeraXClassifier tag text may be split over multiple lines for readability. Whitespace characters around :: are ignored.

src

src is the folder containing the source code for the Python package that implements the bundle functionality. The ChimeraX devel command, used for building and installing bundles, automatically includes all .py files in src as part of the bundle. (Additional files may also be included using bundle information tags such as DataFiles as shown in Bundle Example: Add a Tool.) The only required file in src is __init__.py. Other .py files are typically arranged to implement different types of functionality. For example, cmd.py is used for command-line commands; tool.py or gui.py for graphical interfaces; io.py for reading and saving files, etc.

src/__init__.py

The command registration code is essentially the same as Bundle Example: Hello World, except that the command information, ci, is used to get the full name (as listed in bundle_info.xml) of the command to be registered, and the corresponding function and description are retrieved from the cmd module.

src/cmd.py

cmd.py contains the functions that implement the bundle commands. For example, the cofm function is called when the user issues a tutorial cofm command. To report the center of mass of a set of atoms, cofm requires several parameters supplied by the user:

  1. the atoms of interest,

  2. in which coordinate system to do the computation (using the atomic coordinates from the input file, or include geometric transformations relative to other models), and

  3. whether the center calculation is weighted by the atomic masses.

It then takes the parameters, computes the center of mass, and reports the result to the ChimeraX log. The missing link is how the user-typed command gets translated into a call to cofm. This is the purpose of the call to chimerax.core.commands.register in the register_command method in __init__.py. The register call tells ChimeraX to associate a function and description with a command name. In this case, cofm and cofm_desc are the function and description associated with the command tutorial cofm. When the user types a command that starts with tutorial cofm (or some abbreviation thereof), ChimeraX parses the input text according to a standard syntax, maps the input words to function arguments using the command description, and then calls the function.

The standard syntax of ChimeraX commands is of the form:

command required_arguments optional_arguments

command is the command name, possibly abbreviated and multi-word. Required arguments appear immediately after the command. If there are multiple required arguments, they must be specified in a prespecified order, i.e., they must all be present and are positional. Optional arguments appear after required arguments. They are typically keyword-value pairs and, because they are keyword-based, may be in any order.

A command description instance describes how to map input text to Python values. It contains a list of 2-tuples for required arguments and another for optional arguments. The first element of the 2-tuple is a string that matches one of the command function parameter names. The second element is a “type class”. ChimeraX provides a variety of built-in type classes such as BoolArg (Boolean), IntArg (integer), AtomsArg (container of atoms), and AtomSpecArg (atom specifier). See chimerax.core.commands for the full list. The order of the required parameters list (in the command description) must match the expected order for required arguments (in the input text).

cofm() is the function called from __init__.py when the user enters the cofm command. It retrieves the array of atoms, their coordinates, and their center of mass by calling the internal function _get_cofm() and reports the result via session.logger, an instance of chimerax.core.logger.Logger.

cofm_desc contains the description of what arguments are required or allowed for the cofm command. The details of its declaration are described in the comments in the example.

highlight() is the function called from __init__.py when the user enters the highlight command. Like cofm(), it retrieves the array of atoms, their coordinates, and their center of mass by calling _get_cofm(). It then

  1. computes the distances from each atom to the center of mass using Numpy (line 104),

  2. sorts the atom indices by distances so that indices of atoms that are closer to the center of mass are towards the front of the sort result (argsort(distances)), and select the first count indices (line 110),

  3. turn the array of indices into an array of atoms (line 113), and

  4. finally, set the color of the selected atoms (line 117). The colors attribute of the atomic array is an Nx4 array of integers, where N is the number of atoms and the rows (of 4 elements) are the RGBA values for each atom. The color argument to highlight() is an instance of chimerax.core.colors.Color, whose uint8x4() returns its RGBA value as an array of four (x4) 8-bit integers (uint8).

_get_cofm(), used by both cofm() and highlight(), is passed three arguments:

  • atoms, the atoms specified by the user, if any.

  • transformed, whether to retrieve transformed (scene) or untransformed (original) coordinates. Untransformed coordinates can typically be used when only a single model is involved because the atoms are fixed relative to each other. Transformed coordinates must be used when distances among multiple models are being computed (i.e., the models must all be in same coordinate system).

  • weighted, whether to include atomic mass as part of the center of mass computation. Frequently, an unweighted average of atomic coordinates, which is simpler and faster to compute, is sufficient for qualitative analysis.

If the user did not choose specific atoms (when atoms is None), the usual ChimeraX interpretation is that all atoms should be used (lines 139-141). chimerax.atomic.all_atoms() returns an array of atoms from all open models. Transformed and untransformed coordinates are accessed using the scene_coords and coords attributes of the atom array, respectively (lines 148-151). If atomic mass need not be included, the “center of mass” is simply the average of the coordinates (line 157); if a weighted calculation is required, (a) the atomic masses are retrieved by atoms.elements.masses (line 159), (b) the coordinates are scaled by the corresponding atomic masses (line 160), and (c) the weighted average is computed (line 161).

For performance, ChimeraX makes use of NumPy arrays in many contexts. The container for atoms is typically a chimerax.atomic.Collection instance, as are those for bonds, residues, and atomic structures. Fetching the same attribute, e.g., coordinates, from a collection of molecular data, e.g., atoms, usually results in a NumPy array. Although code involving NumPy arrays is sometimes opaque, they are typically much more efficient than using Python loops.

src/docs/user/commands/tutorial.html

The documentation for the tutorial command should be written in HTML 5 and saved in a file whose name matches the command name and has suffix .html, i.e., tutorial.html. If the bundle command is a subcommand of an existing command (e.g. color bundlecoloring) then any spaces should be replaced by underscores. When help files are included in bundles, documentation for the commands may be displayed using the help command, the same as built-in ChimeraX commands. The directory structure is chosen to allow for multiple types of documentation for a bundle. For example, developer documentation such as the bundle API are saved in a devel directory instead of user; documentation for graphical tools are saved in user/tools instead of user/commands.

While the only requirement for documentation is that it be written as HTML, it is recommended that developers write command help files following the above template, with:

  • a banner linking to the documentation index,

  • a usage section with a summary of the command syntax,

  • text describing each command in the bundle, and

  • an address for contacting the bundle author.

Note that the target links used in the HTML file are all relative to ... Even though the command documentation HTML file is stored with the bundle, ChimeraX treats the links as if the file were located in the commands directory in the developer documentation tree. This creates a virtual HTML documentation tree where command HTML files can reference each other without having to be collected together.

Building and Testing Bundles

To build a bundle, start ChimeraX and execute the command:

devel build PATH_TO_SOURCE_CODE_FOLDER

Python source code and other resource files are copied into a build sub-folder below the source code folder. C/C++ source files, if any, are compiled and also copied into the build folder. The files in build are then assembled into a Python wheel in the dist sub-folder. The file with the .whl extension in the dist folder is the ChimeraX bundle.

To test the bundle, execute the ChimeraX command:

devel install PATH_TO_SOURCE_CODE_FOLDER

This will build the bundle, if necessary, and install the bundle in ChimeraX. Bundle functionality should be available immediately.

To remove temporary files created while building the bundle, execute the ChimeraX command:

devel clean PATH_TO_SOURCE_CODE_FOLDER

Some files, such as the bundle itself, may still remain and need to be removed manually.

Building bundles as part of a batch process is straightforward, as these ChimeraX commands may be invoked directly by using commands such as:

ChimeraX --nogui --exit --cmd 'devel install PATH_TO_SOURCE_CODE_FOLDER exit true'

This example executes the devel install command without displaying a graphics window (--nogui) and exits immediately after installation (exit true). The initial --exit flag guarantees that ChimeraX will exit even if installation fails for some reason.

Distributing Bundles

With ChimeraX bundles being packaged as standard Python wheel-format files, they can be distributed as plain files and installed using the ChimeraX toolshed install command. Thus, electronic mail, web sites and file sharing services can all be used to distribute ChimeraX bundles.

Private distributions are most useful during bundle development, when circulation may be limited to testers. When bundles are ready for public release, they can be published on the ChimeraX Toolshed, which is designed to help developers by eliminating the need for custom distribution channels, and to aid users by providing a central repository where bundles with a variety of different functionality may be found.

Customizable information for each bundle on the toolshed includes its description, screen captures, authors, citation instructions and license terms. Automatically maintained information includes release history and download statistics.

To submit a bundle for publication on the toolshed, you must first sign in. Currently, only Google sign in is supported. Once signed in, use the Submit a Bundle link at the top of the page to initiate submission, and follow the instructions. The first time a bundle is submitted to the toolshed, it is held for inspection by the ChimeraX team, which may contact the authors for more information. Once approved, all subsequent submissions of new versions of the bundle are posted immediately on the site.

What’s Next