Tells Aten to use the specified <dir> as its data directory (where filters etc are stored). This overrides the ATENDATA shell variable.

Specifies that the unit of length used in any models and grid data that follow is Bohr rather than Å, and should be converted to the latter.

When specified, each subsequent command given with the -c or --command switches will be stored but not executed. Once all model files specified on the command-line are loaded, each stored command is executed on each loaded model, before being saved to the same filename. In this way, batch processing of multiple files can be performed. The GUI is not started if --batch is specified. If model export filters are not available for one or more loaded models, any changes will not be saved. It is advisable to work on a copy of the model files when using this command, or to export to a different format in order to preserve the original files (see the --export switch).

For example, to transmute all iron atoms into cobalt for a series of xyz files named 'complex_001.xyz', 'complex_002.xyz' etc.

bob@pc: ~> aten --batch -c 'select(Fe); transmute(Co);'

Force recalculation of bonding in loaded models, regardless of whether the filter used any of the rebond commands (see the Bond Commands).

Provides a command or compound command to execute. Commands should be enclosed in single quotes (to prevent the shell from misquoting any character strings) and individual commands separated with semicolons. Commands provided in this way can be used to set up Aten in the way you want it from the command line, perform operations on model files before loading the GUI, or perform operations on model files without loading the GUI at all.

For example, to start the GUI with a new model named 'cube' that has a cubic cell of 30 Å side length:

bob@pc:~> aten -c 'newmodel("cube"); cell(30,30,30,90,90,90);'

Similarly, to load a model and make a duplicate copy of the atoms (pasted into the same model):

bob@pc:~> aten original.xyz -c 'selectall(); copy(); paste(10,10,10);'

In both cases the GUI initialises itself without being told - this can be prevented with the quit command. Consider the last example - to save the newly-expanded model and quit without ever launching the GUI:

bob@pc:~> aten original.xyz -c 'selectall; copy; paste(10,10,10); savemodel("xyz", "pasted.xyz"); quit;'

Multiple sets of commands may be given:

bob@pc:~> aten source.xyz -c 'selectall; copy' target.xyz -c 'paste(10,10,10);'

Take care here - the commands provided act on the current model, i.e. the one that was most recently loaded. Of course, there are commands that select between the loaded models (see the list of model commands) but that would confuse this supposedly simple example, wouldn't it?

Sets the size limit for trajectory loading, in kilobytes. If an entire trajectory will fit into this cache, all frames in the trajectory are loaded immediately. If not, frames will be read from disk as and when required.

Force translation of non-periodic models centre-of-geometry to the origin, even if the centre was not used in the corresponding filter.

Enables debugging of subroutine calls so that program execution can be traced, or enables extra debug output from specific types of routines (if <type> is given). Warning - this creates a lot of output, most of which is incomprehensible to people with their sanity still intact, but is useful to track the program up to the point of, say, a hideous crash. Valid <type> options are listed in Output Types.

Creates a 'floating' variable <name> which is of type 'double' and that can be accessed from any subsequent script, command, or filter. Note that declarations of variables with the same name made in scripts, commands and filters will override any passed value names in order to avoid conflicts and breaking of existing filters and scripts. The intended use is to be able to pass values easily from the command-line into scripts or one-line commands.

For example, in a bash shell:

bob@pc:~> for num in 10.0 50.5 100.0; do aten --double d=$num -c 'printf("Value is %f\n", d); quit();' done

For each model file specified on the command line, it is loaded and immediately saved in the format specified by <nickname>. The GUI is not started.

For instance, to convert three DL_POLY CONFIG files and an xyz into mol2 format:

bob@pc:~> aten --export mol2 bio1.CONFIG bio2.CONFIG watercell.CONFIG random.xyz

If specified in conjunction with the --batch switch, commands may be applied to each loaded model file before it is saved.

Manually map assigned atom typenames in an expression to the names defined here when expressions are written to a file. For example:

bob@pc:~> aten --ff spc.ff data/test/water.xyz --exportmap "OW=Ospc,H=Hspc" -c 'saveexpression("dlpoly", "water.FIELD"); quit();'

writes the water forcefield with the OW and HW atomtype names mapped to Ospc and Hspc respectively.

For any forthcoming model files provided as arguments on the command line, the specified model import filter is used to load them, regardless of their filename extension (or, indeed, actual format). Since Aten tends not to determine file formats by looking at their content, this is useful for when you know that file is in a particular format, but with an extension that doesn't help Aten recognise it as such.

Loads the specified forcefield file, making it the current forcefield. If the desired forcefield is present in either Aten's installed data/ directory or in your own '.aten/ff' directory (see Installation), then just the filename need be given as Aten searches these locations by default.

Load the specified <file> as if it were a filter file, installing any filters defined within it. Any filters already loaded that have the same 'nickname', 'id' etc. will be hidden by those loaded from <file>. See Overriding Existing Filters for more information.

Force folding of atoms to within the boundaries of the unit cell (if one is present) in loaded models, even if the command fold was not used in the corresponding filter.

Loads the specified grid data file, associating it to the current model, and making it the current grid. A model (even an empty one) must exist for a grid to be loaded.

Show the possible command-line switches and a short description of their meaning.

Starts Aten in interactive mode, where commands are typed and immediately executed. The GUI is not started by default, but may be invoked.

Creates a 'floating' variable <name> which is of type 'int'. See the --double switch for a full description.

Preserves the last stored view of models when the GUI starts, retaining any model rotations and camera transformations performed in scripts or on the command line (normally, the view is reset to display the entire model on startup).

If specified, for each model loaded the original atom names in the file will be preserved as a series of forcefield types generated within a new forcefield created specifically for the model. Elements are still determined from conversion of the atom names, and may still be mapped with the --map option. This option is useful for quickly creating a skeleton set of forcefield types from an existing model with type names, or to allow quick import and export of typed configurations without requiring the original forcefield file to be loaded.

Manually map atom typenames occurring in model files to elements according to the rules defined here. For example:

bob@pc:~> aten --map 'CX=C,N_=P'

will result in atoms called 'CX' being mapped to carbon, and atoms called 'N_' mapped to phosphorus (for whatever reason). These mappings are attempted prior to any z-mapping scheme defined in the filter, and so will take precedence over standard typename-to-element conversions.

Create a new, empty model.

Prevent recalculation of bonding in loaded models, overriding filter directives. This basically means that, if a filter tries to run the rebond command, then specifying --nobond will prevent it.

Prevent translation of non-periodic models centre-of-geometry to the origin, overriding filter directives.

Prevent initial folding of atoms to within the boundaries of the unit cell (if one is present) in loaded models, overriding the use of the fold command in the corresponding filters.

Prevent loading of fragments from both standard ans user locations on startup.

Prevent generation of fragment icons, used in the Fragment Library Window.

Prevent generation of symmetry-equivalent atoms from spacegroup information in loaded models, overriding any occurences of the pack command is used in the corresponding filter.

Don't read in any system-stored Qt settings on startup (such as window positions, toolbar visibilities etc.) using the defaults instead.

Force generation of symmetry-equivalent atoms from spacegroup information in loaded models, even if the command pack was not used in the corresponding filter.

Specifies that the script file is to be loaded and run before moving on to the next command-line argument. A script file is just a plain text file that contains sequence of commands to be executed, written in the command language style.

Creates a 'floating' variable <name> which is of type 'string'. See the --double switch for a full description.

Associates a trajectory file with the last loaded / current model.

Set the maximum number of undo levels per model, or -1 for unlimited (the default).

Switch on verbose reporting of program actions.

Override the names to elements z-mapping style defined in file filters. For a list of possible mapping types see ZMapping Types.