A Gromacs command class acts as a factory function that produces an instance of a gromacs command (gromacs.core.GromacsCommand) with initial default values.
By convention, a class has the capitalized name of the corresponding Gromacs tool; dots are replaced by underscores to make it a valid python identifier.
The list of Gromacs tools to be loaded is configured in gromacs.config.gmx_tool_groups.
It is also possible to extend the basic commands and patch in additional functionality. For example, the GromacsCommandMultiIndex class makes a command accept multiple index files and concatenates them on the fly; the behaviour mimics Gromacs’ “multi-file” input that has not yet been enabled for all tools.
Initialize instance.
See the documentation for gromacs.core.GromacsCommand for details.
Run the command; make a combined multi-index file if necessary.
Combine multiple index file into a single one and return appropriate kwargs.
Calling the method combines multiple index files into a a single temporary one so that Gromacs tools that do not (yet) support multi file input for index files can be used transparently as if they did.
If a temporary index file is required then it is deleted once the object is destroyed.
| Returns : | The method returns the input keyword arguments with the necessary changes to use the temporary index files. |
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| Keywords : | Only the listed keywords have meaning for the method:
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| Example : | Used in derived classes that replace the standard run() (or __init__()) methods with something like: def run(self,*args,**kwargs):
kwargs = self._fake_multi_ndx(**kwargs)
return super(G_mindist, self).run(*args, **kwargs)
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Clean up temporary multi-index files if they were used.
In this example we create two instances of the gromacs.tools.Trjconv command (which runs the Gromacs trjconv command):
import gromacs.tools as tools
trjconv = tools.Trjconv()
trjconv_compact = tools.Trjconv(ur='compact', center=True, boxcenter='tric', pbc='mol',
input=('protein','system'),
doc="Returns a compact representation of the system centered on the protein")
The first one, trjconv, behaves as the standard commandline tool but the second one, trjconv_compact, will by default create a compact representation of the input data by taking into account the shape of the unit cell. Of course, the same effect can be obtained by providing the corresponding arguments to trjconv but by naming the more specific command differently one can easily build up a library of small tools that will solve a specifi, repeatedly encountered problem reliably. This is particularly helpful when doing interactive work.
Gromacs tool ‘mdrun’.
Set up the command with gromacs flags as keyword arguments.
The following are generic instructions; refer to the Gromacs command usage information that should have appeared before this generic documentation.
As an example, a generic Gromacs command could use the following flags:
cmd = GromacsCommand('v', f=['md1.xtc','md2.xtc'], o='processed.xtc', t=200, ...)
which would correspond to running the command in the shell as
GromacsCommand -v -f md1.xtc md2.xtc -o processed.xtc -t 200
Gromacs command line arguments
Gromacs boolean switches (such as -v) are given as python positional arguments ('v') or as keyword argument (v=True); note the quotes in the first case. Negating a boolean switch can be done with 'nov', nov=True or v=False (and even nov=False works as expected: it is the same as v=True).
Any Gromacs options that take parameters are handled as keyword arguments. If an option takes multiple arguments (such as the multi-file input -f file1 file2 ...) then the list of files must be supplied as a python list.
If a keyword has the python value None then it will not be added to the Gromacs command line; this allows for flexible scripting if it is not known in advance if an input file is needed. In this case the default value of the gromacs tool is used.
Keywords must be legal python keywords or the interpreter raises a SyntaxError but of course Gromacs commandline arguments are not required to be legal python. In this case “quote” the option with an underscore (_) and the underscore will be silently stripped. For instance, -or translates to the illegal keyword or so it must be underscore-quoted:
cmd(...., _or='mindistres.xvg')
Command execution
The command is executed with the run() method or by calling it as a function. The two next lines are equivalent:
cmd(...) cmd.run(...)When the command is run one can override options that were given at initialization or one can add additional ones. The same rules for supplying Gromacs flags apply as described above.
Non-Gromacs keyword arguments
The other keyword arguments (listed below) are not passed on to the Gromacs tool but determine how the command class behaves. They are only useful when instantiating a class. This is mostly of interest to developers.
| Keywords : |
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External tool ‘GridMAT-MD.pl’
GridMAT-MD: A Grid-based Membrane Analysis Tool for use with Molecular Dynamics.
This GridMAT-MD is a patched version of the original GridMAT-MD.pl v1.0.2, written by WJ Allen, JA Lemkul and DR Bevan. The original version is available from the GridMAT-MD home page,
Please cite
W. J. Allen, J. A. Lemkul, and D. R. Bevan. (2009) “GridMAT-MD: A Grid-based Membrane Analysis Tool for Use With Molecular Dynamics.” J. Comput. Chem. 30 (12): 1952-1958.
when using this programme.
Usage:
| Arguments : |
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.
Set up the command class.
The arguments can always be provided as standard positional arguments such as
"-c", "config.conf", "-o", "output.dat", "--repeats=3", "-v", "input.dat"
In addition one can also use keyword arguments such as
c="config.conf", o="output.dat", repeats=3, v=True
These are automatically transformed appropriately according to simple rules:
If this does not work (as for instance for the options of the UNIX find command) then provide options and values in the sequence of positional arguments.