Application Plugins

Module contents

This module contains the import logic for the application plugins.

All code for a new plugin should be placed inside the plugin module itself and not here, follow the template for constructing new app plugins.

longbow.apps.amber module

This is the AMBER plugin module.

This plugin is relatively simple in the fact that adding new executables is as simple as modifying the EXECDATA structure below. See the documentation at http://www.hecbiosim.ac.uk/longbow-devdocs for more information.

longbow.apps.charmm module

This is the CHARMM plugin module.

This plugin is relatively simple in the fact that adding new executables is as simple as modifying the EXECDATA structure below. See the documentation at http://www.hecbiosim.ac.uk/longbow-devdocs for more information.

longbow.apps.charmm.detectsubstitutions(args)

Detect substitutions specified on the commandline.

This method will be called from the hooks within the applications.py module. This is where the applications specific code should be placed so that Longbow can handle substitutions.

longbow.apps.charmm.file_parser(filename, path, files, substitutions=None)

Find dependancy files and add them to the upload list.

Recursive function that will assimilate from charmm input files, a list of dependancy files to be staged to the remote host. The filename will be added to the list and any files mentioned in this included file will also be added and searched. Substitutions is a dictionary of “@” style variables.

longbow.apps.chemshell module

This is the Chemshell plugin module.

This plugin is relatively simple in the fact that adding new executables is as simple as modifying the EXECDATA structure below. See the documentation at http://www.hecbiosim.ac.uk/longbow-devdocs for more information.

longbow.apps.chemshell.rsyncuploadhook(jobs, job)

Override the default rsync upload parameters to null so that rsync basically transfers all files

longbow.apps.desmond module

This is the DESMOND plugin module.

This plugin is relatively simple in the fact that adding new executables is as simple as modifying the EXECDATA structure below. See the documentation at http://www.hecbiosim.ac.uk/longbow-devdocs for more information.

longbow.apps.gromacs module

This is the GROMACS plugin module.

This plugin is relatively simple in the fact that adding new executables is as simple as modifying the EXECDATA structure below. See the documentation at http://www.hecbiosim.ac.uk/longbow-devdocs for more information.

longbow.apps.gromacs.defaultfilename(path, item, initargs)

Process tpr files provided by the -deffnm flag.

The reason this needs a special method is due to the fact that users will supply the name as -deffnm test but the file name might be test.tpr which would make our code miss the file from the upload list.

longbow.apps.lammps module

This is the LAMMPS plugin module.

This plugin is relatively simple in the fact that adding new executables is as simple as modifying the EXECDATA structure below. See the documentation at http://www.hecbiosim.ac.uk/longbow-devdocs for more information.

longbow.apps.lammps.detectsubstitutions(args)

Detect substitutions specified on the commandline.

This method will be called from the hooks within the applications.py module. This is where the applications specific code should be placed so that Longbow can handle substitutions.

longbow.apps.lammps.file_parser(filename, path, files, substitutions=None)

Find dependancy files and add them to the upload list.

Recursive function that will assimilate from charmm input files, a list of dependancy files to be staged to the remote host. The filename will be added to the list and any files mentioned in this included file will also be added and searched. Substitutions is a dictionary of “@” style variables.

longbow.apps.namd module

This is the NAMD plugin module.

This plugin is relatively simple in the fact that adding new executables is as simple as modifying the EXECDATA structure below. See the documentation at http://www.hecbiosim.ac.uk/longbow-devdocs for more information.

longbow.apps.namd.file_parser(filename, path, files, substitutions=None)

Find dependancy files and add them to the upload list.

Recursive function that will assimilate from charmm input files, a list of dependancy files to be staged to the remote host. The filename will be added to the list and any files mentioned in this included file will also be added and searched. Substitutions is a dictionary of “@” style variables.