adaptivemd.OpenMMEngine¶
-
class
adaptivemd.
OpenMMEngine
(system_file, integrator_file, pdb_file, args=None)[source]¶ OpenMM Engine to be used by Adaptive MD
Variables: - system_file (File) – the system.xml file for OpenMM
- integrator_file (File) – the integrator.xml file for OpenMM
- pdb_file (File) – the .pdb file for the topology
- args (str) – a list of arguments passed to the openmmrun.py script
Methods
__init__
(system_file, integrator_file, pdb_file)add_output_type
(name[, filename, stride, ...])Add an output type for a trajectory kind to be generated by this engine args
()Return a list of args of the __init__ function of a class base
()Return the most parent class actually derived from StorableMixin descendants
()Return a list of all subclassed objects extend
(source, length)from_dict
(dct)get_uuid
()Create a new unique ID idx
(store)Return the index which is used for the object in the given store. items
()named
(name)Attach a .name property to an object objects
()Returns a dictionary of all storable objects run
(target)stage
(obj[, target])Short cut to add a file to be staged then_func_import
(project, task, data, inputs)to_dict
()Attributes
ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls
Return the base class base_cls_name
Return the name of the base class cls
Return the class name as a string files
full_strides
list of strides for trajectories that have full coordinates native_stride
The least common multiple stride of all generated trajectories. stage_in
Return a list of actions needed before tasks can be generated