schrodinger.application.desmond.stage.jobs module

class schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates(fh_ref_coord: <built-in function array>, fh_mut_coord: <built-in function array>, sh_ref_coord: <built-in function array>, sh_mut_coord: <built-in function array>)

Bases: object

fh_ref_coord: numpy.array

fh_mut_coord: numpy.array

sh_ref_coord: numpy.array

sh_mut_coord: numpy.array

__init__(fh_ref_coord: numpy.array, fh_mut_coord: numpy.array, sh_ref_coord: numpy.array, sh_mut_coord: numpy.array) → None

class schrodinger.application.desmond.stage.jobs.DesmondJob(task='', gid=None, permanent_restrain=None, permanent_group=None, *arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.Job

static err_handler(job)

__init__(task='', gid=None, permanent_restrain=None, permanent_group=None, *arg, **kwarg)

describe()

class schrodinger.application.desmond.stage.jobs.DesmondBackendJob(*args, **kwargs)

Bases: schrodinger.application.desmond.stage.jobs.DesmondJob

Variables

• is_extend (bool) – Whether this job is the extension of a replica exchange. This variable only matters to jobs associated with ReplicaExchange and DesmondExtend stages.

• added_time (float) – The amount of time to add to the replica exchange stage associated with this job, if it is marked as an extension. If is_extend = False, then this variable is ignored. This variable only matters to jobs associated with ReplicaExchange and DesmondExtend stages.

USE_GPU = True

__init__(*args, **kwargs)

class schrodinger.application.desmond.stage.jobs.FepJob(fepid=None, n_win=None, i_win=None, fepout=None, egout=None, fragname=None, snapcore: Optional[schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates] = None, *arg, **kwarg)

Bases: schrodinger.application.desmond.stage.jobs.DesmondBackendJob, schrodinger.application.desmond.picklejar.Picklable

id = 0

__init__(fepid=None, n_win=None, i_win=None, fepout=None, egout=None, fragname=None, snapcore: Optional[schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates] = None, *arg, **kwarg)

describe()