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 Time(launch, start, end, num_cpu, cpu_time, duration)

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)
USE_GPU = False
property failed: bool
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
property is_for_jc: bool

Whether or not this job should be submitted to job control

property is_incomplete: bool
property is_launchable: bool
property is_restartable
property is_retriable: bool
process_completed_job(jctrl: schrodinger.job.jobcontrol.Job, checkpoint_requested=False, restart_requested=False)

Check for valid output and set status of job, assuming job is already complete.

Parameters

  • checkpoint_requested – Set to True if the job should checkpoint. Default if False.

  • restart_requested – Set to True if the job should checkpoint and restart. Default if False.

requeue(jctrl: schrodinger.job.jobcontrol.Job)
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 Time(launch, start, end, num_cpu, cpu_time, duration)

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)
describe()
static err_handler(job)
property failed: bool
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
property is_for_jc: bool

Whether or not this job should be submitted to job control

property is_incomplete: bool
property is_launchable: bool
property is_restartable
property is_retriable: bool
process_completed_job(jctrl: schrodinger.job.jobcontrol.Job, checkpoint_requested=False, restart_requested=False)

Check for valid output and set status of job, assuming job is already complete.

Parameters

  • checkpoint_requested – Set to True if the job should checkpoint. Default if False.

  • restart_requested – Set to True if the job should checkpoint and restart. Default if False.

requeue(jctrl: schrodinger.job.jobcontrol.Job)
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)
class Time(launch, start, end, num_cpu, cpu_time, duration)

Bases: object

__init__(launch, start, end, num_cpu, cpu_time, duration)
USE_GPU = True
static err_handler(job)
property failed: bool
finish()
get_proc_time()
static get_time(jctrl, num_cpu)
property is_for_jc: bool

Whether or not this job should be submitted to job control

property is_incomplete: bool
property is_launchable: bool
property is_restartable
property is_retriable: bool
process_completed_job(jctrl: schrodinger.job.jobcontrol.Job, checkpoint_requested=False, restart_requested=False)

Check for valid output and set status of job, assuming job is already complete.

Parameters

  • checkpoint_requested – Set to True if the job should checkpoint. Default if False.

  • restart_requested – Set to True if the job should checkpoint and restart. Default if False.

requeue(jctrl: schrodinger.job.jobcontrol.Job)
describe()