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

Initialize self. See help(type(self)) for accurate signature.

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)

Initialize self. See help(type(self)) for accurate signature.

USE_GPU = False

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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

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

USE_GPU = True

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

Bases: object

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

Initialize self. See help(type(self)) for accurate signature.

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

describe()

static err_handler(job)

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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)

Initialize self. See help(type(self)) for accurate signature.

USE_GPU = True

static err_handler(job)

finish()

get_proc_time()

static get_time(jctrl, num_cpu)

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()