schrodinger.application.livedesign.tasks module

LiveDesign protocol tasks.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.livedesign.tasks.CoreAtomsOptions

Bases: StrEnum

MCS = 'mcs'

ALL_HEAVY = 'all_heavy'

ALL = 'all'

CUSTOM = 'custom'

class schrodinger.application.livedesign.tasks.ExecutionModes

Bases: JsonableEnum

NONE = 1

UMBRELLA = 'umbrella'

schrodinger.application.livedesign.tasks.run_task(task: CmdJobTask, task_type: str, safe_access_path: str = None)

Check the task to see if it completed successfully. Will raise a RuntimeError if the job failed or a FileNotFoundError is the output file does not exist. If safe_access_path is given, the path will be locked during the task starting process, usually used for shared OPLS directory.

Parameters:

• task – job_utils task object

• task_type – Calculation performed by the task

• safe_access_path – File to check for safe access

schrodinger.application.livedesign.tasks.register_task_output_files(task: CmdJobTask, backend: schrodinger.job.jobcontrol._Backend | None)

Register the output files of a task with the backend

Parameters:

• task – job_utils task object

• backend – Backend object to track output files

schrodinger.application.livedesign.tasks.parse_task_output_ids(task: CmdJobTask, corp_ids: set)

Get the corporate IDs of the structures remaining in task output and IDs of the structures dropped by task.

Some tasks (e.g. MacroCycleDockingTask) rename output structure titles so that they no longer match the input Corporate IDs. These tasks set renames_output_titles = True. When that flag is present the title-based comparison is skipped: if the output file contains any structures all input IDs are considered remaining; otherwise all are considered dropped.

Parameters:

• task – job_utils task object

• corp_ids – Set of corporate IDs of the input structures

class schrodinger.application.livedesign.tasks.LigPrepTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a LigPrep task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

ligprep_infile: TaskFile

A parameter of the class.

ligprep_args: str

A parameter of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

ligprep_argsChanged

A pyqtSignal emitted by instances of the class.

ligprep_argsReplaced

A pyqtSignal emitted by instances of the class.

ligprep_infileChanged

A pyqtSignal emitted by instances of the class.

ligprep_infileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

dropped_file: TaskFile

A parameter of the class.

dropped_fileChanged

A pyqtSignal emitted by instances of the class.

dropped_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, ligprep_args=None, ligprep_infile=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.LigFilterTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a LigFilter task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

filter_file: TaskFile

A parameter of the class.

filter_fileChanged

A pyqtSignal emitted by instances of the class.

filter_fileReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, filter_file, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.GlideTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a Glide task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

grid_file: TaskFile

A parameter of the class.

glide_infile: TaskFile

A parameter of the class.

num_poses: int

A parameter of the class.

ref_file: TaskFile

A parameter of the class.

constraint_type: str

A parameter of the class.

report_strain_energy: str

A parameter of the class.

use_confgenx: str

A parameter of the class.

mcs_timeout_no_skip: str

A parameter of the class.

opls: TaskFile

A parameter of the class.

constraint_typeChanged

A pyqtSignal emitted by instances of the class.

constraint_typeReplaced

A pyqtSignal emitted by instances of the class.

glide_infileChanged

A pyqtSignal emitted by instances of the class.

glide_infileReplaced

A pyqtSignal emitted by instances of the class.

grid_fileChanged

A pyqtSignal emitted by instances of the class.

grid_fileReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

mcs_timeout_no_skipChanged

A pyqtSignal emitted by instances of the class.

mcs_timeout_no_skipReplaced

A pyqtSignal emitted by instances of the class.

num_posesChanged

A pyqtSignal emitted by instances of the class.

num_posesReplaced

A pyqtSignal emitted by instances of the class.

oplsChanged

A pyqtSignal emitted by instances of the class.

oplsReplaced

A pyqtSignal emitted by instances of the class.

ref_fileChanged

A pyqtSignal emitted by instances of the class.

ref_fileReplaced

A pyqtSignal emitted by instances of the class.

report_strain_energyChanged

A pyqtSignal emitted by instances of the class.

report_strain_energyReplaced

A pyqtSignal emitted by instances of the class.

use_confgenxChanged

A pyqtSignal emitted by instances of the class.

use_confgenxReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

csv_file: TaskFile

A parameter of the class.

parsed_inp_file: TaskFile

A parameter of the class.

skip_csv: TaskFile

A parameter of the class.

keyword_dict: dict

A parameter of the class.

csv_fileChanged

A pyqtSignal emitted by instances of the class.

csv_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

keyword_dictChanged

A pyqtSignal emitted by instances of the class.

keyword_dictReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

parsed_inp_fileChanged

A pyqtSignal emitted by instances of the class.

parsed_inp_fileReplaced

A pyqtSignal emitted by instances of the class.

skip_csvChanged

A pyqtSignal emitted by instances of the class.

skip_csvReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

FormatInpFile()

Parse the Glide input file and combine command line arguments and Glide defaults into a final validated Glide input file

classmethod create_task(task_name, ligands_file, grid_file, glide_infile, num_poses, ref_file=None, constraint_type=None, report_strain_energy=None, use_confgenx=None, mcs_timeout_no_skip=None, opls=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.AlignLigandsTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create an align_ligands task using in the input, output and job settings. The alignment_args is a list of arguments that align_ligands takes

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

alignment_args: str

A parameter of the class.

alignment_argsChanged

A pyqtSignal emitted by instances of the class.

alignment_argsReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, alignment_args, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.FlexAlignTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a flex_align task using in the input, output and job settings. The alignment_args is a list of arguments that align_ligands takes

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

refligs_file: TaskFile

A parameter of the class.

flex_align_args: str

A parameter of the class.

flex_align_argsChanged

A pyqtSignal emitted by instances of the class.

flex_align_argsReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

refligs_fileChanged

A pyqtSignal emitted by instances of the class.

refligs_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, refligs_file, flex_align_args, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.TugAlignTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a tug_align task using in the input, output and job settings

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

ref_ligand_file: TaskFile

A parameter of the class.

receptor_structure: TaskFile

A parameter of the class.

tug_align_args: str

A parameter of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

receptor_structureChanged

A pyqtSignal emitted by instances of the class.

receptor_structureReplaced

A pyqtSignal emitted by instances of the class.

ref_ligand_fileChanged

A pyqtSignal emitted by instances of the class.

ref_ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

tug_align_argsChanged

A pyqtSignal emitted by instances of the class.

tug_align_argsReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, ref_ligand_file, receptor_structure=None, tug_align_args=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.EpikClassicTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create an Epik Classic task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

epik_classic_infile: TaskFile

A parameter of the class.

epik_classic_args: str

A parameter of the class.

epik_classic_argsChanged

A pyqtSignal emitted by instances of the class.

epik_classic_argsReplaced

A pyqtSignal emitted by instances of the class.

epik_classic_infileChanged

A pyqtSignal emitted by instances of the class.

epik_classic_infileReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, epik_classic_args=None, epik_classic_infile=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.EpikTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create an Epik task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

mode: str

A parameter of the class.

epik_args: str

A parameter of the class.

epik_argsChanged

A pyqtSignal emitted by instances of the class.

epik_argsReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

modeChanged

A pyqtSignal emitted by instances of the class.

modeReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, epik_args, mode, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.QikPropTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a QikProp task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

qp_args: str

A parameter of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

qp_argsChanged

A pyqtSignal emitted by instances of the class.

qp_argsReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

mae_file: TaskFile

A parameter of the class.

qp_out_file: TaskFile

A parameter of the class.

qp_csv_file: TaskFile

A parameter of the class.

qp_qpsa_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

mae_fileChanged

A pyqtSignal emitted by instances of the class.

mae_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

qp_csv_fileChanged

A pyqtSignal emitted by instances of the class.

qp_csv_fileReplaced

A pyqtSignal emitted by instances of the class.

qp_out_fileChanged

A pyqtSignal emitted by instances of the class.

qp_out_fileReplaced

A pyqtSignal emitted by instances of the class.

qp_qpsa_fileChanged

A pyqtSignal emitted by instances of the class.

qp_qpsa_fileReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, qp_args, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.MemPermTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a Prime Membrane Permeability task using in the input, output and job settings

sub_log_file

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

csv_file

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

permeability_args: str

A parameter of the class.

name: str

A parameter of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

permeability_argsChanged

A pyqtSignal emitted by instances of the class.

permeability_argsReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

sub_log_file: TaskFile

A parameter of the class.

csv_file: TaskFile

A parameter of the class.

csv_fileChanged

A pyqtSignal emitted by instances of the class.

csv_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

sub_log_fileChanged

A pyqtSignal emitted by instances of the class.

sub_log_fileReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, permeability_args=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.CanvasSearchTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a canvasSearch task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

rule_file: TaskFile

A parameter of the class.

name: str

A parameter of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

rule_fileChanged

A pyqtSignal emitted by instances of the class.

rule_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

counts_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

counts_fileChanged

A pyqtSignal emitted by instances of the class.

counts_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, rule_file, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.CovDockTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a canvasSearch task using in the input, output and job settings

parser

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

cdock

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

covdock_opts

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

multi_value_keywords

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

receptor_file: TaskFile

A parameter of the class.

covdock_inp_file: TaskFile

A parameter of the class.

cons_file: TaskFile

A parameter of the class.

ref_file: TaskFile

A parameter of the class.

cdock_file: TaskFile

A parameter of the class.

reaction_type: str

A parameter of the class.

num_poses: str

A parameter of the class.

core_atoms: str

A parameter of the class.

core_constraint_smarts: str

A parameter of the class.

core_rmsd: str

A parameter of the class.

ligand_smarts_pattern: str

A parameter of the class.

macrocycle: bool

A parameter of the class.

cdock_fileChanged

A pyqtSignal emitted by instances of the class.

cdock_fileReplaced

A pyqtSignal emitted by instances of the class.

cons_fileChanged

A pyqtSignal emitted by instances of the class.

cons_fileReplaced

A pyqtSignal emitted by instances of the class.

core_atomsChanged

A pyqtSignal emitted by instances of the class.

core_atomsReplaced

A pyqtSignal emitted by instances of the class.

core_constraint_smartsChanged

A pyqtSignal emitted by instances of the class.

core_constraint_smartsReplaced

A pyqtSignal emitted by instances of the class.

core_rmsdChanged

A pyqtSignal emitted by instances of the class.

core_rmsdReplaced

A pyqtSignal emitted by instances of the class.

covdock_inp_fileChanged

A pyqtSignal emitted by instances of the class.

covdock_inp_fileReplaced

A pyqtSignal emitted by instances of the class.

ligand_smarts_patternChanged

A pyqtSignal emitted by instances of the class.

ligand_smarts_patternReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

macrocycleChanged

A pyqtSignal emitted by instances of the class.

macrocycleReplaced

A pyqtSignal emitted by instances of the class.

num_posesChanged

A pyqtSignal emitted by instances of the class.

num_posesReplaced

A pyqtSignal emitted by instances of the class.

reaction_typeChanged

A pyqtSignal emitted by instances of the class.

reaction_typeReplaced

A pyqtSignal emitted by instances of the class.

receptor_fileChanged

A pyqtSignal emitted by instances of the class.

receptor_fileReplaced

A pyqtSignal emitted by instances of the class.

ref_fileChanged

A pyqtSignal emitted by instances of the class.

ref_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

parsed_inp_file: TaskFile

A parameter of the class.

grid_file: TaskFile

A parameter of the class.

grid_fileChanged

A pyqtSignal emitted by instances of the class.

grid_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

parsed_inp_fileChanged

A pyqtSignal emitted by instances of the class.

parsed_inp_fileReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

CreateInpFile()

Parse the CovDock input file, updating the settings and write a new inp file

classmethod create_task(task_name, ligands_file, receptor_file, covdock_inp_file, cons_file, ref_file, cdock_file, reaction_type, num_poses, core_atoms, core_constraint_smarts, core_rmsd, ligand_smarts_pattern, macrocycle, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.PrimeMMGBSATask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a prime_mmgbsa task using in the input, output and job settings. The prime_mmgbsa_args is a list of arguments that prime_mmgbsa takes

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

pv_file: TaskFile

A parameter of the class.

prime_mmgbsa_args: str

A parameter of the class.

watermap: TaskFile

A parameter of the class.

flexdist: float

A parameter of the class.

ntop_poses: int

A parameter of the class.

flexdistChanged

A pyqtSignal emitted by instances of the class.

flexdistReplaced

A pyqtSignal emitted by instances of the class.

ntop_posesChanged

A pyqtSignal emitted by instances of the class.

ntop_posesReplaced

A pyqtSignal emitted by instances of the class.

prime_mmgbsa_argsChanged

A pyqtSignal emitted by instances of the class.

prime_mmgbsa_argsReplaced

A pyqtSignal emitted by instances of the class.

pv_fileChanged

A pyqtSignal emitted by instances of the class.

pv_fileReplaced

A pyqtSignal emitted by instances of the class.

watermapChanged

A pyqtSignal emitted by instances of the class.

watermapReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, pv_file, watermap, flexdist, ntop_poses, prime_mmgbsa_args, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.LigandStrainTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a ligand_strain task using in the input, output and job settings. The ligand_strain_args is a list of arguments that ligand_strain takes

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligand_file: TaskFile

A parameter of the class.

ligand_strain_args: str

A parameter of the class.

ligand_fileChanged

A pyqtSignal emitted by instances of the class.

ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

ligand_strain_argsChanged

A pyqtSignal emitted by instances of the class.

ligand_strain_argsReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligand_file, ligand_strain_args, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.StrainRescoreTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a StrainRescore task using in the input, output and job settings. The strain_rescore_args is a list of arguments that strain_rescore.py takes

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligand_file: TaskFile

A parameter of the class.

strain_rescore_args: str

A parameter of the class.

ligand_fileChanged

A pyqtSignal emitted by instances of the class.

ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

strain_rescore_argsChanged

A pyqtSignal emitted by instances of the class.

strain_rescore_argsReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

local_st_file: TaskFile

A parameter of the class.

global_st_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

global_st_fileChanged

A pyqtSignal emitted by instances of the class.

global_st_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

local_st_fileChanged

A pyqtSignal emitted by instances of the class.

local_st_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligand_file, strain_rescore_args, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.RBSSTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a RBSS task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

protein_file: TaskFile

A parameter of the class.

rbss_yaml: TaskFile

A parameter of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

protein_fileChanged

A pyqtSignal emitted by instances of the class.

protein_fileReplaced

A pyqtSignal emitted by instances of the class.

rbss_yamlChanged

A pyqtSignal emitted by instances of the class.

rbss_yamlReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

out_csv: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_csvChanged

A pyqtSignal emitted by instances of the class.

out_csvReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, protein_file, rbss_yaml, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.IFDMDCongenericTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a IFD-MD_congeneric.py task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

pv_file: TaskFile

A parameter of the class.

subhost: str

A parameter of the class.

subprocs: int

A parameter of the class.

oplsdir: str

A parameter of the class.

report_full_output_maes: bool

A parameter of the class.

smarts_pattern_overrides: str

A parameter of the class.

lig_titles: list[str]

A parameter of the class.

lig_titlesChanged

A pyqtSignal emitted by instances of the class.

lig_titlesReplaced

A pyqtSignal emitted by instances of the class.

oplsdirChanged

A pyqtSignal emitted by instances of the class.

oplsdirReplaced

A pyqtSignal emitted by instances of the class.

pv_fileChanged

A pyqtSignal emitted by instances of the class.

pv_fileReplaced

A pyqtSignal emitted by instances of the class.

report_full_output_maesChanged

A pyqtSignal emitted by instances of the class.

report_full_output_maesReplaced

A pyqtSignal emitted by instances of the class.

smarts_pattern_overridesChanged

A pyqtSignal emitted by instances of the class.

smarts_pattern_overridesReplaced

A pyqtSignal emitted by instances of the class.

subhostChanged

A pyqtSignal emitted by instances of the class.

subhostReplaced

A pyqtSignal emitted by instances of the class.

subprocsChanged

A pyqtSignal emitted by instances of the class.

subprocsReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, pv_file, subhost=None, subprocs=1, oplsdir=None, report_full_output_maes=False, smarts_pattern_overrides=None, lig_titles=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.MCSDockingTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a MCSDocking task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

grid_file: TaskFile

A parameter of the class.

mcs_docking_in: TaskFile

A parameter of the class.

num_poses: int

A parameter of the class.

ref_file: TaskFile

A parameter of the class.

is_multi_receptor: bool

A parameter of the class.

grid_fileChanged

A pyqtSignal emitted by instances of the class.

grid_fileReplaced

A pyqtSignal emitted by instances of the class.

is_multi_receptorChanged

A pyqtSignal emitted by instances of the class.

is_multi_receptorReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

mcs_docking_inChanged

A pyqtSignal emitted by instances of the class.

mcs_docking_inReplaced

A pyqtSignal emitted by instances of the class.

num_posesChanged

A pyqtSignal emitted by instances of the class.

num_posesReplaced

A pyqtSignal emitted by instances of the class.

ref_fileChanged

A pyqtSignal emitted by instances of the class.

ref_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

csv_file: TaskFile

A parameter of the class.

parsed_inp_file: TaskFile

A parameter of the class.

skip_csv: TaskFile

A parameter of the class.

csv_fileChanged

A pyqtSignal emitted by instances of the class.

csv_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

parsed_inp_fileChanged

A pyqtSignal emitted by instances of the class.

parsed_inp_fileReplaced

A pyqtSignal emitted by instances of the class.

skip_csvChanged

A pyqtSignal emitted by instances of the class.

skip_csvReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

FormatInpFile()

Parse the Glide input file and combine command line arguments and Glide defaults into a final validated Glide input file

classmethod create_task(task_name, ligands_file, grid_file, mcs_docking_in, num_poses, ref_file=None, is_multi_receptor=False, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.MultisimTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a multisim task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

msj_file: TaskFile

A parameter of the class.

st_file: TaskFile

A parameter of the class.

config_file: TaskFile

A parameter of the class.

opls_dir: str

A parameter of the class.

execution_mode: ExecutionModes

A parameter of the class.

config_fileChanged

A pyqtSignal emitted by instances of the class.

config_fileReplaced

A pyqtSignal emitted by instances of the class.

execution_modeChanged

A pyqtSignal emitted by instances of the class.

execution_modeReplaced

A pyqtSignal emitted by instances of the class.

msj_fileChanged

A pyqtSignal emitted by instances of the class.

msj_fileReplaced

A pyqtSignal emitted by instances of the class.

opls_dirChanged

A pyqtSignal emitted by instances of the class.

opls_dirReplaced

A pyqtSignal emitted by instances of the class.

st_fileChanged

A pyqtSignal emitted by instances of the class.

st_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

out_cms: TaskFile

A parameter of the class.

out_eaf: TaskFile

A parameter of the class.

trj_dir: str

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_cmsChanged

A pyqtSignal emitted by instances of the class.

out_cmsReplaced

A pyqtSignal emitted by instances of the class.

out_eafChanged

A pyqtSignal emitted by instances of the class.

out_eafReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

trj_dirChanged

A pyqtSignal emitted by instances of the class.

trj_dirReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths(execution_mode)

classmethod create_task(task_name, st_file, msj_file, execution_mode, config_file=None, opls_dir=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.EventAnalysisTask(*args, _param_type=<object object>, **kwargs)

Bases: SubprocessCmdTask

Create a event_analysis.py task using in the input, output and job settings

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

eaf_file: TaskFile

A parameter of the class.

eaf_fileChanged

A pyqtSignal emitted by instances of the class.

eaf_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

out_file: TaskFile

A parameter of the class.

out_png: TaskFile

A parameter of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

out_pngChanged

A pyqtSignal emitted by instances of the class.

out_pngReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, eaf_file, task_dir=None)

makeCmd()

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.Trj2maeTask(*args, _param_type=<object object>, **kwargs)

Bases: SubprocessCmdTask

Create a trj2mae.py task using in the input, output and job settings

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

cms_file: TaskFile

A parameter of the class.

trj_dir: str

A parameter of the class.

trj_slice: str

A parameter of the class.

extract_asl: str

A parameter of the class.

align_asl: str

A parameter of the class.

align_aslChanged

A pyqtSignal emitted by instances of the class.

align_aslReplaced

A pyqtSignal emitted by instances of the class.

cms_fileChanged

A pyqtSignal emitted by instances of the class.

cms_fileReplaced

A pyqtSignal emitted by instances of the class.

extract_aslChanged

A pyqtSignal emitted by instances of the class.

extract_aslReplaced

A pyqtSignal emitted by instances of the class.

trj_dirChanged

A pyqtSignal emitted by instances of the class.

trj_dirReplaced

A pyqtSignal emitted by instances of the class.

trj_sliceChanged

A pyqtSignal emitted by instances of the class.

trj_sliceReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

out_file: TaskFile

A parameter of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, cms_file, trj_dir, trj_slice, extract_asl, align_asl, task_dir=None)

makeCmd()

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.FFBuilderTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a ffbuilder task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligand_file: TaskFile

A parameter of the class.

opls_dir: TaskFile

A parameter of the class.

ligand_fileChanged

A pyqtSignal emitted by instances of the class.

ligand_fileReplaced

A pyqtSignal emitted by instances of the class.

opls_dirChanged

A pyqtSignal emitted by instances of the class.

opls_dirReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_dir: str

A parameter of the class.

out_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_dirChanged

A pyqtSignal emitted by instances of the class.

out_dirReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligand_file, opls_dir=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

getOutputOPLSArchive()

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.PhaseScreenTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a Phase screen task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

hypo_file: TaskFile

A parameter of the class.

phase_args: str

A parameter of the class.

phase_match: str

A parameter of the class.

hypo_fileChanged

A pyqtSignal emitted by instances of the class.

hypo_fileReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

phase_argsChanged

A pyqtSignal emitted by instances of the class.

phase_argsReplaced

A pyqtSignal emitted by instances of the class.

phase_matchChanged

A pyqtSignal emitted by instances of the class.

phase_matchReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, hypo_file, phase_args=None, phase_match=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.PeptideDockingTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Task that runs peptide docking with the crankshift workflow

job_config: JobConfig

A parameter of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

peptide_st: Structure

A parameter of the class.

peptide_fpath: TaskFile

A parameter of the class.

grid_file: TaskFile

A parameter of the class.

num_steps: int

A parameter of the class.

num_simulations: int

A parameter of the class.

randomize_input: bool

A parameter of the class.

grid_fileChanged

A pyqtSignal emitted by instances of the class.

grid_fileReplaced

A pyqtSignal emitted by instances of the class.

num_simulationsChanged

A pyqtSignal emitted by instances of the class.

num_simulationsReplaced

A pyqtSignal emitted by instances of the class.

num_stepsChanged

A pyqtSignal emitted by instances of the class.

num_stepsReplaced

A pyqtSignal emitted by instances of the class.

peptide_fpathChanged

A pyqtSignal emitted by instances of the class.

peptide_fpathReplaced

A pyqtSignal emitted by instances of the class.

peptide_stChanged

A pyqtSignal emitted by instances of the class.

peptide_stReplaced

A pyqtSignal emitted by instances of the class.

randomize_inputChanged

A pyqtSignal emitted by instances of the class.

randomize_inputReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

writePeptideFile()

setOutputFile()

classmethod create_task(task_name: str, peptide_structure: Structure, grid_file: str, num_simulations: int | None = None, num_steps: int | None = None, hostname=None, procs=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.AbModelingTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a AbModeling task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

modeling_infile: list[TaskFile]

A parameter of the class.

modeling_mode: str

A parameter of the class.

modeling_infileChanged

A pyqtSignal emitted by instances of the class.

modeling_infileReplaced

A pyqtSignal emitted by instances of the class.

modeling_modeChanged

A pyqtSignal emitted by instances of the class.

modeling_modeReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

dropped_file: TaskFile

A parameter of the class.

dropped_fileChanged

A pyqtSignal emitted by instances of the class.

dropped_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, modeling_infile, modeling_mode=None, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.AbHumanizationTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a Antibody Humanization task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

modeling_infile: TaskFile

A parameter of the class.

graft_residues: str

A parameter of the class.

modeling_mode: str

A parameter of the class.

scheme: str

A parameter of the class.

use_humanization_cdr: str

A parameter of the class.

graft_residuesChanged

A pyqtSignal emitted by instances of the class.

graft_residuesReplaced

A pyqtSignal emitted by instances of the class.

modeling_infileChanged

A pyqtSignal emitted by instances of the class.

modeling_infileReplaced

A pyqtSignal emitted by instances of the class.

modeling_modeChanged

A pyqtSignal emitted by instances of the class.

modeling_modeReplaced

A pyqtSignal emitted by instances of the class.

schemeChanged

A pyqtSignal emitted by instances of the class.

schemeReplaced

A pyqtSignal emitted by instances of the class.

use_humanization_cdrChanged

A pyqtSignal emitted by instances of the class.

use_humanization_cdrReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

dropped_file: TaskFile

A parameter of the class.

dropped_fileChanged

A pyqtSignal emitted by instances of the class.

dropped_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, modeling_infile, graft_residues, use_humanization_cdr, scheme, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.ConfGenTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create conformers using confgenx the input, output and job settings.

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

maxconf: int

A parameter of the class.

stereo: int

A parameter of the class.

force_field: str

A parameter of the class.

dont_vary_nitrogens: str

A parameter of the class.

keep_amides: str

A parameter of the class.

dont_vary_nitrogensChanged

A pyqtSignal emitted by instances of the class.

dont_vary_nitrogensReplaced

A pyqtSignal emitted by instances of the class.

force_fieldChanged

A pyqtSignal emitted by instances of the class.

force_fieldReplaced

A pyqtSignal emitted by instances of the class.

keep_amidesChanged

A pyqtSignal emitted by instances of the class.

keep_amidesReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

maxconfChanged

A pyqtSignal emitted by instances of the class.

maxconfReplaced

A pyqtSignal emitted by instances of the class.

stereoChanged

A pyqtSignal emitted by instances of the class.

stereoReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, maxconf, stereo, force_field, dont_vary_nitrogens, keep_amides, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.GlideWSTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a Glide task using in the input, output and job settings

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

model_file: TaskFile

A parameter of the class.

input_file: TaskFile

A parameter of the class.

docking_method: str

A parameter of the class.

docking_methodChanged

A pyqtSignal emitted by instances of the class.

docking_methodReplaced

A pyqtSignal emitted by instances of the class.

input_fileChanged

A pyqtSignal emitted by instances of the class.

input_fileReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

model_fileChanged

A pyqtSignal emitted by instances of the class.

model_fileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

csv_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

csv_fileChanged

A pyqtSignal emitted by instances of the class.

csv_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, model_file, input_file, docking_method, hostname=None, num_subjobs=None, task_dir=None)

FormatInpFile()

Parse the Glide WS input file and overwrite a few keywords with command line arguments, and write out a new input file for Glide WS job.

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.SurfaceAnalysisTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Create a Surface Analysis task using in the input, output and job settings

csv_file

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

log_file

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

modeling_infile: TaskFile

A parameter of the class.

modeling_infileChanged

A pyqtSignal emitted by instances of the class.

modeling_infileReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

csv_file: TaskFile

A parameter of the class.

log_file: TaskFile

A parameter of the class.

csv_fileChanged

A pyqtSignal emitted by instances of the class.

csv_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, modeling_infile, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.livedesign.tasks.MacroCycleDockingTask(*args, _param_type=<object object>, **kwargs)

Bases: CmdJobTask

Run macrocycle_docking.py via the CmdJobTask framework.

The command produced by makeCmd is equivalent to:

$SCHRODINGER/run -FROM psp macrocycle_docking.py
    -target_ligand <ligands> -receptor <receptor>
    <binding-site flags> <sampling flags> <output flags>
    [-run_ffbuilder] [-OPLSDIR ...]
    [-dry_run] [-D]

-JOBNAME and -HOST are appended automatically by the task framework in _customizeCmd and must not appear in makeCmd.

renames_output_titles = True

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: JobConfig

driver_host_settings: HostSettings

A parameter of the class.

driver_host_settingsChanged

A pyqtSignal emitted by instances of the class.

driver_host_settingsReplaced

A pyqtSignal emitted by instances of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

class Input(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

ligands_file: TaskFile

A parameter of the class.

receptor_file: TaskFile

A parameter of the class.

template_ligand: TaskFile

A parameter of the class.

template_ligand_asl: str

A parameter of the class.

binding_site_asl: str

A parameter of the class.

target_nconf: int

A parameter of the class.

conformers_mae: TaskFile

A parameter of the class.

n_output_poses: int

A parameter of the class.

cpu_subhost: str

A parameter of the class.

n_cpu: int

A parameter of the class.

run_ffbuilder: bool

A parameter of the class.

oplsdir: str

A parameter of the class.

dry_run: bool

A parameter of the class.

debug: bool

A parameter of the class.

binding_site_aslChanged

A pyqtSignal emitted by instances of the class.

binding_site_aslReplaced

A pyqtSignal emitted by instances of the class.

conformers_maeChanged

A pyqtSignal emitted by instances of the class.

conformers_maeReplaced

A pyqtSignal emitted by instances of the class.

cpu_subhostChanged

A pyqtSignal emitted by instances of the class.

cpu_subhostReplaced

A pyqtSignal emitted by instances of the class.

debugChanged

A pyqtSignal emitted by instances of the class.

debugReplaced

A pyqtSignal emitted by instances of the class.

dry_runChanged

A pyqtSignal emitted by instances of the class.

dry_runReplaced

A pyqtSignal emitted by instances of the class.

ligands_fileChanged

A pyqtSignal emitted by instances of the class.

ligands_fileReplaced

A pyqtSignal emitted by instances of the class.

n_cpuChanged

A pyqtSignal emitted by instances of the class.

n_cpuReplaced

A pyqtSignal emitted by instances of the class.

n_output_posesChanged

A pyqtSignal emitted by instances of the class.

n_output_posesReplaced

A pyqtSignal emitted by instances of the class.

oplsdirChanged

A pyqtSignal emitted by instances of the class.

oplsdirReplaced

A pyqtSignal emitted by instances of the class.

receptor_fileChanged

A pyqtSignal emitted by instances of the class.

receptor_fileReplaced

A pyqtSignal emitted by instances of the class.

run_ffbuilderChanged

A pyqtSignal emitted by instances of the class.

run_ffbuilderReplaced

A pyqtSignal emitted by instances of the class.

target_nconfChanged

A pyqtSignal emitted by instances of the class.

target_nconfReplaced

A pyqtSignal emitted by instances of the class.

template_ligandChanged

A pyqtSignal emitted by instances of the class.

template_ligandReplaced

A pyqtSignal emitted by instances of the class.

template_ligand_aslChanged

A pyqtSignal emitted by instances of the class.

template_ligand_aslReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: _CmdJobTaskOutput

out_file: TaskFile

A parameter of the class.

csv_file: TaskFile

A parameter of the class.

csv_fileChanged

A pyqtSignal emitted by instances of the class.

csv_fileReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

out_fileChanged

A pyqtSignal emitted by instances of the class.

out_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

setOutputPaths()

classmethod create_task(task_name, ligands_file, receptor_file, template_ligand=None, template_ligand_asl=None, binding_site_asl=None, target_nconf=None, conformers_mae=None, n_output_poses=None, cpu_subhost='localhost', n_cpu=1, run_ffbuilder=False, oplsdir=None, dry_run=False, debug=False, hostname=None, num_subjobs=None, task_dir=None)

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

job_settingsChanged

A pyqtSignal emitted by instances of the class.

job_settingsReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.