schrodinger.application.fragment_virtual_screening.frag_vs_stages module

class schrodinger.application.fragment_virtual_screening.frag_vs_stages.StageInfo(stage_dict)

Bases: object

__init__(stage_dict)

A simple class that stores the information of each fragment VS stage.

Parameters

stage_dict (dict) – a dictionary that defines the stage.

to_dict()

Convert the instance to a dictionary so that it could be future dumped to a yaml file.

Returns

a dictionary that defines the stage.

Return type

dict

class schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage(stage_info, frag_vs_workflow=None)

Bases: object

Base class for different virtual screening stages.

__init__(stage_info, frag_vs_workflow=None)

Initialize the virtual screening stage.

Parameters
  • stage_info. – a StageInfo instance that holds current stage’s information

  • frag_vs_workflow (FragmentVSWorkflow instance) – current fragment virtual screening job.

updateStageDict()

Update the stage status and paths of necessary files in self.stage_info. Write the stage status to the workflow. Dump the workflow status .yaml file.

static validateStage(stage_info)

Validate input argument file for the workflow.

Parameters

stage_info. – a StageInfo instance that holds current stage’s information

static registerJobcontrolInputs(stage_info, job_specs_args_builder)

Register the input files for current stage with jobcontrol.

Parameters
class schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage(stage_info, frag_vs_workflow=None)

Bases: schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage

Implementation of Glide docking stage in fragment VS workflow. Input argument file (args_file) should be similar to Glide docking input file except for supporting the Glide command line arguments ‘NSTRUCT’ and ‘NJOBS’ as keywords and not supporting keywords ‘LIGANDFILE’, ‘GRIDFILE’.

app_name = 'Glide'
run()

Create Glide docking job with input argument file and input ligand file. NSTRUCT and NJOBS can be included in the argument file. Run the Glide docking job. Write the poses of the best ligands to a .maegz file which will be the input file for the next stage.

static validateStage(stage_info)

Validate the input argument file. Exit if the validation failed.

Parameters

stage_info. (StageInfo) – a StageInfo instance that holds current stage’s information

static registerJobcontrolInputs(stage_info, job_specs_args_builder)

Register the input files for current stage with jobcontrol.

Parameters
__init__(stage_info, frag_vs_workflow=None)

Initialize the virtual screening stage.

Parameters
  • stage_info. – a StageInfo instance that holds current stage’s information

  • frag_vs_workflow (FragmentVSWorkflow instance) – current fragment virtual screening job.

updateStageDict()

Update the stage status and paths of necessary files in self.stage_info. Write the stage status to the workflow. Dump the workflow status .yaml file.

class schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage(stage_info, frag_vs_workflow=None)

Bases: schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage

Implementation of AL-Glide stage in fragment VS workflow. The inputs are specified by input arguments file.

app_name = 'AL-Glide'
makeInputArgsFile()

Update the paths of the files that were specified in the AL-Glide’s input arguments file to absolute runtime path.

Returns

path of the new input argument file.

Return type

str

run()

Build the input arguments file and input command line for the current AL-Glide stage. Parse the AL-Glide inputs. Run the AL-Glide job. Write the poses of the best ligands to a .maegz file which will be the input file for the next stage.

static runALGlide(al_glide_args)

Run AL-Glide job with parsed arguments. Return the result csv file and pose file.

Parameters

al_glide_args (argparse.Namespace) – parsed AL-Glide arguments

Returns

path of the result csv file, path of the pose file

Return type

str, str

static restart(stage_info)

Whether current stage should be restarted.

static validateStage(stage_info)

Validate the input argument file. Exit if the validation failed.

Parameters

stage_info. – a StageInfo instance that holds current stage’s information

static registerJobcontrolInputs(stage_info, job_specs_args_builder)

Register the input files for current stage with jobcontrol.

Parameters
__init__(stage_info, frag_vs_workflow=None)

Initialize the virtual screening stage.

Parameters
  • stage_info. – a StageInfo instance that holds current stage’s information

  • frag_vs_workflow (FragmentVSWorkflow instance) – current fragment virtual screening job.

updateStageDict()

Update the stage status and paths of necessary files in self.stage_info. Write the stage status to the workflow. Dump the workflow status .yaml file.