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

registerJobcontrolInputs(job_specs_args_builder)¶

Register the input files for current stage with jobcontrol.

Parameters

stage_info. – a StageInfo instance that holds current stage’s information
job_specs_args_builder (launchapi.JobSpecificationArgsBuilder) – job arguments builder

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

Bases: schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage

Implementation of BigQuery query stage in fragment VS workflow. Input argument file (args_file) requires the specification of two files: 1. QUERY_OPTIONS_FILE - a yaml file containing 4 BQ related parameters, see YAML_ARGNAMES_HELP definition in bq_query_task.py. 2. QUERY_SQL_FILE - an SQL command file containing the SQL commands for the query to be carried out. This stage queries a list of ligands with conditions defined in the SQL file, generates and then downloads one or more CSV files containing the queried ligands with SMILES strings and names. A list of the CSV files are stored in stage_info.output_file_list, thus can be used as input file list for the next stage, usually Glide.

app_name = 'Query'¶

run()¶

static validateStage(stage_info)¶: Validate by checking: 1. whether the google cloud library is available (through bq_query_task module); 2. whether the SQL and query_options files exist.

registerJobcontrolInputs(job_specs_args_builder)¶

Register the input files for current stage with jobcontrol.

Parameters

stage_info. – a StageInfo instance that holds current stage’s information
job_specs_args_builder (launchapi.JobSpecificationArgsBuilder) – job arguments builder

__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.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'¶

__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.

infile_setup()¶

docking_config_setup()¶

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

registerJobcontrolInputs(job_specs_args_builder)¶

Register the input files for current stage with jobcontrol.

Parameters: job_specs_args_builder (launchapi.JobSpecificationArgsBuilder) – job arguments builder

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 runtime path relative to the job directory.

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

registerJobcontrolInputs(job_specs_args_builder)¶

Register the input files for current stage with jobcontrol.

Parameters: job_specs_args_builder (launchapi.JobSpecificationArgsBuilder) – job arguments builder

__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.WScoreSIPStage(stage_info, frag_vs_workflow=None)¶

Bases: schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage

Implementation of WScore score in place stage in fragment VS workflow. Input argument file (args_file) requires WSCORE_GRID_FILE and WSCORE_WMAP_FILE. This stage follows a Glide stage, takes the Glide output poses as input, and carries out a score in place calculation.

app_name = 'WScoreSIP'¶

infile_setup()¶

get_ws_grid_wmap_files()¶

get_ws_sip_docking_config(ws_grid_fname, ws_wmap_fname)¶

static validateStage(stage_info)¶: Validate by checking whether the wscore grid file and watermap files exist.

__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.

docking_config_setup()¶

registerJobcontrolInputs(job_specs_args_builder)¶

Register the input files for current stage with jobcontrol.

Parameters: job_specs_args_builder (launchapi.JobSpecificationArgsBuilder) – job arguments builder

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.

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.WScoreStage(stage_info, frag_vs_workflow=None)¶

Bases: schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage

app_name = 'WSCORE'¶

run()¶: Create Wscore docking job with input argument file and input ligand file. Run the WScore docking job. Write the poses of the best ligands to a .maegz file which will be the input file for the next stage.

static restart(stage_info)¶: Restartability of WScore job is not implemented yet.

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

registerJobcontrolInputs(job_specs_args_builder)¶

Register the input files for current stage with jobcontrol.

Parameters: job_specs_args_builder (launchapi.JobSpecificationArgsBuilder) – job arguments builder

__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.ALABFEPStage(stage_info, frag_vs_workflow=None)¶

Bases: schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage

app_name = 'AL-ABFEP'¶

makeInputArgsFile()¶

Update the paths of the files that were specified in the AL-ABFEP’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-ABFEP stage. Parse the AL-ABFEP inputs. Run the AL-ABFEP job. Write the poses of the best ligands to a .maegz file which will be the input file for the next stage.

runALABFEP(al_abfep_args)¶

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

Parameters: al_abfep_args (argparse.Namespace) – parsed AL-ABFEP arguments
Returns: path of the result csv file, path of the pose file
Return type: str, str

static sortResultByScore(input_pose_file_list, fep_prediction_error_file_list, optimization_target, sorted_output_pose_file, sorted_output_csv_file)¶

Sorted all the ABFEP scored ligands. Dump their ABFEP input poses to a .mae file. Dump their ABFEP calculation results to a .csv file

Parameters

input_pose_file_list (list(str)) – list of .mae files that contain ABFEP input poses
fep_prediction_error_file_list (list(str)) – list of .csv files that contain ABFEP results.
optimization_target (str) – ML optimization target (dG, LE and LLE etc.)
sorted_output_pose_file (str) – a .mae file contains the sorted ligands’ ABFEP input poses
sorted_output_csv_file (str) – a .csv file contains the sorted ligands’ ABFEP results.

registerJobcontrolInputs(job_specs_args_builder)¶

Register the input files for current stage with jobcontrol.

Parameters: job_specs_args_builder (launchapi.JobSpecificationArgsBuilder) – job arguments builder

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

__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.