schrodinger.application.matsci.jwsteps module¶

Steps for use in Workflows

schrodinger.application.matsci.jwsteps.import_driver(dpath)¶

class schrodinger.application.matsci.jwsteps.ParentPathInfo(subdirs, names, outfiles)¶

Bases: tuple

names¶: Alias for field number 1

outfiles¶: Alias for field number 2

subdirs¶: Alias for field number 0

exception schrodinger.application.matsci.jwsteps.JobCreationError¶

Bases: Exception

Raised when a job cannot be created

class schrodinger.application.matsci.jwsteps.BaseWorkflow(struct, options, count, jobq, strcleaner=None, logger=None, subhierarchy=None, robust=False, max_retries=None)¶

Bases: schrodinger.application.matsci.jaguarworkflows.WorkFlow

Base Workflow class

getSteps()¶

Create all the steps required for this workflow

This method should almost certainly be overridden by any child class. The example given here is just that - an example

write(writer, *args, **kwargs)¶

Write out the structure for this workflow and all the child structures

Parameters: writer (schrodinger.StructureWriter) – The writer to use to write the structure

writeSmap(filename)¶

Write smap files for steps that need them and the smap file for the entire job

Parameters: filename (str) – The name of the output structure file
Return type: str or None
Returns: The name of the written smap file or None if no file written

class schrodinger.application.matsci.jwsteps.SubdirectoryStepMixin(*args, **kwargs)¶

Bases: object

A mixin to handle some common functionality for steps that run in subdirectories

__init__(*args, **kwargs)¶: See parent class for documentation

finishProcessingJobControlJob()¶: Add all the subjob files to the backend

setSubDir()¶: Determine the absolute path to this step’s subdirectory so that we can always access it no matter what the current directory is

class schrodinger.application.matsci.jwsteps.BaseStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.SubdirectoryStepMixin, schrodinger.application.matsci.jaguarworkflows.Step

A base class for Steps that are not simple Jaguar jobs. Because this step fires off a Python script that itself fires off Jaguar jobs, we have to modify a number of methods that dealt with the jaguar .in file directly or expected standard Jaguar output.

PROCS = 1¶

STEP_NAME = 'Base Step'¶

JOB_BASE = 'base'¶

DRIVER_PATH = 'driver_dir/driver.py'¶

DRIVER = None¶

FLAGS = {}¶

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_INPUT_NAME_FLAG = ''¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = False¶

FLAGS_ADD_DOUBLE_DASH = False¶

CAN_CREATE_TRAJECTORY = False¶

REQUIRES_CMS_INPUT = False¶

REQUIRES_TRAJECTORY_INPUT = False¶

OUTPUTS_CMS = False¶

USES_JC = True¶

USES_MULTI_SUBJOBS = False¶

USES_THREADS = False¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

BUILTIN_WF_FILE = None¶

SPLITTER = False¶

COMBINER = False¶

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Create a BaseStep object

Parameters

procs (int) – The number of processors to allocate to steps of this class
tag – str(tag) will be added to the end of the job name and step name
flags (dict) – Command line argument flags in addition to, or that override, the class FLAGS variable. Keys are flag names (“-flag”), values are values for that flag. For flags that take no value, use None as the value. To turn off (not include in the command line) a flag in the class FLAGS variable, use the DO_NOT_USE_FLAG constant as the value.
archive (bool) – If True, instead of copying the subdirectory and individual files, will tar.gz up the entire subdirectory and copy that back.
monitor_globs (list) – List of valid file globs (i.e. ["*.zip"]) that should be monitored for and copied back to the original job directory when they appear. Note that the interaction of archive and moitor_globs is such that if both are specified, the result will be a subdirectory with the monitored files AND an archive of the entire subdirectory (including any monitored files that remain when this step completes).
full_command (list) – the full command line for this step including the driver path, etc. but without $SCHRODINGER/run. The command will be used “as is” except for replacing some pre-defined tokens with job-specific strings - see the createCommand function. Each item of the list is a word of the command line invocation.
local_files (list) – A list of file paths to copy into the job subdirectory before running the command
input_file (str) – The name of the file containing the input structures/data. It is ignored if there is a parent for this step.
cpu_hostname (str) – The name of the host to run CPU processes on
gpu_hostname (str) – The name of the host to run GPU processes on
umbrella (str) – Whether to run drivers that have GPU subjobs in umbrella mode or not. Should be one of UMBRELLA_ALWAYS (always run in umbrella mode even if the flag is not provided), UMBRELLA_NEVER (never run in umbrella mode even if the flag is provided) or UMBRELLA_PER_FLAG (obey the presence or absence of the -md_umbrella flag for this step). This parameter is only used if both cpu_hostname and gpu_hostname are given - if not, UMBRELLA_ALWAYS is enforced.
splitter (bool) – True if this step splits the workflow into parallel workflows, False if it does not. Note that this keyword is ignored if the SPLITTER class constant is True.
split_index (int) – If this step STARTS a new split workflow, the 1-based index of that workflow. Otherwise, just use 1 to indicate that it is the same workflow as the parent step.
split_tag (str) – An extra tag to add to the step name to distinguish between the same stage in parallel workflows
child_stages (list) – A list of child stages that need steps to be created from them. Each item is a jaguar_multistage_workflow_utils.StageData instance. This list contains one StageData item for each child stage no matter how many steps will be created from that stage due to splitting the workflow. For instance, if a workflow is A-B-C-D, and B is a splitter step that splits the workflow into 3 workflows, child_stages for B should be [C], not [C, C, C].
use_jc (bool) – True if the step should use job control, False if not. The default value of None defaults to the class USES_JC constant.
tpp (int) – The number of threads per process. Serial processes use 1 thread. This will be added to the step command via -TPP tpp.

See parent class for additional documentation

Raises: ValueError – if umbrella is not an allowed value

property output_file_names¶

Get the names of all the output structures

Return type: list
Returns: Each item of the list is a the name of an output file. The step subdirectory path is NOT prepended to the file name.

getParentalInformation()¶

Get information about parent and required step names, output and subdirectories.

Return type: (ParentalPathInfo, ParentalPathInfo)
Returns: The first item gives information about the parent job, the second item gives cumulative information about the required steps. In cases where there is multiple information, such as the parent output file names, or multiple required step names, etc, the data is provided as space-delimited strings. The subdirectory paths and output file names are relative to the overall job directory.

addParentalInformationProperties(struct)¶

Add parental subdirectory properties to the structure

Parameters: struct (schrodinger.structure.Structure) – The structure to add properties to

setStructOrCMSProperty(nottaduck, prop, value)¶

Set the given property to value on nottaduck, whether nottaduck is a Structure object or CMS object

Parameters

nottaduck (structure.Structure or cms.Cms) – The structure-like object to set the property on
prop (str) – The property to set
value – The value of the property

writeInput(struct)¶

Write the input file

Parameters: struct (structure.Structure, cms.Cms, or None) – The structure to write. If None it will write the input file. If struct is a cms, only an mae will be written if this class does not require cms input.

getNumSplits()¶

Get the number of parallel workflows this step will create. A 1 indicates that this step does not split the workflow.

Return type: int
Returns: The number of parallel workflows this step creates. 1 means it does not split the workflow

start()¶: Start the job - create the input and write it, adding necessary output files to make sure they get copied back

noJobAction()¶: Subclasses that do not run a job can overwrite this method to perform their action when the step is run.

removeIncomingProperties(struct)¶

Remove properties on the structure that may have come from previous steps and that we do not want to propagate through this step

Parameters: struct (structure.Structure) – The structure to remove properties from

getStructure()¶

Get the starting structure for this step

Overrides the parent class to get the initial structure for this workflow if the Step has no parent.

Return type: schrodinger.structure.Structure, None, or str
Returns: The starting structure for this step. None if input is not a structure. str if the starting structure is actually a file structures, in which case the return value is the path to the file.

getStructForChild(index=1)¶

Get the structure from this step to pass on to a child step

Parameters: index (int) – The 1-based index of the structure to get. Should be 1 unless this step is splitting the workflow into parallel workflows, in which case it is the index of the workflow that will run this structure. Unused in the base class, but subclasses may use this parameter.
Return type: structure.Structure, cms.Cms, or str
Returns: The structure the child step should use. If a str is returned, it is the path to the input structure file

setWAMProperty(oname, structs)¶

Some workflow types set the WAM property on the structure file rather than the structure. The WAM property needs to be on the structure in order for the WAM to get passed into the final structure file.

Parameters

oname (str) – The name of the structure file
structs (list) – Each item of the list is a Structure or Cms object that needs to have the WAM property set on it

getOutput(quiet=False)¶

Read in the results of the calculation

Parameters: quiet (bool) – If True, no error messages will be printed. If False, (default) error messages will be printed. Also, if True, self.ok will not be set to False if the output file cannot be read.
Return type: None or list
Returns: None if the calculation failed, or a list of output structures from a successful calculation.

getFirstOutputStructure()¶

Get the first output structure from the results

Return type: structure.Structure
Returns: The structure to write to the output file

getStructsForWriting()¶

Get the structures from this step to write to the final Workflow file

Return type: list of schrodinger.structure.Structure or str
Returns: A list of structures to write or the string constant NO_STRUCTURES to indicate that the step is intentionally returning no structures. An empty list will indicate expected structures were not found.

getInputName()¶

Get the name of the input structure file

Return type: str
Returns: The input structure file name

getInputPath()¶

Get the full path to the input file

Return type: str
Returns: The full path to the input file

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

finish()¶: Finish this step, including processing any output

write(writer, props=None, hierarchy=None)¶

Add the final structure for this step to the output structure file

Parameters

writer (schrodinger.StructureWriter) – The writer to use to write the structure
props (dict) – A dictionary of property/value pairs to add to the property dictionary of this object.
hierarchy (list) – The project group hierarchy for this result - each item is a str

processSmapInfo()¶

Create an smap file in the subjob directory to enable Maestro’s little blue v and s buttons if the user manually imports the subjob output. Also copy smap-eligible files to the main job directory and pass back the file information needed for writing the main job smap file.

Return type: list
Returns: Each item of the list is a file name that should appear in the main job smap file for this step.

createCommand()¶

Create the command line

Return type: list
Returns: The command line in list form
Raises: JobCreationError – If the command cannot be created

addTPPIfNeeded(cmd)¶

Add, or replace, the value of TPP in the command as needed.

Parameters: cmd (list) – The command line as a list of strings. The list is modified in-place

adjustCommandForQueue(cmd)¶

Add subhost and umbrella flags that direct this step’s subjobs to the correct host. Modifies the given command list in place.

Parameters: cmd (list) – The current command line as a list of strings

createJob()¶

Create the job command and object

Return type: jobutils.RobustSubmissionJob
Returns: The job object to run

canDriverUseUmbrella()¶

Check whether the driver for this step knows the -md_umbrella flag

Return type: bool
Returns: True if -md_umbrella is a known flag, False if not

determineQueueResource(cmd)¶

Determine what resource this job should request

Parameters: cmd (list) – The command line as a list of strings
Return type: str or None
Returns: The resource (cpu, gpu or None) this job should request

createQJobFromCommand(cmd)¶

Create the JobDJ job from the list of command line arguments. The job will be set to run in the Step subdirectory.

Return type: jobutils.RobustSubmissionJob
Returns: A job object that can be added to JobDJ

processOutput(output)¶

Process the output of a job during the finish part of the step

Parameters: output – The output of the job. Type may vary in subclasses

archiveSubDir()¶: Archive this step’s subdirectory and add it to the backend for copy back

finishProcessingJobControlJob()¶: Override the parent method to archive the directory if requested

periodicMaintenance()¶: This method is periodically called while the workflow is running

monitorFiles()¶: Check for any requested files that need to be copied back immediately

class schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

Step to perform a macromodel conformational search

STEP_NAME = 'ConfSearch'¶

JOB_BASE = 'csearch'¶

DRIVER_PATH = 'bmin'¶

PROGRAM_NAME = 'Macromodel Conformational Search'¶

FLAGS = {}¶

FLAGS_ADD_INPUT_NAME = False¶

FLAGS_ADD_JOB_NAME = False¶

BUILTIN_WF_FILE = 'single_stage_macromodel_conformational_search.wfw'¶

SPLITTER = True¶

getComUtil()¶

Get the macromodel com utility that holds the settings to write

Return type: schrodinger.application.macromodel.utils.comUtil
Returns: The comUtil object with settings

writeCom()¶: Write out the Macromodel com file

getComName()¶

Get the name of the com file for this step

Return type: str
Returns: The name of the com file

writeInput(struct)¶: Override the parent method to also write the com file

getNumSplits()¶

Get the number of parallel workflows this step will create. A 1 indicates that this step does not split the workflow.

Return type: int
Returns: The number of parallel workflows this step creates. 1 means it does not split the workflow

getStructForChild(index=1)¶

Get the structure from this step to pass on to a child step

Parameters: index (int) – The 1-based index of the structure to get. Should be 1 unless the child step is the first step of a split workflow. In that case, this is the index of the split workflow. Unused in the base class, but subclasses that split workflows may use this.
Return type: structure.Structure or cms.Cms
Returns: The structure the child step should use

getStructsForWriting()¶

Get the structures from this step to write to the final Workflow file

Return type: list of schrodinger.structure.Structure
Returns: A list of structures to write

class schrodinger.application.matsci.jwsteps.VoidStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

A step for running the Distributed Voids driver

STEP_NAME = 'Distribute voids'¶

JOB_BASE = 'voids'¶

DRIVER_PATH = 'distribute_voids_gui_dir/distribute_voids_driver.py'¶

DRIVER = <module 'distribute_voids_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/distribute_voids_gui_dir/distribute_voids_driver.py'>¶

FLAGS = {'-force': None, '-void_pct': 10}¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.FreeVolumeStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

A step for running the Distributed Voids driver

STEP_NAME = 'Free volume'¶

JOB_BASE = 'freevol'¶

DRIVER_PATH = 'free_volume_analysis_gui_dir/free_volume_analysis_driver.py'¶

DRIVER = <module 'free_volume_analysis_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/free_volume_analysis_gui_dir/free_volume_analysis_driver.py'>¶

BUILTIN_WF_FILE = 'single_stage_free_volume.wfw'¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.BaseMetaJaguarWorkflowStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

Base Step for MatSci workflows that themselves run Jaguar subjobs

FLAGS_ADD_TPP = True¶

class schrodinger.application.matsci.jwsteps.JaguarStep(*args, keywords=None, esp_for_md=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseMetaJaguarWorkflowStep

A step for running a single Jaguar calculation

STEP_NAME = 'Jaguar'¶

JOB_BASE = 'jag'¶

DRIVER_PATH = None¶

DRIVER = None¶

FLAGS_ADD_JOB_NAME = False¶

THREADS = True¶

__init__(*args, keywords=None, esp_for_md=False, **kwargs)¶

Create a JaguarStep instance

Parameters

keywords (dict) – Keys are keyword names, values are keyword values. This parameter overrides the keystring argument of the base class. If keywords is not given, keystring will be used if keystring is given.
esp_for_md (bool) – After Jaguar finishes, store the ESP charges as custom forcefield charges in the .01.mae file

See parent class for additional information

writeInput(struct)¶

Write the input file

Type: structure.Structure or None
Parameters: struct – The structure to write. If None it will write the input file.

getInputName()¶

Get the name of the input structure file

Return type: str
Returns: The input structure file name

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

createCommand()¶

Create the command line

Return type: list
Returns: The command line in list form

processSmapInfo()¶

Create an smap file in the subjob directory to enable Maestro’s little blue v and s buttons if the user manually imports the subjob output. Also copy smap-eligible files to the main job directory and pass back the file information needed for writing the main job smap file.

Return type: list
Returns: Each item of the list is a file name that should appear in the main job smap file for this step.

processOutput(output)¶

Process the output of a job during the finish part of the step

Parameters: output (list) – The only item in the list is the output structure

class schrodinger.application.matsci.jwsteps.BDEStep(*args, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseMetaJaguarWorkflowStep

A step for running the Bond Dissociation Energy workflow

KEYS = {'basis': 'MIDIXL', 'dftname': 'B3LYP', 'iaccg': 3, 'igeopt': 1, 'isymm': 0, 'maxit': 100, 'nofail': 1, 'nops_opt_switch': 10}¶

STEP_NAME = 'BDE'¶

JOB_BASE = 'bde'¶

DRIVER_PATH = 'bond_dissociation_gui_dir/bond_dissociation_driver.py'¶

DRIVER = <module 'bond_dissociation_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/bond_dissociation_gui_dir/bond_dissociation_driver.py'>¶

FLAGS = {'-allow_hx': 'no', '-bonds': None, '-states': 's0'}¶

FLAGS_ADD_DOUBLE_DASH = True¶

__init__(*args, **kwargs)¶

Create a BDEStep instance.

See parent class for additional documentation.

getStructsOfType(stype)¶

A generator for structures of the given type from BDE results

Parameters: stype (str) – The type of structure to get ‘Reactants’, ‘Reactions’, ‘Fragments’
Return type: Iterator
Returns: Iterator of schrodinger.Structure for the request type

getStructsForWriting()¶

Get the structure to write for this step. It will be the reactant structure

Return type: list of schrodinger.Structure
Returns: The reactant structure

class schrodinger.application.matsci.jwsteps.HOFStep(*args, high=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseMetaJaguarWorkflowStep

A step for running the Heat of Formation workflow

PROCS = 2¶

STEP_NAME = 'HOF'¶

JOB_BASE = 'hof'¶

DRIVER_PATH = 'jaguar'¶

FLAGS = {'-method_sp': 'M06-2X', '-scalfr': '0.9806', '-zpe': None, 'deltah.py': None, 'run': None}¶

FLAGS_ADD_JOB_NAME = False¶

HOF_PROP = 'r_j_Delta_H_of_Formation(298K)_(kcal/mol)'¶

__init__(*args, high=False, **kwargs)¶

Create a HOFStep instance.

Parameters: high (bool) – True if we are computing heat of formation at the high level of accuracy

See parent class for additional documentation.

outputStructurePath()¶

Get the path to the subjob subdirectory that contains the results

Return type: str
Returns: The path to the subdirectory inside the subjob’s directory that holds the results.

getInputName()¶

Get the name of the input structure file

Return type: str
Returns: The input structure file name

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.CustomMaeStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

A step for running custom scripts that output a .mae file

STEP_NAME = 'Custom'¶

JOB_BASE = 'custom'¶

USES_JC = False¶

USES_MULTI_SUBJOBS = True¶

USES_THREADS = True¶

class schrodinger.application.matsci.jwsteps.BaseDesmondStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

Base class for steps that use Desmond as the main engine or produce a cms file

OUTPUTS_CMS = True¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'gpu'¶

__init__(*args, maestro_in=False, **kwargs)¶

Create a BaseDesmondStep instance

Parameters: maestro_in (bool) – If true, the class will write a Maestro input file (.maegz) rather than a CMS (.cms) file

See parent class for additional documentation

REQUIRES_CMS_INPUT = True¶

getStructsForWriting()¶

Get the output Maestro structure derived from the output CMS system

Return type: list of schrodinger.Structure
Returns: The output Maestro structure

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

getInputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

getTrajectoryName()¶

Get the name of the output trajectory directory

Return type: str or None
Returns: The output trajectory directory name or None if this step does not create trajectories

class schrodinger.application.matsci.jwsteps.ReplicateMakerMixin¶

Bases: object

A mixin for built-in workflows that can optionally produce multiple structures that split the workflow

property output_file_names¶

Get the names of all the output structures

Return type: list
Returns: Each item of the list is a the name of an output file. The step subdirectory path is NOT prepended to the file name.

getOutputEnding()¶

Get the output file ending based on the command line flags

Return type: str
Returns: The output file ending appropriate for CMS or MAE output

getOutputFileNamePattern()¶

A glob pattern that matches output file names

Return type: str
Returns: The pattern to use when globbing for output files

getNumSplits()¶

Get the number of parallel workflows this step will create. A 1 indicates that this step does not split the workflow.

Return type: int
Returns: The number of parallel workflows this step creates. 1 means it does not split the workflow

getStructForChild(index=1)¶

Get the structure from this step to pass on to a child step

Parameters: index (int) – The 1-based index of the structure to get. Should be 1 unless this step is splitting the workflow into parallel workflows, in which case it is the index of the workflow that will run this structure. Unused in the base class, but subclasses may use this parameter.
Return type: structure.Structure or cms.Cms
Returns: The structure the child step should use

getStructsForWriting()¶

Get the structures from this step to write to the final Workflow file

Return type: list of schrodinger.structure.Structure
Returns: A list of structures to write

class schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep(*args, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.ReplicateMakerMixin, schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs the Disordered System Builder.

STEP_NAME = 'Disordered system'¶

JOB_BASE = 'dsb'¶

DRIVER_PATH = 'disordered_system_builder_gui_dir/disordered_system_builder_driver.py'¶

DRIVER = <module 'disordered_system_builder_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/disordered_system_builder_gui_dir/disordered_system_builder_driver.py'>¶

FLAGS = {'-forcefield': 'S-OPLS', '-grid': None, '-pack': None, '-split_components': None}¶

REQUIRES_CMS_INPUT = False¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

USES_MULTI_SUBJOBS = True¶

BUILTIN_WF_FILE = 'single_stage_disorder_system_single_component.wfw'¶

MAE_ENDING = '_amorphous.maegz'¶

CMS_ENDING = '_system-out.cms'¶

__init__(*args, **kwargs)¶

Create a DisorderedSystemBuilderStep instance

See parent class for additional documentation

getOutputEnding()¶

Get the output file ending based on the command line flags

Return type: str
Returns: The output file ending appropriate for CMS or MAE output

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.PolymerBuilderStep(*args, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.ReplicateMakerMixin, schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs the Polymer Builder.

STEP_NAME = 'Polymer Builder'¶

JOB_BASE = 'polybuild'¶

DRIVER_PATH = 'polymer_builder_gui_dir/polymer_builder_driver.py'¶

DRIVER = <module 'polymer_builder_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/polymer_builder_gui_dir/polymer_builder_driver.py'>¶

REQUIRES_CMS_INPUT = False¶

FLAGS = {'-simple_input': None}¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

USES_MULTI_SUBJOBS = True¶

BUILTIN_WF_FILE = 'single_stage_polymer_builder.wfw'¶

MAE_NOCELL_ENDING = '-polymer.maegz'¶

MAE_CELL_ENDING = '-amcell.maegz'¶

CMS_ENDING = '_system-out.cms'¶

__init__(*args, **kwargs)¶

Create a PolymerBuilderStep instance

See parent class for additional documentation

getInputName()¶

Get the name of the input structure file

Return type: str
Returns: The input structure file name

removeIncomingProperties(*args, **kwargs)¶: Override the parent method to do nothing since we don’t have a single simple input structure and the properties do not survive the polymer builder.

getOutputEnding()¶

Get the output file ending based on the command line flags

Return type: str
Returns: The output file ending appropriate for CMS or MAE output

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.PrepForMDStep(*args, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs Prepare for MD to create a Desmond system.

STEP_NAME = 'Prepare for MD'¶

JOB_BASE = 'prepmd'¶

DRIVER_PATH = 'prepare_for_md_gui_dir/prepare_for_md_driver.py'¶

DRIVER = <module 'prepare_for_md_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/prepare_for_md_gui_dir/prepare_for_md_driver.py'>¶

FLAGS = {'-forcefield': 'S-OPLS', '-split_components': None}¶

REQUIRES_CMS_INPUT = False¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

BUILTIN_WF_FILE = 'single_stage_prepare_for_md.wfw'¶

__init__(*args, **kwargs)¶

Create a PrepForMDStep object

See parent class for documentation

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.MolecularDynamicsStep(*args, analysis=False, average=None, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs one or more Desmond MD stages

STEP_NAME = 'Relaxation'¶

JOB_BASE = 'relax'¶

ANALYSIS_FRAME_PERCENT = 20¶

CAN_CREATE_TRAJECTORY = True¶

RESOURCE = 'gpu'¶

SUBJOB_RESOURCE = 'gpu'¶

__init__(*args, analysis=False, average=None, **kwargs)¶

Create a MolecularDynamicsStep object

Parameters

analysis (bool) – Whether to perform a trajectory analysis on the last MD stage
average (int) – What percent of the final MD stage trajectory to average the cell size over

See parent class for documentation

addVelocityIfNeeded(kwargs)¶

Add the velocity write keyword if there will be analysis done

Parameters: kwargs (dict) – dict of current keyword/value pairs - modified if velocity is needed

getStringers()¶

Create the stringers that define each MD stage

Return type: list
Returns: A list of MSJStringer objects

writeMSJFile()¶: Write the MSJ file for this step

writeInput(struct)¶

Write the input structure file and msj file

Parameters: struct (structure.Structure or None) – The structure to write. If None it will write the input file.

getMSJName()¶

Get the name of the MSJ file

Return type: str
Returns: The MSJ file name

createJob()¶

Form the command line and create a job for the queue

Return type: jobutils.RobustSubmissionJob
Returns: The job to add to the JobDJ

processOutput(output)¶

Process the output of a job during the finish part of the step

Parameters: output – The output of the job. If it evaluates to False, no processing is done. Otherwise it is unused.

class schrodinger.application.matsci.jwsteps.BaseRelaxationStep(*args, temp=300.0, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.MolecularDynamicsStep

A base class for relaxation step

STEP_NAME = 'BaseRelaxation'¶

JOB_BASE = 'baserelax'¶

__init__(*args, temp=300.0, **kwargs)¶

Create a base relaxation object

Parameters: temp (float) – Temperature for the final relaxation step

See parent class for documentation

getStringers()¶

Create the stringers that define each MD stage

Raises: NotImplementedError – Overwrite this method
Return type: str
Returns: A list of MSJStringer objects

class schrodinger.application.matsci.jwsteps.MatSciMDRelaxationStep(*args, temp=300.0, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseRelaxationStep

A step that runs a MatSci MD relaxation protocol

STEP_NAME = 'MSRelaxation'¶

JOB_BASE = 'msrelax'¶

getStringers()¶

Create the stringers that define each MD stage

Return type: str
Returns: A list of MSJStringer objects

class schrodinger.application.matsci.jwsteps.CompressiveRelaxationStep(*args, temp=300.0, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseRelaxationStep

A step that runs a compressive relaxation protocol

STEP_NAME = 'CompressRelaxation'¶

JOB_BASE = 'comprelax'¶

getStringers()¶

Create the stringers that define each MD stage

Return type: str
Returns: A list of MSJStringer objects

class schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation1Step(*args, temp=300.0, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseRelaxationStep

A step that runs first Semi-Crystalline relaxation protocol

STEP_NAME = 'SemiCrystalRelaxation1'¶

JOB_BASE = 'semicrystalrelax1'¶

getStringers()¶

Create the stringers that define each MD stage

Return type: str
Returns: A list of MSJStringer objects

class schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation2Step(*args, temp=300.0, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseRelaxationStep

A step that runs second Semi-Crystalline relaxation protocol

STEP_NAME = 'SemiCrystalRelaxation2'¶

JOB_BASE = 'semicrystalrelax2'¶

getStringers()¶

Create the stringers that define each MD stage

Return type: str
Returns: A list of MSJStringer objects

class schrodinger.application.matsci.jwsteps.SingleMDStep(*args, params=None, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.MolecularDynamicsStep

A step that runs a single MD simulation

STEP_NAME = 'md'¶

JOB_BASE = 'md'¶

STRINGER_CLASS¶: alias of schrodinger.application.matsci.desconfig.MDMSJStringer

__init__(*args, params=None, **kwargs)¶

Create a MatSciMDRelaxationStep object

Parameters: temp (dict) – Keyword arguments to pass to the STRINGER_CLASS

See parent class for documentation

getStringers()¶

Create the stringers that define each MD stage

Return type: list
Returns: A list of MSJStringer objects

class schrodinger.application.matsci.jwsteps.SingleBrownieStep(*args, params=None, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.SingleMDStep

A step that runs a single Brownie step

STEP_NAME = 'brownie'¶

JOB_BASE = 'brownie'¶

STRINGER_CLASS¶: alias of schrodinger.application.matsci.desconfig.BrownieMSJStringer

class schrodinger.application.matsci.jwsteps.MDCustomMSJStep(*args, msj=None, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.MolecularDynamicsStep

A step that runs MD with a custom MSJ file

STEP_NAME = 'Customized MD'¶

JOB_BASE = 'custom_md'¶

CAN_CREATE_TRAJECTORY = True¶

__init__(*args, msj=None, **kwargs)¶

Create a MSCustomMSJStep object

Parameters: msj (str) – The of the msj file to use

See parent class for documentation

writeMSJFile()¶: Write the MSJ file for this step

getMSJName()¶

Get the name of the MSJ file

Return type: str
Returns: The MSJ file name

class schrodinger.application.matsci.jwsteps.TgStep(*args, melting=False, bilinear=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a Tg calculation

STEP_NAME = 'Tg'¶

JOB_BASE = 'tg'¶

DRIVER_PATH = 'thermophysical_properties_gui_dir/thermophysical_properties_driver.py'¶

DRIVER = <module 'thermophysical_properties_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/thermophysical_properties_gui_dir/thermophysical_properties_driver.py'>¶

FLAGS = {'-density_stage_time': 20, '-frame_interval': 200.0, '-job_order': 'max_first', '-load_temp_structure': 200.0, '-max_convergence_retries': 5, '-max_temp': 600, '-min_temp': 200, '-temp_step': 25}¶

FLAGS_INPUT_NAME_FLAG = '-icms'¶

CAN_CREATE_TRAJECTORY = True¶

USES_MULTI_SUBJOBS = True¶

BUILTIN_WF_FILE = 'single_stage_Tg.wfw'¶

__init__(*args, melting=False, bilinear=False, **kwargs)¶

Create a TgStep object

Parameters

melting (bool) – If True, temps will run from low to high. Otherwise, (default), they will run from high to low.
bilinear (bool) – If True, the Tg fit will be done via the bilinear method. Otherwise, (default), it will be done via hyperbola

See parent class for additional documentation

processOutput(output)¶

Process the output of a job during the finish part of the step. This computes the Tg via fit of temperature vs density.

Parameters: output (list) – The output of the job. The first item should be the structure (Cms or Structure) that contains the density vs temperature properties.

class schrodinger.application.matsci.jwsteps.StressStrainStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a Stress-Strain calculation

STEP_NAME = 'Stress'¶

JOB_BASE = 'stress'¶

DRIVER_PATH = 'stress_strain_gui_dir/stress_strain_driver.py'¶

DRIVER = <module 'stress_strain_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/stress_strain_gui_dir/stress_strain_driver.py'>¶

CAN_CREATE_TRAJECTORY = True¶

BUILTIN_WF_FILE = 'single_stage_stress_strain.wfw'¶

class schrodinger.application.matsci.jwsteps.DiffusionMSDStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a MSD Diffusion calculation

STEP_NAME = 'Diffusion by MSD'¶

JOB_BASE = 'diffusion_msd'¶

DRIVER_PATH = 'diffusion_coefficient_gui_dir/diffusion_coefficient_msd_driver.py'¶

DRIVER = <module 'diffusion_coefficient_msd_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/diffusion_coefficient_gui_dir/diffusion_coefficient_msd_driver.py'>¶

CAN_CREATE_TRAJECTORY = True¶

BUILTIN_WF_FILE = 'single_stage_diffusion_msd.wfw'¶

getTrajectoryName()¶

Get the name of the output trajectory directory

Return type: str
Returns: The output trajectory directory name

class schrodinger.application.matsci.jwsteps.DiffusionGKStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a velocity autocorrelation Diffusion calculation

STEP_NAME = 'Diffusion by GK'¶

JOB_BASE = 'diffusion_vel'¶

DRIVER_PATH = 'diffusion_coefficient_gui_dir/diffusion_coefficient_gk_driver.py'¶

DRIVER = <module 'diffusion_coefficient_gk_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/diffusion_coefficient_gui_dir/diffusion_coefficient_gk_driver.py'>¶

CAN_CREATE_TRAJECTORY = True¶

BUILTIN_WF_FILE = 'single_stage_diffusion_gk.wfw'¶

getTrajectoryName()¶

Get the name of the output trajectory directory

Return type: str
Returns: The output trajectory directory name

class schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a polymer crosslink calculation

STEP_NAME = 'Crosslinking'¶

JOB_BASE = 'xlink'¶

FLAGS_INPUT_NAME_FLAG = '-icms'¶

DRIVER_PATH = 'polymer_crosslink_gui_dir/polymer_crosslink_driver.py'¶

DRIVER = <module 'polymer_crosslink_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/polymer_crosslink_gui_dir/polymer_crosslink_driver.py'>¶

BUILTIN_WF_FILE = 'single_stage_polymer_crosslink_amide_bond.wfw'¶

class schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a stress-based elastic constants calculation

STEP_NAME = 'Estress'¶

JOB_BASE = 'estress'¶

FLAGS_INPUT_NAME_FLAG = '-icms'¶

DRIVER_PATH = 'elastic_constants_gui_dir/elastic_constants_driver2.py'¶

DRIVER = <module 'elastic_constants_driver2' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/elastic_constants_gui_dir/elastic_constants_driver2.py'>¶

CAN_CREATE_TRAJECTORY = True¶

BUILTIN_WF_FILE = 'single_stage_elastic_constant_stress_based.wfw'¶

class schrodinger.application.matsci.jwsteps.ElasticConstantsStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep

A step that runs a non-stress elastic constants calculation

STEP_NAME = 'Elastic'¶

JOB_BASE = 'elastic'¶

DRIVER_PATH = 'elastic_constants_gui_dir/elastic_constants_driver.py'¶

DRIVER = <module 'elastic_constants_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/elastic_constants_gui_dir/elastic_constants_driver.py'>¶

OUTPUTS_CMS = False¶

USES_MULTI_SUBJOBS = True¶

BUILTIN_WF_FILE = 'single_stage_elastic_constant_energy_based.wfw'¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.PenetrantLoadingStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a Penetrant Loading calculation

STEP_NAME = 'pload'¶

JOB_BASE = 'pload'¶

DRIVER_PATH = 'penetrant_loading_gui_dir/penetrant_loading_driver.py'¶

DRIVER = <module 'penetrant_loading_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/penetrant_loading_gui_dir/penetrant_loading_driver.py'>¶

CAN_CREATE_TRAJECTORY = True¶

BUILTIN_WF_FILE = 'single_stage_penetrant_loading.wfw'¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

getTrajectoryName()¶

Get the name of the output trajectory directory

Return type: str
Returns: The output trajectory directory name

class schrodinger.application.matsci.jwsteps.ViscosityStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a viscosity calculation

STEP_NAME = 'Viscosity'¶

JOB_BASE = 'viscosity'¶

DRIVER_PATH = 'viscosity_gui_dir/viscosity_gk_driver.py'¶

DRIVER = <module 'viscosity_gk_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/viscosity_gui_dir/viscosity_gk_driver.py'>¶

CAN_CREATE_TRAJECTORY = False¶

BUILTIN_WF_FILE = 'single_stage_viscosity.wfw'¶

class schrodinger.application.matsci.jwsteps.SurfaceTensionStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a surface tension calculation

STEP_NAME = 'Surface Tension'¶

JOB_BASE = 'surface_tension'¶

DRIVER_PATH = 'surface_tension_gui_dir/surface_tension_driver.py'¶

DRIVER = <module 'surface_tension_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/surface_tension_gui_dir/surface_tension_driver.py'>¶

CAN_CREATE_TRAJECTORY = True¶

BUILTIN_WF_FILE = 'single_stage_surface_tension.wfw'¶

getTrajectoryName()¶

Get the name of the output trajectory directory

Return type: str
Returns: The output trajectory directory name

class schrodinger.application.matsci.jwsteps.EvaporationStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs an evaporation calculation

STEP_NAME = 'Evaporation'¶

JOB_BASE = 'evaporation'¶

DRIVER_PATH = 'evaporation_gui_dir/evaporation_driver.py'¶

DRIVER = <module 'evaporation_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/evaporation_gui_dir/evaporation_driver.py'>¶

CAN_CREATE_TRAJECTORY = False¶

BUILTIN_WF_FILE = 'single_stage_evaporation.wfw'¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a Polymer Chain Analysis

STEP_NAME = 'pcan'¶

JOB_BASE = 'pcan'¶

DRIVER_PATH = 'polymer_chain_analysis_gui_dir/polymer_chain_analysis_driver.py'¶

DRIVER = <module 'polymer_chain_analysis_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/polymer_chain_analysis_gui_dir/polymer_chain_analysis_driver.py'>¶

REQUIRES_TRAJECTORY_INPUT = True¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

BUILTIN_WF_FILE = 'single_stage_polymer_chain_analysis.wfw'¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.StructureFactorStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a Structure Factor calculation

STEP_NAME = 'sfactor'¶

JOB_BASE = 'sfactor'¶

DRIVER_PATH = 'structure_factor_gui_dir/structure_factor_driver.py'¶

DRIVER = <module 'structure_factor_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/structure_factor_gui_dir/structure_factor_driver.py'>¶

FLAGS_INPUT_NAME_FLAG = '-cms_file'¶

REQUIRES_TRAJECTORY_INPUT = True¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

BUILTIN_WF_FILE = 'single_stage_structure_factor.wfw'¶

class schrodinger.application.matsci.jwsteps.SimulationProfileStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a Simulation Profile calculation

STEP_NAME = 'profile'¶

JOB_BASE = 'profile'¶

DRIVER_PATH = 'trajectory_density_analysis_gui_dir/trajectory_density_analysis_driver.py'¶

DRIVER = <module 'trajectory_density_analysis_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/trajectory_density_analysis_gui_dir/trajectory_density_analysis_driver.py'>¶

FLAGS_INPUT_NAME_FLAG = '-cms_file'¶

REQUIRES_TRAJECTORY_INPUT = True¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

BUILTIN_WF_FILE = 'single_stage_trajectory_density_analysis.wfw'¶

class schrodinger.application.matsci.jwsteps.CustomCmsStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step for running custom scripts that output a .cms file

STEP_NAME = 'Custom'¶

JOB_BASE = 'custom'¶

USES_JC = False¶

USES_MULTI_SUBJOBS = True¶

USES_THREADS = True¶

class schrodinger.application.matsci.jwsteps.CustomCmsToMaeStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.CustomCmsStep

A step for running custom scripts that take in a .cms file and output .maegz

STEP_NAME = 'Custom'¶

JOB_BASE = 'custom'¶

OUTPUTS_CMS = False¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.CustomTrajectoryStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.CustomCmsStep

A step for running custom scripts that output a .cms file and create trajectories

CAN_CREATE_TRAJECTORY = True¶

class schrodinger.application.matsci.jwsteps.ClusterAnalysisStep(*args, maestro_in=False, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseDesmondStep

A step that runs a Cluster Analysis calculation

STEP_NAME = 'cluster'¶

JOB_BASE = 'cluster'¶

DRIVER_PATH = 'cluster_analysis_gui_dir/cluster_analysis_driver.py'¶

DRIVER = <module 'cluster_analysis_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/cluster_analysis_gui_dir/cluster_analysis_driver.py'>¶

FLAGS_INPUT_NAME_FLAG = '-cms_file'¶

OUTPUTS_CMS = False¶

RESOURCE = 'cpu'¶

SUBJOB_RESOURCE = 'cpu'¶

BUILTIN_WF_FILE = 'single_stage_cluster_analysis.wfw'¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

class schrodinger.application.matsci.jwsteps.BaseNoJobStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

A base class for steps that do not run a job but perform some other action.

PROCS = 0¶

DRIVER_PATH = None¶

DRIVER = None¶

USES_JC = False¶

createCommand()¶

Create the command line

Return type: list
Returns: An empty list because this class does not use the command line

adjustCommandForQueue(cmd)¶

Add subhost and umbrella flags that direct this step’s subjobs to the correct host. Modifies the given command list in place.

This method does nothing in the base class because it does not submit jobs to the queue

Parameters: cmd (list) – The current command line as a list of strings

canDriverUseUmbrella()¶

Check whether the driver for this step knows the -md_umbrella flag

Return type: False
Returns: This class does not submit jobs to the queue so cannot use umbrella mode

determineQueueResource(cmd)¶

Determine what resource this job should request

Parameters: cmd (list) – The command line as a list of strings
Return type: None
Returns: This class does not use queue resources

createQJobFromCommand(cmd)¶

Create the JobDJ job from the list of command line arguments. The job will be set to run in the Step subdirectory.

Return type: None
Returns: This class does not create a job

class schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseNoJobStep

DRIVER_PATH = 'MultipleStructSplitterStep'¶

PROGRAM_NAME = 'Multiple Structure Splitter'¶

SPLITTER = True¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

getNumSplits()¶

Get the number of parallel workflows this step will create. A 1 indicates that this step does not split the workflow.

Return type: int
Returns: The number of parallel workflows this step creates. 1 means it does not split the workflow

getStructForChild(index=1)¶

Get the structure from this step to pass on to a child step

Parameters: index (int) – The 1-based index of the structure to get. Should be 1 unless the child step is the first step of a split workflow. In that case, this is the index of the split workflow. Unused in the base class, but subclasses that split workflows may use this.
Return type: structure.Structure or cms.Cms
Returns: The structure the child step should use

getStructsForWriting(*args, **kwargs)¶: Override the parent method to return no structures

getOutput(*args, **kwargs)¶: Override the parent method to do nothing

processOutput(*args, **kwargs)¶: Override the parent method to do nothing

class schrodinger.application.matsci.jwsteps.ExtractClustersStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

A step for running the Extract Clusters driver

STEP_NAME = 'Extract Clusters'¶

JOB_BASE = 'extract'¶

DRIVER_PATH = 'extract_clusters_gui_dir/extract_clusters_driver.py'¶

DRIVER = <module 'extract_clusters_driver' from '/scr/buildbot/savedbuilds/2024-2/NB/build-134/mmshare-v6.6/python/scripts/extract_clusters_gui_dir/extract_clusters_driver.py'>¶

BUILTIN_WF_FILE = 'single_stage_extract_clusters.wfw'¶

SPLITTER = True¶

getOutputName()¶

Get the name of the output structure file

Return type: str
Returns: The output structure file name

getNumSplits()¶

Get the number of parallel workflows this step will create. A 1 indicates that this step does not split the workflow.

Return type: int
Returns: The number of parallel workflows this step creates. 1 means it does not split the workflow

getStructForChild(index=1)¶

Get the structure from this step to pass on to a child step

Parameters: index (int) – The 1-based index of the structure to get. Should be 1 unless the child step is the first step of a split workflow. In that case, this is the index of the split workflow. Unused in the base class, but subclasses that split workflows may use this.
Return type: structure.Structure or cms.Cms
Returns: The structure the child step should use

getStructsForWriting()¶

Get the structures from this step to write to the final Workflow file

Return type: list of schrodinger.structure.Structure
Returns: A list of structures to write

class schrodinger.application.matsci.jwsteps.CombinerStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, cpu_hostname=None, gpu_hostname=None, umbrella='per_flag', splitter=False, split_index=1, split_tag='', child_stages=None, use_jc=None, tpp=1, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseNoJobStep

DRIVER_PATH = 'Combiner'¶

PROGRAM_NAME = 'Combine Steps'¶

COMBINER = True¶

getStructForChild(index=1)¶

Get the structure from this step to pass on to a child step

Parameters: index (int) – Ignored in this class
Return type: str
Returns: The path relative to the main job directory pointing to the combined structure file

getOutput(*args, **kwargs)¶: Override the parent method to do nothing

write(*args, **kwargs)¶: Override the parent method to do nothing

writeInput(struct)¶

Write the input file

Type: structure.Structure or None
Parameters: struct – The structure to write. If None it will write the input file.