schrodinger.application.matsci.jwsteps module

Steps for use in Workflows

Copyright Schrodinger, LLC. All rights reserved.

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

exception schrodinger.application.matsci.jwsteps.JobCreationError

Bases: Exception

Raised when a job cannot be created

__init__(*args, **kwargs)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

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

Bases: schrodinger.application.matsci.jaguarworkflows.WorkFlow

Base Workflow class

This class does not assume the first step is the main step. Instead, set the main_step property to the main step. This is the step that will get all the workflow properties added to it.

The main step will also be the only step in the main PT group. All other steps will be in a “subjobs” subgroup.

__init__(*args, **kwargs)

Create a Workflow object

Parameters

• struct (schrodinger.structure.Structure) – The initial structure to use for the workflow

• options (argparse Namespace object) – The input options.

• count (int) – A serial number to distinguish this workflow from other workflows. May be used to create a unique base name.

• jobq (JobDJ) – The queue to submit jobs to

• strcleaner (schrodinger.application.matsci.jobutils.StringCleaner or None) – A StringCleaner instance used to guarantee unique workflow base names

• logger (logging.Logger) – The logger for this class

• subhierarchy (str) – If given, the final structure for all steps other than the main step will be placed in a PT subgroup with this name.

• robust (bool) – If True, use the robust Jaguar driver to run Jaguar jobs. If false, use Jaguar directly.

FALLBACK_BASE_NAME = 'structure'

check(log_zero_steps=False)

Check if this workflow is complete. Also, submit the next step(s) if the previous step has finished.

Parameters

log_zero_steps (bool) – log a message if there are zero steps

Return type

bool

Returns

True if the workflow is complete, False if not

generateBaseName(strcleaner, count)

Come up with a base name for this workflow based on the workflow structure title or a fallback name if the title can’t be used. Pass in a StringCleaner object to guarantee uniqueness.

Parameters

• strcleaner (schrodinger.application.matsci.jobutils.StringCleaner or None) – a StringCleaner instance to use for uniquifying names

• count (int) – A serial number to distinguish this workflow from other workflows. May be used to create a unique base name.

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

log(msg, prefix=True, level=20)

Add a message to the log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

periodicMaintenance()

The run_workflows function will call this method periodically - it can be used to perform operations while one of the workflow steps is running

recordFailureStatus()

Set properties based on the success/failure of each step, and write workflow structures to a summary failed file if any step failed

write(writer)

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

Parameters

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

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.JaguarOptimization(*args, **kwargs)

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

Class to run a Jaguar optimization and possibly thermochemistry

This class overrides many of the parent class methods to enable the step to run in a subdirectory. The parent class expects the job to run in the main workflow job directory.

STEP_NAME = 'Optimization'

JOB_BASE = 'opt'

USES_JC = True

__init__(*args, **kwargs)

See parent class for documentation

writeInput()

Override the parent method to work in the subjob directory

createJob()

Override the parent method to work in the subjob directory

start()

Override the parent method to work in the subjob directory

getOutput(*args, **kwargs)

Override the parent method to work in the subjob directory

createSmapFile()

Create the smap file that allows the surfaces to automatically import when the structure is manually imported into Maestro

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

finish()

Do any work required to create properties when the calculation has finished.

If property_name was provided to the constructor, this computes the energy difference between this step and the inherited parent step and stores it in the property name.

finishProcessingJobControlJob()

Add all the subjob files to the backend

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getStructure()

Get the starting structure for this step

Return type

schrodinger.structure.Structure

Returns

The starting structure for this step

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

periodicMaintenance()

This method is periodically called while the workflow is running

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

class schrodinger.application.matsci.jwsteps.BaseResults(parent)

Bases: object

A simple results class to provide the functionality from the jaguarworkflows.Results class that is still needed for non-Jaguar jobs

__init__(parent)

Create a BaseResults class

Parameters

parent (jaguarworkflows.Step) – The class these results are for

getMaeStructure()

Get the resulting Maestro structure for the parent class

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, **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

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseResults

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

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, **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.

See parent class for additional documentation

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

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

writeInput(struct)

Write the input file

Parameters

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

start()

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

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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.

getStructForWriting()

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

Return type

schrodinger.structure.Structure

Returns

The structure to write

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

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

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

Bases: schrodinger.application.matsci.jwsteps.BaseStep

Step to perform a macromodel conformational search

STEP_NAME = 'ConfSearch'

JOB_BASE = 'csearch'

DRIVER_PATH = 'bmin'

FLAGS = {}

FLAGS_ADD_INPUT_NAME = False

FLAGS_ADD_JOB_NAME = False

__init__(*args, **kwargs)

See parent class for documentation

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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

DRIVER = None

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = False

PROCS = 1

REQUIRES_CMS_INPUT = False

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the input structure file

Return type

str

Returns

The input structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

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

Return type

schrodinger.structure.Structure

Returns

The structure to write

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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, **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/2022-2/NB/build-128/mmshare-v5.8/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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = False

PROCS = 1

REQUIRES_CMS_INPUT = False

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, **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.

See parent class for additional documentation

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the input structure file

Return type

str

Returns

The input structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

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

Return type

schrodinger.structure.Structure

Returns

The structure to write

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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, **kwargs)

Bases: schrodinger.application.matsci.jwsteps.BaseStep

Base Step for MatSci workflows that themselves run Jaguar subjobs

FLAGS_ADD_TPP = True

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_INPUT_NAME_FLAG = ''

JOB_BASE = 'base'

OUTPUTS_CMS = False

PROCS = 1

REQUIRES_CMS_INPUT = False

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

STEP_NAME = 'Base Step'

USES_JC = True

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, **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.

See parent class for additional documentation

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the input structure file

Return type

str

Returns

The input structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

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

Return type

schrodinger.structure.Structure

Returns

The structure to write

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/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

processOutput(output)

Find the minimum BDE and store it as a workflow property

Parameters

output – Unused, kept for API compatibility

getStructForWriting()

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

Return type

schrodinger.Structure

Returns

The reactant structure

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = True

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = False

PROCS = 1

REQUIRES_CMS_INPUT = False

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the input structure file

Return type

str

Returns

The input structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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)'

SAVE_PROPS = {'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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

DRIVER = None

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_TPP = True

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = False

REQUIRES_CMS_INPUT = False

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseResults

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

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

Return type

schrodinger.structure.Structure

Returns

The structure to write

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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, **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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = False

PROCS = 1

REQUIRES_CMS_INPUT = False

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, full_command=None, local_files=None, input_file=None, **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.

See parent class for additional documentation

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the input structure file

Return type

str

Returns

The input structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

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

Return type

schrodinger.structure.Structure

Returns

The structure to write

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

class schrodinger.application.matsci.jwsteps.BaseDesmondResults(parent)

Bases: schrodinger.application.matsci.jwsteps.BaseResults

A simple results class to provide the functionality from the jaguarworkflows.Results class that is still needed for Desmond jobs

getMaeStructure()

Get the resulting Maestro structure for the parent class

__init__(parent)

Create a BaseResults class

Parameters

parent (jaguarworkflows.Step) – The class these results are for

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

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

OUTPUTS_CMS = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

JOB_BASE = 'base'

PROCS = 1

REQUIRES_TRAJECTORY_INPUT = False

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

STEP_NAME = 'Base Step'

USES_JC = True

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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

Bases: 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/2022-2/NB/build-128/mmshare-v5.8/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

__init__(*args, **kwargs)

Create a DisorderedSystemBuilderStep instance

See parent class for additional documentation

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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

Bases: 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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/polymer_builder_gui_dir/polymer_builder_driver.py'>

REQUIRES_CMS_INPUT = False

__init__(*args, **kwargs)

Create a PolymerBuilderStep instance

See parent class for additional documentation

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getInputName()

Get the name of the input structure file

Return type

str

Returns

The input structure file name

writeInput(*args, **kwargs)

Overrides the parent method to copy the full input structure file or list of structures from parent rather than write a single structure.

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.

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/prepare_for_md_gui_dir/prepare_for_md_driver.py'>

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

REQUIRES_CMS_INPUT = False

__init__(*args, **kwargs)

Create a PrepForMDStep object

See parent class for documentation

getStructure()

See parent class for documentation

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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

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

Create a MolecularDynamicsStep object

Parameters

• analysis (bool) – Whether to perform a trajectory analysis as the last stage

• average (int) – What percent of the final stage trajectory to average the cell size over

See parent class for documentation

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

getStringers()

Create the stringers that define each 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.

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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 stage

Raises

NotImplementedError – Overwrite this method

Return type

str

Returns

A list of MSJStringer objects

ANALYSIS_FRAME_PERCENT = 20

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Form the command line and create a job for the queue

Return type

jobutils.RobustSubmissionJob

Returns

The job to add to the JobDJ

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getMSJName()

Get the name of the MSJ file

Return type

str

Returns

The MSJ file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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.

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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.

writeMSJFile()

Write the MSJ file for this step

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 stage

Return type

str

Returns

A list of MSJStringer objects

ANALYSIS_FRAME_PERCENT = 20

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Form the command line and create a job for the queue

Return type

jobutils.RobustSubmissionJob

Returns

The job to add to the JobDJ

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getMSJName()

Get the name of the MSJ file

Return type

str

Returns

The MSJ file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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.

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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.

writeMSJFile()

Write the MSJ file for this step

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 stage

Return type

str

Returns

A list of MSJStringer objects

ANALYSIS_FRAME_PERCENT = 20

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Form the command line and create a job for the queue

Return type

jobutils.RobustSubmissionJob

Returns

The job to add to the JobDJ

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getMSJName()

Get the name of the MSJ file

Return type

str

Returns

The MSJ file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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.

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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.

writeMSJFile()

Write the MSJ file for this step

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 stage

Return type

str

Returns

A list of MSJStringer objects

ANALYSIS_FRAME_PERCENT = 20

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Form the command line and create a job for the queue

Return type

jobutils.RobustSubmissionJob

Returns

The job to add to the JobDJ

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getMSJName()

Get the name of the MSJ file

Return type

str

Returns

The MSJ file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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.

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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.

writeMSJFile()

Write the MSJ file for this step

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 stage

Return type

str

Returns

A list of MSJStringer objects

ANALYSIS_FRAME_PERCENT = 20

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Form the command line and create a job for the queue

Return type

jobutils.RobustSubmissionJob

Returns

The job to add to the JobDJ

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getMSJName()

Get the name of the MSJ file

Return type

str

Returns

The MSJ file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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.

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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.

writeMSJFile()

Write the MSJ file for this step

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.desmondutils.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 stage

Return type

list

Returns

A list of MSJStringer objects

ANALYSIS_FRAME_PERCENT = 20

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Form the command line and create a job for the queue

Return type

jobutils.RobustSubmissionJob

Returns

The job to add to the JobDJ

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getMSJName()

Get the name of the MSJ file

Return type

str

Returns

The MSJ file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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.

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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.

writeMSJFile()

Write the MSJ file for this step

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.desmondutils.BrownieMSJStringer

ANALYSIS_FRAME_PERCENT = 20

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

addVelocityIfNeeded(kwargs)

Add the velocity write keyword if there will be an analysis stage

Parameters

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

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Form the command line and create a job for the queue

Return type

jobutils.RobustSubmissionJob

Returns

The job to add to the JobDJ

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getMSJName()

Get the name of the MSJ file

Return type

str

Returns

The MSJ file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStringers()

Create the stringers that define each stage

Return type

list

Returns

A list of MSJStringer objects

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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.

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

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.

writeMSJFile()

Write the MSJ file for this step

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/2022-2/NB/build-128/mmshare-v5.8/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'

SAVE_PROP_STARTS = {'r_matsci_Density(g/cm3)_@_'}

CAN_CREATE_TRAJECTORY = True

__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.

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

USES_JC = True

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/stress_strain_gui_dir/stress_strain_driver.py'>

SAVE_PROP_STARTS = {'r_matsci_Strain', 'r_matsci_Stress'}

CAN_CREATE_TRAJECTORY = True

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/polymer_crosslink_gui_dir/polymer_crosslink_driver.py'>

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/elastic_constants_gui_dir/elastic_constants_driver2.py'>

SAVE_PROPS = {'r_matsci_Bulk_Modulus_(MPa)', "r_matsci_Lame'_Lambda_(MPa)", "r_matsci_Lame'_Mu", 'r_matsci_Poisson_Ratio', 'r_matsci_Shear_Modulus_(MPa)', 'r_matsci_Universal_Anisotropy', "r_matsci_Young's_Modulus_(MPa)"}

CAN_CREATE_TRAJECTORY = True

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/elastic_constants_gui_dir/elastic_constants_driver.py'>

SAVE_PROP_STARTS = {'r_matsci_Strain'}

OUTPUTS_CMS = False

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = True

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = '-icms'

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {'r_matsci_Bulk_Modulus_(MPa)', "r_matsci_Lame'_Lambda_(MPa)", "r_matsci_Lame'_Mu", 'r_matsci_Poisson_Ratio', 'r_matsci_Shear_Modulus_(MPa)', 'r_matsci_Universal_Anisotropy', "r_matsci_Young's_Modulus_(MPa)"}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/penetrant_loading_gui_dir/penetrant_loading_driver.py'>

CAN_CREATE_TRAJECTORY = True

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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/polymer_chain_analysis_gui_dir/polymer_chain_analysis_driver.py'>

SAVE_PROPS = {'r_matsci_End-to-end_Distance_(Ang.)', 'r_matsci_End_Dist_Time_End_(ns)', 'r_matsci_End_Dist_Time_Start_(ns)', 'r_matsci_Extended_Chain_Length_(Ang.)', 'r_matsci_Mean_Fractional_Anisotropy', 'r_matsci_Mean_Squared_End_Distance_(Ang.^2)', 'r_matsci_Mean_Squared_Radius_Of_Gyration_(Ang.^2)', 'r_matsci_Persistence_Length_(Ang.)', 'r_matsci_Radius_Of_Gyration_(Ang.)', 's_matsci_End_Dist_File', 's_matsci_End_Internal_Dist_File', 's_matsci_Moment_of_Inertia_File', 's_matsci_Radius_of_Gyration_File', 's_matsci_Torsional_File'}

REQUIRES_TRAJECTORY_INPUT = True

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/structure_factor_gui_dir/structure_factor_driver.py'>

SAVE_PROPS = {'r_matsci_sq_resolution', 's_matsci_sq_method'}

FLAGS_INPUT_NAME_FLAG = '-cms_file'

REQUIRES_TRAJECTORY_INPUT = True

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/trajectory_density_analysis_gui_dir/trajectory_density_analysis_driver.py'>

FLAGS_INPUT_NAME_FLAG = '-cms_file'

REQUIRES_TRAJECTORY_INPUT = True

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = False

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

DRIVER = None

DRIVER_PATH = 'driver_dir/driver.py'

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

FLAGS_INPUT_NAME_FLAG = ''

JOB_BASE = 'custom'

OUTPUTS_CMS = True

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

STEP_NAME = 'Custom'

USES_JC = False

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

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/2022-2/NB/build-128/mmshare-v5.8/python/scripts/cluster_analysis_gui_dir/cluster_analysis_driver.py'>

FLAGS_INPUT_NAME_FLAG = '-cms_file'

ARCHIVED_INPUT = ['.in', '.mae', '.maegz']

ARCHIVED_KEEPERS = {'.smap', '.spm', '.vib', '.vis'}

CAN_CREATE_TRAJECTORY = False

FLAGS = {}

FLAGS_ADD_DOUBLE_DASH = False

FLAGS_ADD_INPUT_NAME = True

FLAGS_ADD_JOB_NAME = True

FLAGS_ADD_TPP = False

OUTPUTS_CMS = False

PROCS = 1

REQUIRES_CMS_INPUT = True

REQUIRES_TRAJECTORY_INPUT = False

RESULTS_CLASS

alias of schrodinger.application.matsci.jwsteps.BaseDesmondResults

SAVE_PROPS = {}

SAVE_PROP_STARTS = {}

USES_JC = True

__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

addParentalSubdirProperties(struct)

Add parental subdirectory properties to the structure

Parameters

struct (cms.Cms or schrodinger.structure.Structure) – The structure to add properties to

archiveFiles()

Create a tar.gz archive of all jaguar files and then removes any files that are no longer needed.

archiveSubDir()

Archive this step’s subdirectory and add it to the backend for copy back

calcsDone()

Check to see if the calculation finished

If finished and the job failed, self.ok will be set to False

Return type

bool

Returns

True if the calculation finished, False if not

canStart()

Check to see if this job can start - if the parent job(s) have finished successfully.

Return type

bool

Returns

True if the job can start, False if not

createCommand()

Create the command line

Return type

list

Returns

The command line in list form

Raises

JobCreationError – If the command cannot be created

createJob()

Create the job command and object

Return type

jobutils.RobustSubmissionJob

Returns

The job object to run Macromodel

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

finish()

Finish this step, including processing any output

finishProcessingJobControlJob()

Override the parent method to archive the directory if requested

getCMSSystem()

Get the output CMS system

Return type

cms.Cms

Returns

The output system

getInput(override_uhf=True, override_solvent=True)

Get the JaguarInput object for this step, setting the keywords as required.

Return type

None or jaguar_input.JaguarInput

Returns

None if an error occured, or the jaguar_input.JaguarInput object to use for this step

getInputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name

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.

getParentalSubdirectories()

Get the subdirectory names for parents and required stages

Return type

str, str

Returns

The parent subdirectory, and a space-separated string of all required stage subdirectories. The subdirectory paths are relative to the overall job directory.

getStructForWriting()

Get the output Maestro structure derived from the output CMS system

Return type

schrodinger.Structure

Returns

The output Maestro structure

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 or None

Returns

The starting structure for this step. None if input is not a structure.

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

handleFileLinkProperties(struct)

Fix existing Jaguar file link properties and add any new ones

Parameters

struct (structure.Structure) – The structure with the properties

log(msg, prefix=True, level=20)

Add a message to the parent workflow’s log file

Parameters

• msg (str) – The message to add

• prefix (bool) – Whether to add information about the workflow and step name to the front of the message string

• level (int) – A logging constant indicating the priority level of the message

monitorFiles()

Check for any requested files that need to be copied back immediately

periodicMaintenance()

This method is periodically called while the workflow is running

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

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

setKeywords(input, keystring)

Set the keywords for this job

Parameters

• input (jaguar_input.JaguarInput) – The JaguarInput object to set the keywords on

• keystring (str) – Space separated keyword=value pairs. Each pair must contain an equals sign

setSubDir()

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

start()

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

storeFilenames()

Store file names associated with this job before we delete the job object

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

writeInput(struct)

Write the input file

Parameters

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

getOutputName()

Get the name of the output structure file

Return type

str

Returns

The output structure file name