schrodinger.application.matsci.jwsteps module¶

Steps for use in Workflows

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

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. The only options used by this module is options.host, which are used by Step objects. Other options may be used by custom classes.
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
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.

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

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

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.

__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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

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

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, **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 BaseResults

STEP_NAME = 'Base Step'¶

JOB_BASE = 'base'¶

DRIVER_PATH = 'driver_dir/driver.py'¶

FLAGS = {}¶

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = False¶

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=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).

See parent class for additional documentation

writeInput(struct)¶

Write the input structure file

Parameters:	struct (structure.Structure) – The structure to write

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
Returns:	The starting structure 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.

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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

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

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

FLAGS_ADD_TPP = False¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseResults

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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

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
Returns:	The starting structure for this step

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

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, **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'¶

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

getOutputName()¶

Get the name of the output structure file

Return type:	str
Returns:	The output structure file name

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = False¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseResults

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=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).

See parent class for additional documentation

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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.

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
Returns:	The starting structure for this step

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

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

Parameters:	struct (structure.Structure) – The structure to write

class schrodinger.application.matsci.jwsteps.BaseMetaJaguarWorkflowStep(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=None, **kwargs)¶

Bases: schrodinger.application.matsci.jwsteps.BaseStep

Base Step for MatSci workflows that themselves run Jaguar subjobs

FLAGS_ADD_TPP = True¶

DRIVER_PATH = 'driver_dir/driver.py'¶

FLAGS = {}¶

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

JOB_BASE = 'base'¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseResults

STEP_NAME = 'Base Step'¶

__init__(*args, procs=1, tag=None, flags=None, archive=False, monitor_globs=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).

See parent class for additional documentation

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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

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
Returns:	The starting structure for this step

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

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

Parameters:	struct (structure.Structure) – The structure to write

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'¶

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

__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

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = True¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseResults

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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

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
Returns:	The starting structure for this step

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

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

Parameters:	struct (structure.Structure) – The structure to write

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¶

__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

processOutput(output)¶

Retrieve the heat of formation information from the output structure

Parameters:	output (list) – A list with the output structure as the first item

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_TPP = True¶

RESULTS_CLASS¶: alias of BaseResults

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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.

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
Returns:	The starting structure for this step

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

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

Parameters:	struct (structure.Structure) – The structure to write

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

RESULTS_CLASS¶: alias of BaseDesmondResults

__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

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

DRIVER_PATH = 'driver_dir/driver.py'¶

FLAGS = {}¶

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = False¶

JOB_BASE = 'base'¶

PROCS = 1¶

STEP_NAME = 'Base Step'¶

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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.

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
Returns:	The starting structure for this step

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

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

Parameters:	struct (structure.Structure) – The structure to write

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'¶

FLAGS = {'-forcefield': 'OPLS3e', '-grid': None, '-pack': None, '-split_components': None}¶

__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

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = False¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseDesmondResults

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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.

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
Returns:	The starting structure for this step

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

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

Parameters:	struct (structure.Structure) – The structure to write

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'¶

FLAGS = {'-forcefield': 'OPLS3e', '-split_components': None}¶

__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

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = False¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseDesmondResults

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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.

getStructForWriting()¶

Get the output Maestro structure derived from the output CMS system

Return type:	`schrodinger.Structure`
Returns:	The output Maestro structure

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

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

Parameters:	struct (structure.Structure) – The structure to write

class schrodinger.application.matsci.jwsteps.MolecularDynamicsStep(*args, analysis=False, **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¶

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

Create a MolecularDynamicsStep object

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

See parent class for documentation

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

Parameters:	struct (structure.Structure) – The structure to write

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:	`jaguarworkflows.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.

DRIVER_PATH = 'driver_dir/driver.py'¶

FLAGS = {}¶

FLAGS_ADD_INPUT_NAME = True¶

FLAGS_ADD_JOB_NAME = True¶

FLAGS_ADD_TPP = False¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseDesmondResults

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

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:	`jaguarworkflows.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

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
Returns:	The starting structure for this step

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

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.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'¶

FLAGS = {'-density_stage_time': 20, '-frame_interval': 200.0, '-gpu': None, '-job_order': 'max_first', '-load_temp_structure': 200.0, '-max_convergence_retries': 5, '-max_temp': 600, '-min_temp': 200, '-temp_step': 25}¶

FLAGS_ADD_INPUT_NAME = False¶

FLAGS_ADD_JOB_NAME = False¶

__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

FLAGS_ADD_TPP = False¶

PROCS = 1¶

RESULTS_CLASS¶: alias of BaseDesmondResults

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

calcsDone()¶

Check to see if the calculation finished successfully

Return type:	bool
Returns:	True if the calculation finished and was successful, 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

createJob()¶

Create the job command and object

Return type:	`jaguarworkflows.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:	`jaguarworkflows.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

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
Returns:	The starting structure for this step

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. 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.

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

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

Parameters:	struct (structure.Structure) – The structure to write

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