schrodinger.application.matsci.jaguar_multistage_workflow_utils module¶

Utilities for Jaguar multistage workflow.

schrodinger.application.matsci.jaguar_multistage_workflow_utils.set_up_logger(related_filename)¶

Set up the logger used in this module.

Parameters: related_filename (str) – the base name of this file name will be used as the base name of the log file name if not running under job control, otherwise the job name will be used

schrodinger.application.matsci.jaguar_multistage_workflow_utils.parse_yes_no_setting(setting, keyword)¶

Translate an English word into a boolean if possible

Parameters

setting (str) – The text (true/false/yes/no/on/off etc) to convert
keyword (str) – The associated keyword to show in error messages

Return type

bool

Returns

True if the setting translates to Truthy, False if it translates to Falsey

Raises

InvalidStageFileError – If setting can’t be translated

exception schrodinger.application.matsci.jaguar_multistage_workflow_utils.InvalidStageFileError¶

Bases: Exception

Class for any exception that occurs when reading in a settings file

exception schrodinger.application.matsci.jaguar_multistage_workflow_utils.MissingDataError¶

Bases: Exception

Raised when an expected structure property for Analysis is not found

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine(line, index)¶

Bases: object

Base class for lines that take keyword=value parameters

TAG = 'BASE'¶

ALL_KEYS = {}¶

__init__(line, index)¶

Create a ParameterLine object

Parameters

line (str) – The line to parse from the input file
index (int) – The 1-based index of this stage

Raises

InvalidStageFileError – If something is wrong with the line

getKeywords(line)¶

Parse the line into a set of keyword-value pairs

Parameters: line (str) – The line to parse from the input file
Return type: dict
Returns: Keys are lowercase keywords, values are values
Raises: InvalidStageFileError – If something is wrong with the line

validateKeywords(keywords, index)¶

Validate and pull information from the keywords

Parameters

keywords (dict) – Keys are class constant keywords
index (int) – The 1-based index of this stage

Raises

InvalidStageFileError – If something is wrong with the line

classmethod writeParameterLine(keywords, datafile)¶

Write a line with these settings to the given file

Parameters

keywords (dict) – The current settings
datafile (file) – The file object to write to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine(line, index)¶

Bases: schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine

Holds general information about a custom script

Used in the meta workflow driver but not the Jaguar multistage workflow

TAG = 'CUSTOM'¶

INPUT = 'input'¶

OUTPUT = 'output'¶

TRAJECTORY = 'trajectory'¶

PATH = 'path'¶

USE_JC = 'use_jc'¶

ALL_KEYS = {'input', 'output', 'path', 'trajectory', 'use_jc'}¶

MAEGZ = 'maegz'¶

CMS = 'cms'¶

OTHER = 'other'¶

ALLOWED_INPUT = {'cms', 'maegz', 'other'}¶

ALLOWED_OUTPUT = {'cms', 'maegz'}¶

DO_NOT_CHECK_PATH = 'Not_located'¶

validateKeywords(keywords, index)¶

Validate and pull information from the keywords

Parameters

keywords (dict) – Keys are class constant keywords
index (int) – The 1-based index of this stage

Raises

InvalidStageFileError – If something is wrong with the line

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine(line, index)¶

Bases: schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine

Holds general information about a stage: name, parent, etc.

Used in the meta workflow driver but not the Jaguar multistage workflow

TAG = 'INFO'¶

NAME = 'name'¶

PARENT = 'parent'¶

MAIN = 'main'¶

REQUIRES = 'requires'¶

SPLITTER = 'splitter'¶

SUBJOBS = 'subjobs'¶

THREADS = 'threads'¶

ALL_KEYS = {'main', 'name', 'parent', 'requires', 'splitter', 'subjobs', 'threads'}¶

__init__(line, index)¶

Create a StageInfoLine object

Parameters

line (str) – The line to parse from the input file
index (int) – The 1-based index of this stage

Raises

InvalidStageFileError – If something is wrong with the line

validateKeywords(keywords, index)¶

Validate and pull information from the keywords

Parameters

keywords (dict) – Keys are class constant keywords
index (int) – The 1-based index of this stage

Raises

InvalidStageFileError – If something is wrong with the line

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams(line, partial=False)¶

Bases: object

Holds information about an MD simulation stage

MD = 'md'¶

BROWNIE = 'brownie'¶

MS_RELAX = 'matsci_relaxation'¶

COMPRESSIVE_RELAX = 'compress_relaxation'¶

SEMI_CRYSTALLINE1_RELAX = 'semi_crystal_relaxation1'¶

SEMI_CRYSTALLINE2_RELAX = 'semi_crystal_relaxation2'¶

CUSTOM_MSJ = 'custom'¶

TYPE = 'type'¶

ENSEMBLE = 'ensemble'¶

TIME = 'time'¶

TEMP = 'temp'¶

PRESSURE = 'pressure'¶

TIMESTEP = 'timestep'¶

TRJINT = 'trj_interval'¶

TRJINT_STRINGER = 'trajectory_dot_interval'¶

SEED = 'seed'¶

SEED_STRINGER = 'random_seed'¶

ANALYSIS = 'analysis'¶

AVERAGE = 'average'¶

ANISOTROPIC = 'anisotropic'¶

PATH = 'path'¶

ALL_KEYS = ['ensemble', 'time', 'temp', 'pressure', 'seed', 'analysis', 'average', 'timestep', 'trj_interval', 'anisotropic', 'path']¶

PATH_ONLY = {'path'}¶

TEMP_ONLY = {'temp'}¶

RAW_MD_KEYS = {'analysis', 'anisotropic', 'average', 'ensemble', 'pressure', 'seed', 'temp', 'time', 'timestep', 'trj_interval'}¶

ALLOWED_KEYS = {'brownie': {'analysis', 'anisotropic', 'average', 'ensemble', 'pressure', 'seed', 'temp', 'time', 'timestep', 'trj_interval'}, 'compress_relaxation': {'temp'}, 'custom': {'path'}, 'matsci_relaxation': {'temp'}, 'md': {'analysis', 'anisotropic', 'average', 'ensemble', 'pressure', 'seed', 'temp', 'time', 'timestep', 'trj_interval'}, 'semi_crystal_relaxation1': {'temp'}, 'semi_crystal_relaxation2': {'temp'}}¶

__init__(line, partial=False)¶

Create a Simulation instance from a line of text

Expected tab-delimited format:: type=stype temp=300…

Parameters

line (str) – The line of text to create the instance from
partial (bool) – True if partially-incomplete data is allowed

Raises

InvalidStageFileError – If something is wrong with the line

validateKeywords()¶

Validate and parse information from the keywords

Raises: InvalidStageFileError – If something is wrong with the line

validateMSJPath()¶

Validate that the msj file was given, exists and associated cfg files also exist

Raises: InvalidStageFileError – If any condition is not met

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.CommandLine(line)¶

Bases: object

Holds information about a workflow command line

INPUT_MASK = '$input'¶

TRAJ_MASK = '$trj'¶

PARENT_OUTFILE_MASK = '$parent_outfile'¶

__init__(line)¶

Create a CommandLine instance from a line of text

Expected tab-delimited format:: [$SCHRODINGER/run] driver_path command line tokens

Any string in the command that depends on a job-specific name should be given as simply $input. For instance, in a command such as:

$SCHRODINGER/run driver.py -flob hobnob -j jobname.txt jobname.maegz

The command should be provided is:

$SCHRODINGER/run driver.py -flob hobnob -j $input.txt $input.maegz

$input will be replaced at runtime with the name of the job

If a trajectory path from the previous step is part of the command, that should be given as just $trj (i.e. -trj $trj)

Command line values that have a space in them - such as an ASL string - should be put inside double quotes: “mol.num 7”

Parameters: line (str) – The line of text to create the instance from
Raises: InvalidStageFileError – If something is wrong with the line

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParentStageData(line)¶

Bases: object

Holds and manipulates data about a parent stage

__init__(line)¶

Create a ParentStageData instance from a line of text

Expected tab-delimited format:: parent_stage_# [WAVEFUNCTION] [HESSIAN] [ANALYSIS]

Parameters: line (str) – The line of text to create the instance from

static writeInheritableParentDataToFile(parent, wavefunction, hessian, datafile)¶

Write inheritable parent stage data to a file in a format that this class can read in.

Parameters

parent (int) – The stage number of the parent stage
wavefunction (bool) – Whether to use the wavefunction from the parent stage
hessian (bool) – Whether to use the hessian from the parent stage
datafile (file) – The file to write the data to

static writeNonInheritableParentDataToFile(parents, datafile)¶

Write noninheritable parent stage data to a file in a format that this class can read in.

Parameters

parents (list) – the stage numbers of the parent stages
datafile (file) – the file to write the data to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint(line)¶

Bases: object

Holds and manipulates data about geometry constraints

__init__(line)¶

Create a GeomConstraint instance from a line of text

Expected tab-delimited format:: entry_id target value index index …

Parameters: line (str) – The line of text to create the instance from

static writeData(eid, target, ctype, idxs, afile)¶

Write the given data to file.

Parameters

eid (str) – the entry ID
target (float or None) – the target value for the constraint if there is one
ctype (int) – the Jaguar constraint type
idxs (list) – contains indices of atoms defining the constraint
afile (file) – the file to write the data to

static writeModelDataToFile(model, datafile, eid)¶

Write geometry constraint data from a model to a file in a format that this class can read in

Parameters

model (schrodinger.application.jaguar.gui.tabs.optimization_tab. ContraintCoordinatesModel) – The model containing restraints to write
datafile (file) – The file to write the data to
eid (str) – The entry id for this geometry constraint

static writeDictDataToFile(adict, datafile)¶

Write geometry constraint data from a dictionary to a file in a format that this class can read in

Parameters

adict (dictionary) – keys are entry IDs, values are lists of GeomConstraint
datafile (file) – The file to write the data to

applyToJaguarInput(jagin)¶

Apply this geometry constraint to a JaguarInput object

Parameters: jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object to apply this constraint to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord(line)¶

Bases: object

Holds and manipulates data about active coordinates

__init__(line)¶

Create an ActiveCoord instance from a line of text

Expected tab-delimited format:: entry_id type index index …

Parameters: line (str) – The line of text to create the instance from

static writeData(eid, ctype, idxs, afile)¶

Write the given data to file.

Parameters

eid (str) – the entry ID
ctype (int) – the Jaguar active coordinate type
idxs (list) – contains indices of atoms defining the active coordinate
afile (file) – the file to write the data to

static writeModelDataToFile(model, datafile, eid)¶

Write active coordinate data using a geometry constraint model to a file in a format that this class can read in

Parameters

model (schrodinger.application.jaguar.gui.tabs.optimization_tab. ContraintCoordinatesModel) – The model containing active coordinates to write
datafile (file) – The file to write the data to
eid (str) – The entry id for this active coordinate

static writeDictDataToFile(adict, datafile)¶

Write active coordinate data from the given dictionary to a file in a format that this class can read in

Parameters

adict (dict) – keys are entry IDs, values are lists of ActiveCoord
datafile (file) – The file to write the data to

applyToJaguarInput(jagin)¶

Apply this active coordinate to a JaguarInput object

Parameters: jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object to apply this active coordinate to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis(line)¶

Bases: object

Holds and manipulates data about by-atom basis sets

__init__(line)¶

Create a AtomBasis instance from a line of text

Expected tab-delimited format:: entry_id index basis_set

Parameters: line (str) – The line of text to create the instance from

static writeData(eid, anum, basis, afile)¶

Write the given data to file.

Parameters

eid (str) – the entry ID
anum (int) – the atom number
basis (str) – the basis
afile (file) – the file to write the data to

static writeModelDataToFile(model, datafile)¶

Write by-atom basis set data from a model to a file in a format that this class can read in

Parameters

model (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets. basis_set_widgets.BasisSetModel) – The model containing restraints to write
datafile (file) – The file to write the data to

static writeDictDataToFile(adict, datafile)¶

Write by-atom basis set data from a dictionary to a file in a format that this class can read in

Parameters

adict (dict) – keys are entry IDs, values are lists of AtomBasis
datafile (file) – The file to write the data to

applyToJaguarInput(jagin)¶

Apply this basis set to a JaguarInput object

Parameters: jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object to apply this atom basis set to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint(line)¶

Bases: object

Holds and manipulates data about by-atom charge constraints

__init__(line)¶

Create a ChargeConstraint instance from a line of text

Expected tab-delimited format:: entry_id index basis_set

Parameters: line (str) – The line of text to create the instance from

static writeData(eid, charge, weights, afile)¶

Write the given data to file.

Parameters

eid (str) – the entry ID
charge (float) – the charge
weights (dict) – keys are atom indices, values are float weights
afile (file) – the file to write the data to

static writeModelDataToFile(model, datafile)¶

Write by-atom charge constraint data from a model to a file in a format that this class can read in

Parameters

model (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets. basis_set_widgets.ChargeConstraintsModel) – The model containing restraints to write
datafile (file) – The file to write the data to

static writeDictDataToFile(adict, datafile)¶

Write by-atom charge constraint data from a dictionary to a file in a format that this class can read in

Parameters

adict (dict) – keys are entry IDs, values are lists of ChargeConstraint
datafile (file) – The file to write the data to

applyToJaguarInput(jagin)¶

Apply this charge constraint to a JaguarInput object

Parameters: jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object to apply this constraint to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords(line, use_eid=True)¶

Bases: object

Holds and manipulates data about keywords

__init__(line, use_eid=True)¶

Create a StageKeywords instance from a line of text

Expected tab-delimited format:: entry_id keyword=value keyword=value …

Parameters

line (str) – The line of text to create the instance from
use_eid (bool) – If True, require the line to start with an entry id. If False, the line should not start with an entry id.

static writeKeywordsToFile(keywords, datafile)¶

Write keyword data to a file in a format that this class can read in

Parameters

keywords (dict) – keys are entry IDs, values dicts with Jaguar (key, value) pairs
datafile (file) – The file to write the data to

static writeDictDataToFile(adict, datafile)¶

Write keyword data from the given dictionary to a file in a format that this class can read in

Parameters

adict (dict) – keys are entry IDs, values are lists of StageKeywords
datafile (file) – The file to write the data to

applyToJaguarInput(jagin)¶

Apply these keywords to a JaguarInput object

Parameters: jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object to apply these keywords to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.QMMoleculeKeywords(*args, **kwargs)¶

Bases: schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords

A StageKeywords subclass with additional properties for Meta Workflows

ESP_FOR_MD = 'esp_for_md'¶

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

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.ExtraSectionData¶

Bases: object

Holds and manipulates text for extra sections

__init__()¶

Create an ExtraSectionData instance

Use addLine to add a line of text

addLine(line)¶

Add a line of text to the extra section text block

Parameters: line (str) – The line of text to add to the extra section block

addToJaguarInput(input_file)¶

Add this block of text at the bottom of a jaguar input file

Parameters: input_file (file) – The input file to add the text to

static writeSectionsToFile(sections, datafile)¶

Write extra sections data to a file in a format that this class can read in

Parameters

sections (str) – The extra text to add
datafile (file) – The file to write the data to

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.OverrideKeywords(line)¶

Bases: object

Holds and manipulates data about override keywords - these are keywords that either can’t be set by the GUI or override the values set in the GUI. They apply to all structures

__init__(line)¶

Create a OverrideKeywords instance from a line of text

Expected tab-delimited format:: keyword=value keyword=value …

Parameters: line (str) – The line of text to create the instance from

static writeKeyStringToFile(keystring, datafile)¶

Write override keyword data to a file in a format that this class can read in

Parameters

keystring (str) – the string of keyword=value pairs to write
datafile (file) – The file to write the data to

applyToJaguarInput(jagin)¶

Apply these keywords to a JaguarInput object

Parameters: jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object to apply these keywords to

schrodinger.application.matsci.jaguar_multistage_workflow_utils.get_property_keys_from_keywords(keywords)¶

Return Jaguar output structure property keys that are created from the given input keywords.

Parameters: keywords (dict) – Jaguar keywords
Return type: list
Returns: structure property keys

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.AnalyzeStageData(line)¶

Bases: object

Holds and manipulates data about an analysis stage

__init__(line)¶

Create an Analyze instance from a line of text

Expected tab-delimited format:: stage_idx property_key property_key float str stage_idx stage_idx…

Parameters: line (str) – The line of text to create the instance from

static writeAnalyzeDataToFile(data, datafile)¶

Write analyze data to a file in a format that this class can read in.

Parameters

data (list) – contains (parent_st_idx, key, parent_key, prefactor, function, parent_idx, parent_idx, …) tuples
datafile (file) – the file to write the data to

getThermoKeys(parent_st_dict)¶

Return the thermochemistry keys for this analyze stage term.

Parameters: parent_st_dict (dict) – contains parent index, structure pairs
Return type: list
Returns: the thermochemistry keys

schrodinger.application.matsci.jaguar_multistage_workflow_utils.write_stages_file(stages, file_path)¶

Write stages to a file with the given path.

Parameters

stages (list) – contains StageData
file_path (str) – the file path

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData(index)¶

Bases: object

Hold and manipulate all the settings for a stage in the workflow

DATA_CLASSES = {'ACTIVE_COORDINATES': <class 'schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord'>, 'ATOM_BASIS': <class 'schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis'>, 'CHARGE_CONSTRAINTS': <class 'schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint'>, 'GEOM_CONSTRAINTS': <class 'schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint'>, 'KEYWORDS': <class 'schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords'>}¶

__init__(index)¶

Create a StageData instance

Parameters: index (int) – The 1-based index of this stage

parseDataLine(line, ltype, partial=False)¶

Parse a data line

Parameters

line (str) – The line of data to parse
ltype (str) – The type of data in this line. Should be a module constant PARENT, EXTRA_SECTIONS, ANALYZE, or one of the DATA_CLASSES keys
partial (bool) – True if partially-incomplete data is allowed

applyEntryData(jagin, eid)¶

Apply all entry data for entry eid to the given JaguarInput object

Parameters

jagin (schrodinger.application.jaguar.input.JaguarInput) – The JaguarInput object to apply the data to
eid (str) – The ID of the entry whose data should be applied

getKeywords(eid=None)¶

Get the keywords for this stage for the given eid. If no eid is given, keywords for a random entry will be returned.

Parameters: eid (str or None) – If str, keywords for this entry will be supplied. If None, a random entry will be chosen.
Return type: dict
Returns: keys are keywords, values are values for that keyword

getPropertyKeys(st=None)¶

Return output structure property keys that are created by this stage.

Parameters: st (schrodinger.structure.Structure or None) – if given and the stage is an analysis stage then the thermochemistry wildcards are considered
Return type: list
Returns: structure property keys

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSWorkFlow(*args, **kwargs)¶

Bases: schrodinger.application.matsci.jaguarworkflows.WorkFlow

A Jaguar Multistage WorkFlow object that controls all the steps for an entry

__init__(*args, **kwargs)¶

Create a JSMWorkFlow instance

Parameters

stages (list) – A list of StageData objects, one for each step in the workflow
smap_name (str) – The name of the master smap file
hierarchical (bool) – in the output structure file hierarchically group structures by stage using a job name and original structure title header

See parent class for additional documentation

getSteps()¶: Create all the steps for this workflow, one for each stage

class schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep(stage, *args, **kwargs)¶

Bases: schrodinger.application.matsci.jaguarworkflows.Step

A step in the Jaguar Multistage Workflow

__init__(stage, *args, **kwargs)¶

Create a JMSStep instance

Parameters: stage (StageData) – The settings for this step

See parent class for additional documentation

getThermoExts(parent_st_dict)¶

Return the thermochemistry extensions for this stage.

Parameters: parent_st_dict (dict) – contains parent index, structure pairs
Return type: list
Returns: the thermochemistry extensions

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

getStructure()¶: Overwrite the parent class method to return the structure from the inheritable parent step if an inheritable parent exists, otherwise return the original structure

getInput()¶

Overwrite the parent class method to avoid setting default keywords values and to apply data from the StageData class for this step

Return type: schrodinger.application.jaguar.input.JaguarInput or None
Returns: The JaguarInput object for this step, or None if it could not be created.

getJaguarRestartFileName()¶

Get the name of the Jaguar restart file for this step - the restart file contains the wavefunction and hessian

Return type: str
Returns: The name of the Jaguar restart file for this step

writeInput()¶: Overwrite the parent class method to copy data from the parent step and add extra section data from the StageData object

finishProcessingJobControlJob()¶: Add any files to the backend that the Jaguar subjob preserved

write(writer, **kwargs)¶

In addition to the parent method, also compile any smap data into the master smap file.

See parent method for additional documentation

schrodinger.application.matsci.jaguar_multistage_workflow_utils.create_workflows(options, jobq, stages, smap_name=None, hierarchical=True, workflow_class=None, robust=False, tmp_logger=None, max_retries=None)¶

Create a workflow for each structure

Parameters

options (argparse.Namespace) – The command line options
jobq (schrodinger.job.queue.JobDJ) – The JobDJ to run subjobs with
stages (list) – A list of StageData objects to create JMSStep from
smap_name (str) – The name of the master smap file
hierarchical (bool) – in the output structure file hierarchically group structures by stage using a job name and original structure title header
workflow_class (Jaguar multistage workflow) – Jaguar multistage workflow or any other custom jaguar workflow
robust (bool) – If True, use the robust Jaguar driver to run Jaguar jobs. If false, use Jaguar directly.
tmp_logger (logging.Logger or None) – output logger or None if there isn’t one
max_retries (int or None) – see queue.JobControlJob

schrodinger.application.matsci.jaguar_multistage_workflow_utils.parse_stage_data(data, meta=False, partial=False)¶

Parse data in settings file format into a list of stages

Parameters

data (list or file) – The data to parse. Can be a list of strings with each item a line of data, or a an open file
meta (bool) – If True, this is a meta workflow-like data file. If False, this is a jaguarworkflows-like data file
partial (bool) – True if partially-incomplete data is allowed

Return type

list

Returns

A list of StageData objects

Raises

InvalidStageFileError – if there is an issue

schrodinger.application.matsci.jaguar_multistage_workflow_utils.read_stage_datafile(filename, meta=False)¶

Read in a settings file. Logs an error and exists if an error occurs while reading the file.

Parameters

filename (str) – The name of the settings file to read
meta (bool) – If True, this is a meta workflow-like data file. If False, this is a jaguarworkflows-like data file

Return type

list

Returns

A list of StageData objects

Raises

InvalidStageFileError – if there is an issue

schrodinger.application.matsci.jaguar_multistage_workflow_utils.validate_jaguarlike_stages(stages)¶

Validate the information for jaguarworkflows-like stages

Parameters: stages (list) – contains StageData
Raises: InvalidStageFileError – if there is an issue

schrodinger.application.matsci.jaguar_multistage_workflow_utils.validate_metalike_stages(stages)¶

Validate the stage information for meta workflows-like stages

Parameters: stages (list) – contains StageData
Raises: InvalidStageFileError – if there is an issue

schrodinger.application.matsci.jaguar_multistage_workflow_utils.validate_stages(stages, meta=False)¶

Validate stages.

Parameters

stages (list) – contains StageData
meta (bool) – If True, this is a meta workflow-like data file. If False, this is a jaguarworkflows-like data file

Raises

InvalidStageFileError – if there is an issue

schrodinger.application.matsci.jaguar_multistage_workflow_utils.log_error(msg)¶

Add a message to the log file and exit with an error code

Parameters: msg (str) – The message to log

schrodinger.application.matsci.jaguar_multistage_workflow_utils.log(msg, timestamp=False, pad=False, pad_below=False)¶

Add a message to the log file

Parameters

msg (str) – The message to log
pad (bool) – Whether to pad above this message with a blank line
pad_below (bool) – Whether to pad below this message with a blank line
timestamp (bool) – Whether to print a timestamp with the message

schrodinger.application.matsci.jaguar_multistage_workflow_utils.create_smap(basename, output_name, smap_dict=None, finalize_empty=False)¶

Create the master smap file that will map property files (.vib, .vis, etc) to structures in the compiled structure file

Parameters

basename (str) – The base name of all job files
output_name (str) – The name of the output structure file
smap_dict (dict) – keys are file names, values are indices, the values are not entry IDs but rather the counting indices (1-based) of the structure in the given output_name file that the given file name key is associated with, values can also be lists of indices for example if a given file name is used for multiple indices
finalize_empty (bool) – whether to proceed with finalizing the smap file even if an empty smap_dict has been passed as input

Return type

str

Returns

The name of the smap file created

schrodinger.application.matsci.jaguar_multistage_workflow_utils.finalize_smap(smap_name, backend, finalize_empty=False)¶

Finish the master smap file and add it to the jobcontrol backend if necessary

Parameters

smap_name (str) – The name of the master smap file
backend (schrodinger.job.jobcontrol._Backend) – The job control backend or None if there is no backend
finalize_empty (bool) – whether to proceed with finalizing the smap file even if an empty smap_dict has been passed as input