schrodinger.pipeline.stage module

Base classes for Pipeline stages.

To create a stage instance:

stageobj = YourStage(<stagename>)

# Add keywords:

stageobj['NUM_RINGS'] = 2
stageobj['UNIQUEFIELD'] = 's_m_title'

# Add input objects:
# ligand_files is list of file names
ligandsobj = pipeio.Structures(ligand_files)
stageobj.setInput(1, 'INPUT1', ligandsobj)

# Tell the stage where to save it's output:
stageobj.setOutputName(1, 'OUTPUT')

# Integers (1) are position numbers.
# INPUT1 is the name of the input object

# Run the stage:

outputs =

# outputs is now a dictionary of output objects

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.pipeline.stage.get_time(t1, t2=0)

Returns a string of the time difference between t2 and t1 in human readable format. t2 and t1 are times, as returned by time.time()

class schrodinger.pipeline.stage.Stage(stagename, specs=None, allow_extra_keywords=False, cleanup=True, inpipeline=False, driver_dir=None)

Bases: collections.UserDict

__init__(stagename, specs=None, allow_extra_keywords=False, cleanup=True, inpipeline=False, driver_dir=None)

This is the Stage class. Derive your own class from it.

  • stagename – full name for this stage (<jobname>-<stagename>)

  • specs – ConfigObj specification for the supported keywords

  • allow_extra_keywords – Whether to allow keywords that are not in the specification.

  • cleanup – Whether to remove intermediate files

  • inpipeline – Whether the state is running within a Python Pipeline. If the stage is manually created, do NOT set this flag. Python Pipeline will set it as needed.

  • driver_dir – Directory in which the driver is running.


Validates the stored keywords. This is done by converting <self> to a ConfigObj instance, and calling validate() on it. The validated keywords are then updated back to <self>. This is done as part of Ev:87429


Return verbosity of thos stage (for JobDJ)


If a stage has a main product associated with it, the stage should overwrite this method with a method that returns the product string. For example, the LigPrepStage.mainProduct() will return “ligprep” Used by Pipeline.


Specify which product this stage is part of. Will determine which host the subjobs are run on.

addExpectedInput(position, type, required=True)

A stage can accept one or more pipeio input objects. Use this method to specify the type of input object that is expected at each position.

position - an integer starting at 1. type - structures/grids/etc. required - whether this input always needs to be specified

addExpectedOutput(position, type, always=True)

A stage can return one or more pipeio objects. Use this method to specify the type of object that will be returned and whether or not it will always be produced by the stage.

position - an integer starting at 1. type - structures/grids/etc. always - whether this output is always produced


Return the directory in which the stage is running


Specify a product that is required for this stage to run; optionally minimum version.

Example: product=”mmshare”


Raises RuntimeError if any of the required products are not installed or the version installed is less that minimum required version. It is possible to override this method. See for example.


Return the runtime-path of a file that user specified Prints an error and exits if file does not exist.


Similar to requiredProduct() but can be used to specify required products at runtime. For example, ConvertStage doesn’t know what products are required for conversion until runtime. Raises RuntimeError if product is not installed.


Returns True if the user requested optional output at <position>

setOutput(position, obj)

Use this method at the end of operate() to set the output.


Returns the output IO object of the stage at specified position. Use this method after running the stage to get its output objects


This method dumps all the variables of the Stage to a restart file. Run it every time an important step is performed.


Gets called after the Stage joins pipeline. Meant to be used to initialize non-persistent context.

checkFile(file, error='File does not exist:')

Raise exception if specified file does not exist. The message that is printed can be specified.

checkFiles(files, error='File does not exist')

Raise expetion if any file does not exist.


Prints specified objects to the stage log file. No EOF return


Print an info line to the log file


Print a debug line to the log file


Print a warning line to the log file


Print an error line to the log file


Print an error line to the log file and exit with code 1


Print the value of each keyword for this stage to the stream specified as <fh>. Used by Pipeline


OVERWRITE: Make sure that all parameters are valid.


Returns True if this stage has started.


Returns True if this stage’s operate() exited successfully.


OVERWRITE: Return False if something is wrong with the input files or the parameter, otherwise return True.


Return stagename (jobname of the stage)


Return a dictionary of variable name of the inputs at each position. Key:position, value:name

setInput(position, name=None, obj=None)

Specify an input to use for this stage. position - input specified is for this position name - Variable name of this IO object obj - the IO object

This method is called by Pipeline.


Use in operate() to get the input object for specified position. Returns None if invalid position is specified.


Iterate through input objects: (position, obj)

setOutputName(position, varname)

Is called by Pipeline when starting the stage. Tell the stage what name to save each output under.


Return a list of output names for each position (dict)


Return the output name for specified position

setJobOptions(subjob_hosts=None, njobs=None, adjust=None, force=None, max_retries=None, cleanup=None)

Tell this stage how to run the subjobs

  • subjob_hosts – list of hosts to run subjobs on

  • njobs – number of subjobs to generate. None means determine automatically.

  • adjust – whether to adjust njobs such that job size is within limits

  • force – whether to continue with job if subjobs fail

  • max_retries – number of times to attempt to restart a subjob If not specified, use SCHRODINGER_MAX_RETRIES or 2.

  • cleanup – whether to delete intermediate files


Returns a list of hosts to run the subjobs on. localhost:1 may be in the list as well. Ideally, pass the output to JobDJ. Format: [ (host1,ncpus), (host2,ncpus) ] Pass this value to JobDJ.


Just like getHostList() but instead of returning a list, returns a host string to be passed to the -HOST argument.


Return True if subjobs are running on the same host as the driver and the stages. This is always the case with JOB_SERVER but not with classic Job Control.


Returns the requested target number of subjobs, and whether or not to adjust that number if it is unreasonable.

If -NJOBS was not specified, the # of CPUs or 10 is returned (whichever is smaller).

Used by Glide DockingStage and _adjustNJobs()

getAdjustedNJobs(total_mol, min_job_size, max_job_size)

Returns the desired number of subjobs, and adjusts it for the the specified min & max job sizes if the user specified ADJUST option. If the number of desired jobs was specified by the user, the number of available cpus is used or 10, whichever is smaller. Specify the number of input ligands and the smallest and largest desired job sizes (Generally job lengths of 1 minute & 24 hours).


Returns a dictionary of options to pass to JobDJ: hosts, max_retries, default_max_retries, verbosity


Use this method to adjust the specified queue.JobDJ instance to the VSW settings.


Returns a pre-set JobDJ instance for the stage to use. It already has it’s hosts, max_retries, max_failures, default_max_retries, and verbosity set.


Return the number of max restarts to use. If -max_retries is specified, returns that value; otherwise if SCHRODINGER_MAX_RETRIES is defined, returns that value; otherwise returns default of 2. Pass this value to JobDJ.


Returns the total number of processors specified in the host string. For queued hosts with no CPU# specification, 10 is added.


Stages should clean up after themselves if this returns True


Gets called periodically in order to update JobDJ’s hosts. Will ask Pipeline for CPUS when needed, and will tell Pipeline when they are no longer needed.

run(idle_function=None, restart_file=None, verbosity=None, logfh=None)

Run the stage.

idle_function - function to call when idle

restart_file - file to periodically dump this instance to

verbosity - there are three verbosity levels: “quiet”, “normal”, and “verbose”

“quiet” - only warnings and errors are printed “normal” - stage progress is printed - default “verbose” - additional debugging info is printed

logfh - where to send the loggin output


Adds the specified file to the stage’s job control record. File must be specified as local (not absolute) path.


OVERWRITE: Perform an operation on the input Objects. use self.setOutput(position, obj) to set output objects

genFileName(extension=None, filenum=None, start=None, end=None)

Generate a file name to be used by the stage. Returns string:

"<full-stagename>", etc.

Depending on given options.

genOutputFileName(position, extension='', filenum=None, start=None, end=None)

Generate a file name to be used by the stage when writing files for the output position <position>. Returns strings:

"<full-varname>", etc.

Depending on given options.

clear() None.  Remove all items from D.
classmethod fromkeys(iterable, value=None)
get(k[, d]) D[k] if k in D, else d.  d defaults to None.
items() a set-like object providing a view on D’s items
keys() a set-like object providing a view on D’s keys
pop(k[, d]) v, remove specified key and return the corresponding value.

If key is not found, d is returned if given, otherwise KeyError is raised.

popitem() (k, v), remove and return some (key, value) pair

as a 2-tuple; but raise KeyError if D is empty.

setdefault(k[, d]) D.get(k,d), also set D[k]=d if k not in D
update([E, ]**F) None.  Update D from mapping/iterable E and F.

If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v

values() an object providing a view on D’s values
schrodinger.pipeline.stage.Restart(restart_file, ignored=None)

Run this function in order to recover a saved Stage instance.