schrodinger.pipeline.stages.rmsd module

A stage for calculating RMSDs for structures in two sets.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.stages.rmsd.RmsdStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for calculating RMSDs for structures in two sets.

First set - original structures Second set - new conformations

The keywords specific to this stage are…

UNIQUEFIELD_REF - Property in the reference set used to match

structures for comparison. If unset, it defaults to the UNIQUEFIELD property. The RMSD is calculated for pairs in which the UNIQUEFIELD_REF value in the reference ligand matches the UNIQUEFIELD value in the modified ligand.

UNIQUEFIELD - Property in the modified set used to match

structures for comparison.

RMSDFIELD - Property to save RMSDs into in the output file

RENUMBER_STRUCTURES - Should be False if atom numbering is the same

between same structure in two input sets

IGNORE_STATES - If True, ignore hydrogens and treat all bonds

as single order.

The stage takes two input structure file sets and generates one output structure file set.

__init__(*args, **kwargs)

See class docstring.


Algorithm: Compare each structure in the original (first) ligands set to every structure in the modified (second) set. If their corresponding UNIQUEFIELD_* properties are the same, calculate RMS for the structure, save it to RMSDFIELD, and write out the structure to the output file.


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

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


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


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.

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.


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


OVERWRITE: Make sure that all parameters are valid.


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.

clear() None.  Remove all items from D.

Print a debug line to the log file


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


Print an error line to the log file


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

classmethod fromkeys(iterable, value=None)
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.

get(k[, d]) D[k] if k in D, else d.  d defaults to None.
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).


Stages should clean up after themselves if this returns True


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.


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


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


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.


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()


Return stagename (jobname of the stage)


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


Return the output name for specified position


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


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


Return the directory in which the stage is running


Return verbosity of thos stage (for JobDJ)


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


Returns True if this stage has started.


Print an info line to the log file


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

items() a set-like object providing a view on D’s items

Iterate through input objects: (position, obj)

keys() a set-like object providing a view on D’s keys

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


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.


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

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.


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


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

Example: product=”mmshare”


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.

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

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

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


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

setOutput(position, obj)

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

setOutputName(position, varname)

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

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


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.


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

values() an object providing a view on D’s values

Print a warning line to the log file