schrodinger.pipeline.stages.gencodes module

Stage for generating and storing codes for ligands/compounds and variants.

It also recombined input ligands into a number of subjobs specified via -NJOBS argument (If -adjust is used, this number is also adjusted based on the MIN_SUBJOB_STS and MAX_SUBJOB_STS keywords.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.stages.gencodes.RecombineStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for generating compound and variant codes, which are stored as properties.

It also recombined input ligands into a number of subjobs specified via -NJOBS argument (If -adjust is used, this number is also adjusted based on the MIN_SUBJOB_STS and MAX_SUBJOB_STS keywords.

See the specs for the keywords specific to this stage.

A ligand/compound is identified by the UNIQUEFIELD property, and structures with the same value of this property are indexed as variants. If UNIQUEFIELD is not specified, each structure is treated as a compound (i.e., there are no variants), and the label for the compound is just the structure index number as all the files and structures are read.

The output structures will have their OUTCOMPOUNDFIELD set to their compound label (either the UNIQUEFIELD property value or the structure index). If OUTCOMPOUNDFIELD is “s_m_title”, the original titles will be saved to the ‘s_pipeline_title_backup’ property.

OUTVARIANTFIELD property (‘s_pipeline_variant’ by default) is set to “<compound_label>-<variant_index>”.

The stage takes one input structure file set and generates one set of output structure files, each containing about 100,000 structures.

__init__(*args, **kwargs)

See class docstring.

operate()

Generates ligand compound and variant codes, and saves the structures into fewer number of files (max 100,000 per file, except a new output file must start with a new compound). Adds the compound label, compound-and-variant, and original title to the output structures as properties. Raises a RuntimeError if the output file format is invalid, if there is a problem reading an input file or writing an output file, or if the UNQIUEFIELD property doesn’t exist for a structure.

JobDJOptions()

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

__contains__(key)
__len__()
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

addOutputFile(filename)

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

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.

checkInputs()

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

checkParameters()

OVERWRITE: Make sure that all parameters are valid.

checkProducts()

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 ligprep.py for example.

clear() → None. Remove all items from D.
copy()
debug(text)

Print a debug line to the log file

dump()

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

error(text)

Print an error line to the log file

exit(text='')

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>-<filenum><extension>"
"<full-stagename>-<start>_<end><extension>"
"<full-stagename><extension>"
"<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>-<filenum><extension>"
"<full-varname>-<start>_<end><extension>"
"<full-varname><extension>"
"<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).

getCleanupRequested()

Stages should clean up after themselves if this returns True

getHostList()

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.

getHostStr()

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

getInput(position)

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

getInputNames()

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

getJobDJ(**kwargs)

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.

getMaxRetries()

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.

getNCpus()

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

getNJobs()

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()

getName()

Return stagename (jobname of the stage)

getOutput(position)

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

getOutputName(position)

Return the output name for specified position

getOutputNames()

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

getRuntimePath(filename)

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

getStageDirectory()

Return the directory in which the stage is running

getVerbosity()

Return verbosity of thos stage (for JobDJ)

hasCompleted()

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

hasStarted()

Returns True if this stage has started.

info(text)

Print an info line to the log file

initNonPersistent(pipeline)

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
iterInputs()

Iterate through input objects: (position, obj)

keys() → a set-like object providing a view on D's keys
lognoret(*args)

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

mainProduct()

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.

outputRequested(position)

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.

reportParameters(fh=None)

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

requiredProduct(product)

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

Example: product=”mmshare”

requiredProductRuntime(product)

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

runJobDJ(jobdj)
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.

setJobDJOptions(jobdj)

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

Parameters:
  • 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
setMainProduct(product)

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

updateJobdj(jobdj)

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.

validateValues(preserve_errors=False)

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
warning(text)

Print a warning line to the log file

class schrodinger.pipeline.stages.gencodes.RestoreTitlesStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for copying titles for each input ligand from the ‘s_pipeline_title_backup’ property to the ‘s_m_title’ property.

The stage takes one input structure file set and generates one set of output structure files, each containing about 100,000 structures.

__init__(*args, **kwargs)

See class docstring.

operate()

For each structure, sets the value of the DESTINATION_FIELD to the the value of the SOURCE_FIELD. If no such value exists, raises a RuntimeError.

JobDJOptions()

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

__contains__(key)
__len__()
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

addOutputFile(filename)

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

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.

checkInputs()

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

checkParameters()

OVERWRITE: Make sure that all parameters are valid.

checkProducts()

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 ligprep.py for example.

clear() → None. Remove all items from D.
copy()
debug(text)

Print a debug line to the log file

dump()

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

error(text)

Print an error line to the log file

exit(text='')

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>-<filenum><extension>"
"<full-stagename>-<start>_<end><extension>"
"<full-stagename><extension>"
"<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>-<filenum><extension>"
"<full-varname>-<start>_<end><extension>"
"<full-varname><extension>"
"<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).

getCleanupRequested()

Stages should clean up after themselves if this returns True

getHostList()

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.

getHostStr()

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

getInput(position)

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

getInputNames()

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

getJobDJ(**kwargs)

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.

getMaxRetries()

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.

getNCpus()

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

getNJobs()

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()

getName()

Return stagename (jobname of the stage)

getOutput(position)

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

getOutputName(position)

Return the output name for specified position

getOutputNames()

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

getRuntimePath(filename)

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

getStageDirectory()

Return the directory in which the stage is running

getVerbosity()

Return verbosity of thos stage (for JobDJ)

hasCompleted()

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

hasStarted()

Returns True if this stage has started.

info(text)

Print an info line to the log file

initNonPersistent(pipeline)

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
iterInputs()

Iterate through input objects: (position, obj)

keys() → a set-like object providing a view on D's keys
lognoret(*args)

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

mainProduct()

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.

outputRequested(position)

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.

reportParameters(fh=None)

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

requiredProduct(product)

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

Example: product=”mmshare”

requiredProductRuntime(product)

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

runJobDJ(jobdj)
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.

setJobDJOptions(jobdj)

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

Parameters:
  • 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
setMainProduct(product)

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

updateJobdj(jobdj)

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.

validateValues(preserve_errors=False)

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
warning(text)

Print a warning line to the log file