schrodinger.pipeline.stages.glide module

Glide Docking & Gridgen stages.

DockingStage - stage for running Glide docking jobs

GridgenStage - stage for generating Glide grids (not functional)

HBOND_CONSTRAINTS: List of constraints in format: “label <atomnum>” METAL_CONSTRAINTS: List of constraints in format: “label <atomnum>” POSIT_CONSTRAINTS: List of constraints in format: “label <x> <y> <z> <radius>” NOE_CONSTRAINTS: List of constraints in format: “label <x> <y> <z> <min> <max>”

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.pipeline.stages.glide.compress(origFile)

Compresses the specified file and removes the original

class schrodinger.pipeline.stages.glide.DockingStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

VSW stage for performing Glide docking

__init__(*args, **kwargs)

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

Parameters

• 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.

checkInputs()

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

recombineInputLigands()

setupJobs()

Docks the structures in ligfiles to the grid <gridprefix>.

processJobOutputs()

write_glide_input_file(ligfile, gridfile, nreport, glide_jobname)

Write Glide docking job input file

mergeGlideOutputs(input_files, num_comps_to_keep, best_by_compound)

Takes in a list of _lib.mae or _pv.mae files, and merges them together based on glidescore. Assumes that the files have already been sorted with glide_sort (default in Glide).

Parameters

• input_files (list of str) – List of docked pose files (PV or LIB).

• num_comps_to_keep (int) – Stop merging when this number of compounds have been reached.

• best_by_compound – whether to keep only the best scoring pose per compound (based on unique ID property).

Returns

Merged file path and number of structures in it (including rec). If none of the structures docked (SIP mode), will return (None, 0).

Return type

(str, int)

generateCsvFile(pre_csv_file, csv_props)

check_subjob_output(glide_jobname)

Will return the output file for the specified subjob. If no valid poses were produced, None is returned. Raises a descriptive RuntimeError if logfile and/or output file is incomplete.

buildDockedLigandsMap()

Builds up a dict of self.docked_ligands from the job names in self.glide_jobnames.

If self._force_jobs is False, the job fails in the event of subjob failure. Otherwise, the errors are logged and the job continues.

operate()

Perform an operation on the input files.

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.

areSubjobsAndStageOnSameHost()

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.

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.glide.GridgenStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

__init__(*args, **kwargs)

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

Parameters

• 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.

operate()

Perform an operation on the input files.

setupJobs()

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.

areSubjobsAndStageOnSameHost()

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.

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.glide.MergeStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for merging up to 999 Glide output files with ‘glide_ensemble_merge’. The input files can be either PV or LIB, and have to be sorted by GlideScoreglide. The output file will also be sorted, and the GlideScores can be offset by a specified value for each input file.

The keywords specific to this stage are…

NREPORT Save only the top NREPORT poses. The default is 0, which

retains all poses.

MAXPERLIG Retain at most MAXPERLIG poses for each ligand

(determined by the structure title). The default is 1. Use 0 to retain all poses.

UNIQUEFIELD Property to uniquely identify compounds by. Default is title.

OFFSETS List of GlideScore offsets (float) to be applied to the

input structures. First item in the list is the offset for the first input, second is for second input, etc. If not specified, all are defaulted to 0.0.

MARKERS List of string lables for each receptor. Each ligand will

be marked by this value depending on which input set it originated from.

The stage takes up to 100 input structure file sets (PV or LIB) and generates a single output pose file.

__init__(*args, **kwargs)

See class docstring.

operate()

Run the ‘glide_ensemble_merge’ script on all the input files from all sets, optionally applying GlideScore offsets to some sets. Generates a single output pose file.

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.

areSubjobsAndStageOnSameHost()

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.

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.glide.GlideSortStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for sorting Glide _pv/lib.mae files. Currently, a sorted file is produced for each input file; that is, the input files are merged and sorted together.

The keywords specific to this stage are…

BLOCK_SORT_BY_TITLE Whether to block-sort the poses by title. If

True (the default), all poses with the same title are grouped and sorted by the INTRATITLE_SORT_KEYS keys. The blocks themselves are sorted by applying the SORT_KEYS to just the top pose in each block.

INTRATITLE_SORT_KEYS The sort key(s) within a title block. The

default is ‘r_i_glide_emodel’ (appropriate for Glide HTVS/SP results). Multiple sort keys must be whitespace-separated.

SORT_KEYS The key(s) for sorting the pose file. If

BLOCK_SORT_BY_TITLE is True, the blocks are sorted by the values of their top pose’s SORT_KEYS properties. Multiple sort keys must be whitespace-separated.

OUTPUT_POSES_PER_TITLE The number of top poses per title to keep.

Applies only if BLOCK_SORT_BY_TITLE is true. The default is 0, which means retain all poses.

INPUT_TYPE Specify whether the receptor is (‘pv’) or is

not (‘lib’) in the file. By default, the type will be determined from the file name (i.e., _pv/lib.mae).

__init__(*args, **kwargs)

See class docstring.

operate()

Sort each input pose file using the application.glide.glideanalysis module. Generates a sorted output pose file for each input pose file.

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.

areSubjobsAndStageOnSameHost()

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.

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