schrodinger.pipeline.pipeio module

Core Pipeline I/O classes (Structures, Grid, and Text, and PhaseDB).

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.pipeio.Grid(gridfile=None)

Bases: schrodinger.pipeline.pipeio.PipeIO

A class to hold a set of grid files (compressed or uncompressed).

check()

Check that the grid file exists.

Raises:RuntimeError – Raised if the file is missing.
getFiles()

Return a list of grid file names, expanded from the representative file name, after checking for their existence.

For compressed grids, the zip file is the only item returned, but for uncompressed grids, all the standard grid component file names are returned.

getPath()

Return the grid file name.

isFilled()
setData(gridfile)

Replace the grid file name.

Parameters:gridfile (str) – The replacement grid file name.
class schrodinger.pipeline.pipeio.PhaseDB(path=None, remote=False)

Bases: schrodinger.pipeline.pipeio.PipeIO

A class to hold the absolute pathname of a Phase database.

check()

Make sure all files in the list exist.

Raises:RuntimeError – Raised if “.” is in the list or if any file can’t be found.
getFiles()

Return the list of files.

getPath()

Returns the path (abolute base name).

For the old format, does NOT include “_phasedb”, for new format DOES include the “.phdb”.

isFilled()
setData(path)

Replace the stored database path.

class schrodinger.pipeline.pipeio.PipeIO

Parent class for all Pipeline I/O classes. Subclasses hold data that is passed between stages during execution.

check()

Make sure that the object is valid. If it’s not valid (e.g. file does not exist), raise a RuntimeError.

This method must be implemented in subclasses.

getCount()

Return the number of items in this object.

This method may be overridden in subclasses.

getFiles()

Return a list of files representing this object.

This method must be implemented in subclasses.

isFilled()

Check whether the object is used or empty.

This method must be implemented in subclasses.

class schrodinger.pipeline.pipeio.Structures(ligs=[], count=None)

Bases: schrodinger.pipeline.pipeio.PipeIO

A class to hold the names of structure files.

check()

Make sure all files in the list exist. Raise a RuntimeError if “.” is in the list, and exit (sys.exit(1)) if any file can’t be found.

count()

Return the number of structures in the set.

getCount(count_if_needed=False)
getFiles()

Return the list of ligand file names after checking that all of them exist via the check method.

isFilled()
setData(ligfiles, count=None)

Replace the list of ligand files with ligfiles.

Raises:RuntimeError – Raised if “.” is in the list.
class schrodinger.pipeline.pipeio.Text(files=[])

Bases: schrodinger.pipeline.pipeio.PipeIO

A class to hold the names of one or more text (or log) files.

check()

Make sure all files in the list exist.

Raises:RuntimeError – Raised if “.” is in the list or if any file can’t be found.
getFiles()

Return the list of text file names after checking that all of them exist.

isFilled()
setData(textfiles)

Replace the list of file names with textfiles.

Raises:RuntimeError – Raised if “.” is in the list.