Module pipeutils

Classes

[hide private]

MultiFileReader
Reads structures from multiple files.

MultiFileWriter
Writes structres to basename-NNN<extension> while never writing more than 100,000 structures to a file.

BackwardsReader
Read a file line by line, backwards.

DotPrinter
Class for printing a progress period or percentage every N number of iterations.

Functions

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countRoots(ligfiles, unique_field="s_m_title")
Counts the nunber of compounds in the supplied files.

get_last_20_lines(logfile)
Given a log file, returns a string of last 20 lines of it.

read_unique_field(st, uniquefield)
Returns the value of the specified property for the specified st (converted to string).

Variables

[hide private]

__doc__ = ...

_version = "$Revision: 1.20 $"

Function Details

[hide private]

countRoots(ligfiles, unique_field="s_m_title")

Counts the nunber of compounds in the supplied files. Compounds are identified by the 'unique_field' property, and all structures that share the same 'unique_field' value are considered variants of the compound. Raises a RuntimeError if there is a problem reading a ligand file or if the 'unique_field' property is missing. Returns a tuple of the total number of structures (i.e., variants) and the total number of compounds.

read_unique_field(st, uniquefield)

Returns the value of the specified property for the specified st (converted to string). If the property does not exist, attempts to read the same property of different type (string/int/float).

If neither is avaible, re-raises the missing property exception.

Variables Details

[hide private]

doc

Value:

"""
Shared functions for Pipeline stages.

Copyright Schrodinger, LLC. All rights reserved.

"""