schrodinger.infra.mmbitset module

A pythonic wrapper for the mmbs library, providing access to bitsets.

The default error handler for the Bitset module is set to mm.error_handler. If no error handler is specified for error_handler arguments, its value is what will be used.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.infra.mmbitset.Bitset(handle=None, manage_handle=True, error_handler=None, size=None)

Bases: object

This class represents a bitset, with each element either 1 or 0.

A bitset is similar conceptually to a Python dictionary that contains keys that are integers from 1 to the length of the bitset, and the value for each key is an on/off boolean (1 or 0).

Bitsets are usually used when keeping track of which atoms in the ct an operation needs to be performed on; in which case the length of the Bitset is the number of atoms in the ct.

An instance of Bitset can be converted to a list containing the elements that are on (i.e. set to 1) via list(bitset) and to a set via set(bitset).

This is an object-oriented wrapper for the underlying MMBS library. All state is stored in the C library. References to instances of this class can be used in direct mmbs library calls, as it will converted to the integer handle when necessary.

__init__(handle=None, manage_handle=True, error_handler=None, size=None)

Initialize an object with an existing MMBS handle or a size.

By default, the MMBS resources will be managed by the object. To keep these from being cleaned up on object deletion, set manage_handle=False.

Parameters

size (int) – The size to use for a newly created bitset.

classmethod from_list(size, on_list)

Alternative constructor; returns a Bitset object initialized from a Python list.

Example usage:

bs = Bitset.from_list(st.atom_total, selected_atoms)

where <st> is the structure object, and <selected_atoms> is a list of atom indices.

Parameters

  • size (int) – The size to use for a newly created bitset.

  • on_list – Turn on the bits that are present in this iterable. Each item should be an int between 1 and <size>.

size()

Return the capacity (i.e. maximum index) of the Bitset.

resize(size)

Modify the capacity of the Bitset.

count()

Return the number of index values that are set to ‘on’.

get(index)

Get the value of the index.

Returns True if the index value is on, False if it is off.

set(index)

Set the index value to ‘on’.

unset(index)

Set the index value to ‘off’.

invert()

Invert the bits in the set.

range(start, finish)

Set all bits in a range from “start” to “finish”

fill()

Set all bits to on.

all()

Are all bits on?

copy()

Create another bitset that is a duplicate of this one.

__len__()

Returns the size of the bitset (Number of ON and OFF bits)