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: schrodinger.infra.mmobject.MmObject

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>.

static initialize(error_handler=None)

Initialize all libs that mmbs is dependent upon.

static terminate()

Terminate the libs that were initiated in Bitset.initialize().

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’.

range(start, finish)

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

fill()

Set all bits to on.

__repr__()

Return a Python representation string for this bitset.

__str__()

Return a string of this bitset.

__class__

alias of builtins.type

__del__()

Decrement the reference count. If the handle is being actively managed, call _delete when it the count hits zero.

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.mmbitset', '__doc__': '\n This class represents a bitset, with each element either 1 or 0.\n\n A bitset is similar conceptually to a Python dictionary that contains\n keys that are integers from 1 to the length of the bitset, and the value\n for each key is an on/off boolean (1 or 0).\n\n Bitsets are usually used when keeping track of which atoms in the ct an\n operation needs to be performed on; in which case the length of the Bitset\n is the number of atoms in the ct.\n\n An instance of Bitset can be converted to a list containing the elements\n that are on (i.e. set to 1) via list(bitset) and to a set via set(bitset).\n\n This is an object-oriented wrapper for the underlying MMBS library. All\n state is stored in the C library. References to instances of this class\n can be used in direct mmbs library calls, as it will converted to the\n integer handle when necessary.\n\n ', '__init__': <function Bitset.__init__>, '_delete': <function Bitset._delete>, 'from_list': <classmethod object>, 'initialize': <staticmethod object>, 'terminate': <staticmethod object>, 'size': <function Bitset.size>, 'resize': <function Bitset.resize>, 'count': <function Bitset.count>, 'get': <function Bitset.get>, 'set': <function Bitset.set>, 'unset': <function Bitset.unset>, 'range': <function Bitset.range>, 'fill': <function Bitset.fill>, '__repr__': <function Bitset.__repr__>, '__str__': <function Bitset.__str__>, '__iter__': <function Bitset.__iter__>, '__len__': <function Bitset.__len__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__()

Return the handle of the object so that the object reference can be used in functions that expect an integer handle.

__iter__()

Return an iterator for this bitset. Loops over all of the ON bits.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.infra.mmbitset'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__len__()

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