Utilities and commonly reused generics

Many helper functions used throughout the rest of the library.

class glypy.utils.base.ClassPropertyDescriptor(fget, fset=None)

Bases: object

Standard Class Property Descriptor Implementation

glypy.utils.base.classproperty(func)

Applies ClassPropertyDescriptor as you would a normal @property descriptor

glypy.utils.base.cyclewarning()

Used to warn users about the presence of cylcical glycans, which are harder to reason about for crossring_cleavages.

glypy.utils.base.make_counter(start=1)

Create a functor whose only internal piece of data is a mutable container with a reference to an integer, start. When the functor is called, it returns current int value of start and increments the mutable value by one.

Parameters:

start: int, optional

The number to start counting from. Defaults to 1.

Returns:

int:

The next number in the count progression.

glypy.utils.base.make_struct(name, fields, debug=False)

A convenience function for defining plain-old-data (POD) objects that are optimized for named accessor lookup, unlike namedtuple. If the named container does not require any special logic and won’t be extended, the resulting structure is best for storing and accessing the data.

Parameters:

name: str

The name of the new class structure

fields: iterable of str

glypy.utils.base.opener(obj, mode='r')

Try to use obj to access a file-object. If obj is a string, assume it denotes a path to a file, and open that file in the specified mode. If obj has an attribute read, assume it itself is a file-like object and return it.

Parameters:

obj: basestring or file-like object

If obj is a base string it is treated like a file path, else if it supports the file-like operation read, return the object unchanged.

mode: str, optional

The mode, if any, to open obj with if it is a file path. Defaults to ‘r’, read

glypy.utils.base.root(structure)

The root protocol function.

Creates a generic method for obtaining the root of a structure representing or containing a glycan graph with a single distinct root.

Parameters:

structure : any

An object that implements the root protocol, containing a tree structure somewhere inside it.

Returns:

Monosaccharide : The root of the Glycan tree

glypy.utils.base.tree(structure)

The tree protocol function.

Creates a generic method for obtaining the Glycan of a structure representing or containing a glycan graph.

Parameters:

structure : any

An object that implements the root protocol, containing a tree structure somewhere inside it.

Returns:

Glycan

class glypy.utils.enum.Enum

Bases: object

A simple class implementing EnumMeta. Useful base type for other enumerated types.

class glypy.utils.enum.EnumMeta

Bases: type

A metaclass for types hosting enumerated members. Class attributes are automatically translated into EnumValue objects with the specified value and a name string matching the specified attribute name. Newly assigned attributes are wrapped dynamically.

The class itself can be treated like a dictionary for looking up these attributes by name or value, and these values can be iterated over.

..note::

Why is this necessary? It’s probably not. I chose to write it initially for compatibility with a previous iteration of the library, but later decided it was worth keeping for two reasons:

1. Avoids stringly-typing the library. Comparison of strings is a slippery slope to raw magic strings littering the codebase.
2. Richer comparison behavior allows these same names to be used in different modes with the same symbol.
3. Namespacing of EnumValue objects makes it easier to avoid accidental name collisions when comparing EnumValues instead of magic strings.

__call__(k)

Attempt to translate the input object k into a data member of the Enum.

First try to find an element of self by hashing it against member names.

Then try to find an element of self by searching for a member in self that is value-equal to k

Otherwise throw a KeyError

Parameters:

k: object

The value to be translated.

Returns:

EnumValue

__setattr__(k, v)

Intercept attribute assignment, wrapping values in EnumValue

Parameters:

k : str

Name to be set

v : object

The value to assign. If it is not of type EnumValue it will be wrapped like EnumValue(self, name=k, value=v)

translate(k)

Attempt to translate the input object k into a data member of the Enum.

First try to find an element of self by hashing it against member names.

Then try to find an element of self by searching for a member in self that is value-equal to k

Otherwise throw a KeyError

Parameters:

k: object

The value to be translated.

Returns:

EnumValue

class glypy.utils.enum.EnumValue(group, name, value, other_names=None)

Bases: object

Represents a wrapper around an value with a name to identify it and more rich comparison logic. A value of an enumerated type

class glypy.utils.multimap.MultiMap(**kwargs)

Bases: object

Implements a simple MultiMap data structure on top of a dictionary of lists

__len__()

Returns the number of items in contents

items()

Returns an iterator over the items of contents. Each item takes the form of (key, value).

keys()

Returns an iterator over the keys of contents An alias of __iter__()

pop(key, value)

Removes value from the collection of values stored at key and returns the tuple (key, value)

Raises:

IndexError

KeyError

values()

Returns an iterator over the values of contents

class glypy.utils.multimap.OrderedMultiMap(**kwargs)

Bases: glypy.utils.multimap.MultiMap

Implements a simple MultiMap data structure on top of a dictionary of lists that remembers the order keys were first inserted in.

__iter__()

Returns an iterator over the keys of contents in the order they were added.

items()

As in MultiMap, but items are yielded in the order their keys were first added.

keys()

Alias of __iter__()