abpytools.utils package

Submodules

abpytools.utils.abpytools_exceptions module

exception abpytools.utils.abpytools_exceptions.NumberingException[source]

Bases: Exception

abpytools.utils.data_loader module

class abpytools.utils.data_loader.DataLoader(data=[], data_type='', amino_acid_property=[])[source]

Bases: object

get_data()[source]

abpytools.utils.downloads module

class abpytools.utils.downloads.Download(url='', verbose=False, timeout=5)[source]

Bases: object

download(user_agent='wswp', num_retries=2)[source]
abpytools.utils.downloads.download(url, verbose, user_agent='wswp', num_retries=2, decoding_format='utf-8', timeout=5)[source]

Function to download contents from a given url

Input:

url: str string with the url to download from

user_agent: str Default ‘wswp’

num_retries: int Number of times to retry downloading if there is an error

verbose: bool Print out url and errors

decoding: “utf-8”

Output:
returns: str string with contents of given url

abpytools.utils.math_utils module

class abpytools.utils.math_utils.Matrix2D

Bases: abpytools.utils.math_utils.Matrix2D_backend

shape
values

Returns data as a list of lists

class abpytools.utils.math_utils.Matrix2D_backend

Bases: object

Cython class to manipulate double precision 2D matrix

n_cols
n_rows
size_
class abpytools.utils.math_utils.NumericalBaseStructure

Bases: object

class abpytools.utils.math_utils.Vector

Bases: object

Lightweight Cython vector class implementation that stores data as C arrays and uses these to perform calculations

add()

Elementwise addition between two vectors.

Args:
other:

Returns:

dot_product()

Vector dot product. Args:

other (Vector): a Vector object to calculate the dot product with

Returns: the dot product between two vectors

exp()
multiply()

Elementwise multiplication between two vectors.

Args:
other:

Returns:

norm()
size
subtract()

Elementwise subtraction between two vectors.

Args:
other:

Returns:

values

Returns:

abpytools.utils.math_utils.dot_product_()

Python API to use Cython dot_product implementation.

Args:
u list: Python list representing vector u v list: Python list representing vector v

Returns: Dot product of u and v

abpytools.utils.python_config module

class abpytools.utils.python_config.PythonConfig[source]

Bases: object

ipython_info
matplotlib_interactive
abpytools.utils.python_config.get_ipython_info()[source]

Module contents