Miscellaneous Tools

This module defines miscellaneous utility functions.

class Everything

A place for everything.

rangeString(lint, sep=' ', rng=' to ', exc=False, pos=True)

Returns a structured string for a given list of integers.

Parameters:

• lint – integer list or array
• sep – range or number separator
• rng – range symbol
• exc – set True if range symbol is exclusive
• pos – only consider zero and positive integers

In [1]: from prody.utilities import rangeString

In [2]: lint = [1, 2, 3, 4, 10, 15, 16, 17]

In [3]: rangeString(lint)
Out[3]: '1 to 4 10 15 to 17'

In [4]: rangeString(lint, sep=',', rng='-')
Out[4]: '1-4,10,15-17'

In [5]: rangeString(lint, ',', ':', exc=True)
Out[5]: '1:5,10,15:18'

alnum(string, alt='_', trim=False, single=False)

Replace non alpha numeric characters with alt. If trim is True remove preceding and trailing arg characters. If single is True, contain only a single joining alt character.

importLA()

Returns one of scipy.linalg or numpy.linalg.

dictElement(element, prefix=None, number_multiples=False)

Returns a dictionary built from the children of element, which must be a xml.etree.ElementTree.Element instance. Keys of the dictionary are tag of children without the prefix, or namespace. Values depend on the content of the child. If a child does not have any children, its text attribute is the value. If a child has children, then the child is the value.

intorfloat(x)

Returns int(x), or float(x) upon ValueError.

startswith(this, that)

Returns True if this or that starts with the other.

showFigure()

Call show() function with block=False argument to avoid blocking behavior in non-interactive sessions. If block keyword argument is not recognized, try again without it.

countBytes(arrays, base=False)

Returns total number of bytes consumed by elements of arrays. If base is True, use number of bytes from the base array.

sqrtm(matrix)

Returns the square root of a matrix.

addEnds(x, y, axis=0)

Finds breaks in x, extends them by one position and adds nan at the corresponding position in y. x needs to be an 1-D array, y can be a matrix of column (or row) vectors

isPDB()

match(string[, pos[, endpos]]) –> match object or None. Matches zero or more characters at the beginning of the string

isURL()

match(string[, pos[, endpos]]) –> match object or None. Matches zero or more characters at the beginning of the string

isSymmetric(M, rtol=1e-05, atol=1e-08)

Checks if the matrix is symmetric.

makeSymmetric(M)

Makes sure the matrix is symmetric.

div0(a, b, defval=0.0)

Performs true_divide but ignores the error when division by zero (result is set to zero instead).

wmean(array, weights, axis=None)

Calculates the weighted average of array given axis.

bin2dec(x)

Converts the binary array to decimal.

fixArraySize(arr, sizes, value=0)

Makes sure that arr is of sizes. If not, pad with value.

decToHybrid36(x, resnum=False)

Convert a regular decimal number to a string in hybrid36 format

hybrid36ToDec(x, resnum=False)

Convert string in hybrid36 format to a regular decimal number

checkIdentifiers(*pdb, **kwargs)

Check whether pdb identifiers are valid, and replace invalid ones with None in place.