Miscellaneous Tools

This module defines miscellaneous utility functions.

class prody.utilities.misctools.Everything

A place for everything.

prody.utilities.misctools.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

prody.utilities.misctools.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.

prody.utilities.misctools.bin2dec(x)

Converts the binary array to decimal.

prody.utilities.misctools.checkIdentifiers(*pdb, **kwargs)

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

prody.utilities.misctools.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.

prody.utilities.misctools.decToHybrid36(x, resnum=False)

Convert a regular decimal number to a string in hybrid36 format

prody.utilities.misctools.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.

prody.utilities.misctools.div0(a, b, defval=0.0)

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

prody.utilities.misctools.fixArraySize(arr, sizes, value=0)

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

prody.utilities.misctools.hybrid36ToDec(x, resnum=False)

Convert string in hybrid36 format to a regular decimal number

prody.utilities.misctools.impLoadModule(name, cmd, path)

Returns an an imported module equivalent to imp.

prody.utilities.misctools.importDec()

Returns an imported module equivalent to numpy testing decorators.

prody.utilities.misctools.importLA()

Returns one of scipy.linalg or numpy.linalg.

prody.utilities.misctools.intorfloat(x)

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

prody.utilities.misctools.isPDB(string, pos=0, endpos=9223372036854775807)

Matches zero or more characters at the beginning of the string.

prody.utilities.misctools.isSymmetric(M, rtol=1e-05, atol=1e-08)

Checks if the matrix is symmetric.

prody.utilities.misctools.isURL(string, pos=0, endpos=9223372036854775807)

Matches zero or more characters at the beginning of the string.

prody.utilities.misctools.makeSymmetric(M)

Makes sure the matrix is symmetric.

prody.utilities.misctools.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

prody.utilities.misctools.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.

prody.utilities.misctools.sqrtm(matrix)

Returns the square root of a matrix.

prody.utilities.misctools.startswith(this, that)

Returns True if this or that starts with the other.

prody.utilities.misctools.wmean(array, weights, axis=None)

Calculates the weighted average of array given axis.