Miscellaneous Tools¶
This module defines miscellaneous utility functions.
-
rangeString
(lint, sep=' ', rng=' to ', exc=False, pos=True)[source]¶ 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)[source]¶ 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
()[source]¶ Returns one of
scipy.linalg
ornumpy.linalg
.
-
dictElement
(element, prefix=None, number_multiples=False)[source]¶ 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)[source]¶ Returns
int(x)
, orfloat(x)
uponValueError
.
-
showFigure
()[source]¶ Call
show()
function withblock=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)[source]¶ Returns total number of bytes consumed by elements of arrays. If base is True, use number of bytes from the base array.
-
addEnds
(x, y, axis=0)[source]¶ 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
-
div0
(a, b, defval=0.0)[source]¶ Performs
true_divide
but ignores the error when division by zero (result is set to zero instead).
-
decToHybrid36
(x, resnum=False)[source]¶ Convert a regular decimal number to a string in hybrid36 format
-
hybrid36ToDec
(x, resnum=False)[source]¶ Convert string in hybrid36 format to a regular decimal number