pyviblib.util.misc

Miscellaneous

Classes

SmartDict

container for storage of overridable options

Command

emulator of lambda functions

PropertiesContainer

class for exposing properties via attributes

Functions

color_html_to_RGB()

convert a color in the HTML format to RGB

color_RGB_to_html()

convert a color in the RGB format to HTML

color_complementary()

generate the complementary of a color

str_to_float()

convenient conversion from string to float

remove_indices_from_list()

remove indices from a list

random_color()

generate a random color

save_matrix()

save a matrix

unique()

make a unique array

is_command_on_path()

check whether a command is on the path

ps2pdf()

convert from PS/EPS to PDF

ppm2gif()

convert from PPM to GIF with Netpbm

rests()

retrieve atomno, i

readconfig_option()

read an option from a section

gen_molecule_name()

generate the molecule name

gen_group_labels()

generate group labels A, B etc.

import_processing()

import and return a processing module

memoize_deterministic()

memoization decorator

Module variables

CACHE_MEMOIZE

a dictionary that holds the memoize cache

LOCK_MEMOIZE

a lock used during memoization

Author:Maxim Fedorovsky

class pyviblib.util.misc.SmartDict(mapping_or_sequence=None, kw=None, default_value=None)

A container for a convenient storage of overridable options.

The class is based on the Python builtin dictionary. It is made up of two containers:

• internal dictionary for the default values
• second dictionary, where the options are first looked up.

The former dictionary is referred to as the default dictionary and the latter one as the reference dictionary.

The following readable and writable property is exposed:

kw

reference dictionary

The following public methods are exported:

update_()

update the reference dictionary

merge()

overwrite the default dictionary with the reference one

Initializer of the class.

Parameters:

• mapping_or_sequence – initial contents of the default dictionary
• kw – reference dictionary
• default_value – returned if a key is found in neither in the default nor in the reference dictionary

merge()

Update the default dictionary with the reference one.

update_(kw)

Update the reference dictionary.

If it is not defined, update the default dictionary.

Parameter:kw – dictionary to update with

class pyviblib.util.misc.Command(func, *args, **kwargs)

Emulator of lambda functions.

The idea is taken from H.P. Langtangen, Python Scripting for Computational Science. Springer Verlag Berlin Heidelberg, 2004. p. 519.

Initializer of the class.

Parameters:

• func – function to be called, must be callable, otherwise an exception is raised
• args – positional arguments to the function
• kwargs – keyword arguments to the function

static fget_attr(obj, name)

Emulate a fget function used by definition of a property (via attribute).

This is a static method of the class.

Parameters:

• obj – supposed to be the first argument of the fget function
• name – name of the attribute

static fset_attr(obj, value, name)

Emulate a fset function used by definition of a property.

This is a static method of the class.

Parameters:

• obj – object
• value – value of the attribute to be set
• name – attribute of the object to be set

class pyviblib.util.misc.PropertiesContainer

Class for exposing properties via attributes.

The following protected methods are called in the constructor:

_check_consistency()

check the consistency of the data passed

_declare_properties()

declare properties

The following protected method should be used for adding properties:

_add_property()

expose a given class attribute as a property

Initializer of the class.

pyviblib.util.misc.color_html_to_RGB(colorstr)

Convert a color in the HTML format to RGB.

Parameter:colorstr – color in the HTML format e.g. ‘#FF0000’ Returns:the tuple of float RGB values

pyviblib.util.misc.color_RGB_to_html(rgb)

Convert a color in the RGB format to HTML.

Parameter:rgb – tuple of float RGB values e.g. (1., 0., 0.) Returns:the color in the HTML format

pyviblib.util.misc.color_complementary(colorstr)

Generate the complementary of a color.

Parameter:colorstr – color in the HTML format e.g. ‘#FF0000’ Returns:the complementary color in the HTML format

pyviblib.util.misc.str_to_float(val, default=0.0)

Convenient conversion from string to float.

If the convertion is failed, return the default value.

Parameters:

• val – string value to converted to float
• default – float value to be returned on error (default 0.)

pyviblib.util.misc.remove_indices_from_list(list_, indices)

Remove indices from a list.

Parameters:

• list – list to be processed
• indices – indices to be removed from the list

No exception is raised if invalid indices are found.

pyviblib.util.misc.random_color()

Generate a random color in the HTML format.

pyviblib.util.misc.save_matrix(mat, filename, value_format='%13.6f', base=1)

Save a matrix.

Parameters:

• mat – matrix to be saved (ndarray)
• filename – file name or file object to save to
• value_format – format for writing elements of the matrix
• base – start index of the matrix

pyviblib.util.misc.unique(arr)

Make a unique array.

Parameter:arr – input ndarray

pyviblib.util.misc.is_command_on_path(cmd)

Check whether a command is on the path.

The function searches in directories specified by the PATH environmental variable.

Parameter:cmd – command name

pyviblib.util.misc.ps2pdf(filesrc, removesrc=True, **options)

Convert an PS/EPS file to PDF with the ps2pdf command.

See also

http://www.cs.wisc.edu/~ghost/doc/AFPL/6.50/Ps2pdf.htm#Options

Parameters:

• filesrc – PS/EPS file
• removesrc – remove the source file after the conversion (default True)
• options – any options recognized by ps2pdf

Returns:

whether the conversion has been successful

pyviblib.util.misc.ppm2gif(ppmname, gifname, tmpdir=None, remove_tmpdir=False, background=None)

Convert a ppm file to gif with Netpbm.

Parameters:

• ppmfile – ppm file
• gifname – gif file
• tmpdir – temp directory (default None), if None, create one and delete anyway
• remove_tmpdir – whether to remove tmpdir when done
• background – if given, it is a color in the HTML format to be made transparent

Raise:

OSError, IOError

pyviblib.util.misc.rests(num, divisor=3)

Retrieve atomno, i.

pyviblib.util.misc.readconfig_option(cfp, section, option, default=None)

Read an option from a section from a ConfigParser.

If the option cannot be read or on error the function returns the default.

Parameters:

• section – name of the section
• option – name of the option
• default – default value

pyviblib.util.misc.gen_molecule_name(filename, maxchar=None)

Generate the molecule name from the full path of a file.

Parameter:maxchar – maximal number of characters in the molecule name

pyviblib.util.misc.gen_group_labels(ngroups)

Generate group labels A, B etc.

Parameter:ngroups – number of groups

pyviblib.util.misc.import_processing()

Import and return a processing module.

pyviblib.util.misc.memoize_deterministic(gen_key)

Memoization decorator.

Parameter:gen_key – a callable that generates a string to identify a function to be memoized