pymatgen.util.io_utils module

This module provides utility classes for io operations.

class AtomicFile(name, mode='w+b', createmode=None, encoding=None)[source]

Bases: object

This is a straight port of Alexander Saltanov’s atomicfile package.

Writeable file object that atomically writes a file. All writes will go to a temporary file. Call close() when you are done writing, and AtomicFile will rename the temporary copy to the original name, making the changes visible. If the object is destroyed without being closed, all your writes are discarded. If an encoding argument is specified, will be called to open the file in the wanted encoding.

  • () (encoding) –

  • ()

  • ()

  • ()


Close the file.


Discard the file.

ask_yesno(question, default=True)[source]
  • () (default) –

  • ()


clean_lines(string_list, remove_empty_lines=True)[source]

Strips whitespace, carriage returns and empty lines from a list of strings.

  • string_list – List of strings

  • remove_empty_lines – Set to True to skip lines which are empty after stripping.


List of clean strings with no whitespaces.

micro_pyawk(filename, search, results=None, debug=None, postdebug=None)[source]

Small awk-mimicking search routine.

‘file’ is file to search through. ‘search’ is the “search program”, a list of lists/tuples with 3 elements; i.e. [[regex,test,run],[regex,test,run],…] ‘results’ is a an object that your search program will have access to for storing results.

Here regex is either as a Regex object, or a string that we compile into a Regex. test and run are callable objects.

This function goes through each line in filename, and if regex matches that line and test(results,line)==True (or test is None) we execute run(results,match),where match is the match object from running Regex.match.

The default results is an empty dictionary. Passing a results object let you interact with it in run() and test(). Hence, in many occasions it is thus clever to use results=self.

Author: Rickard Armiento, Ioannis Petousis