ample.util.ample_util module¶

Various miscellaneous functions

amoptd_fix_path(optd, newroot)[source]¶

Update all the paths in an AMPLE results dictionary to be rooted at newroot

Parameters:	optd (dict) – AMPLE results dictionary newroot (str) – Path to the AMPLE root directory (topdir containing MRBUMP dir etc.)

disable_logging(*args, **kwds)[source]¶

A context manager to disable logging within a block.

Parameters:	logger (logging.Logger) – logger instance highet_level (int) – loglevel that will be set for the duration of the context

extract_tar(archive, directory=None, filenames=None, suffixes=None)[source]¶

Extract one or more files from a tar file into a specified directory

Parameters:	archive (str) – tar archive to extract from directory (str) – directory to extract files into filenames (list) – a list of files to extract from the archive suffixes (list) – only extract a file if the suffix is in the list
Returns:	A list of the extracted files
Return type:	list

filename_append(filename=None, astr=None, directory=None, separator='_')[source]¶: Append astr to filename, before the suffix, and return the new filename.

find_exe(executable, dirs=None)[source]¶

Find the executable exename.

Parameters:	executable (str) – The name of the program or the path to an existing executable dirs (list, tuple, optional) – Additional directories to search for the location

ideal_helices(optd)[source]¶

Get some ideal helices

Parameters:	nresidues (int) – Number of residues to be used
Returns:	pdbs (list) ensemble_options (dict) ensembles_data (list)

is_exe(fpath)[source]¶

Check if an executable exists

Parameters:	fpath (str) – The path to the executable
Returns:
Return type:	bool

is_file(fpath)[source]¶

Check if a file exists

make_workdir(run_dir, ccp4i2=False, MAX_WORKDIRS=100)[source]¶

Make a work directory rooted at run_dir and return its path

Parameters:	run_dir (str) – The path to a run directory where the job was started ccp4i2 (bool, optional) – Indicate if we are running under CCP4I2
Returns:	work_dir – The path to the working directory
Return type:	str

read_amoptd(amoptd_fname)[source]¶

Read a PICKLE-formatted AMPLE options file

Parameters:	amoptd_fname (str) – The path to the PICKLE-formatted AMPLE options file
Returns:	amoptd – AMPLE options from saved state
Return type:	dict

run_command(cmd, logfile=None, directory=None, dolog=True, stdin=None, check=False, **kwargs)[source]¶

Execute a command and return the exit code.

Parameters:	cmd (list) – Command to run as a list stdin (str or filehandle, optional) – Stdin for the command logfile (str, optional) – The path to the logfile directory (str, optional) – The directory to run the job in (cwd assumed) dolog (bool, optional) – Whether to output info to the system log [default: False]
Returns:	returncode – Subprocess exit code
Return type:	int

Notes

We take care of outputting stuff to the logs and opening/closing logfiles

saveAmoptd(*args)[source]¶: Save AMPLE options to a PICKLE-formatted file

See also

save_amoptd()

Warning

This function was deprecated and will be removed in future releases. Please use save_amoptd() instead.

save_amoptd(amoptd)[source]¶

Save AMPLE options to a PICKLE-formatted file

Parameters:	amoptd (dict) – AMPLE options from saved state

tmpFileName()[source]¶: Return a filename for a temporary file

See also

tmp_file_name()

Warning

This function was deprecated and will be removed in future releases. Please use tmp_file_name() instead.

tmp_file_name(delete=True, directory=None, suffix='')[source]¶

Return a filename for a temporary file

Parameters:	delete (bool, optional) – Flag whether the temporary file should be deleted [default: True] directory (str, optional) – Path to a directory to write the files to. suffix (str, optional) – A suffix to the temporary filename