ample.util.ample_util module¶

Various miscellaneous functions

exception FileNotFoundError[source]¶

Bases: exceptions.Exception

amoptd_fix_path(optd, newroot, i2mock=False)[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.)

ccp4_version()[source]¶

Get CCP4 version as a tuple

Returns:	version : tuple Major, minor, and revision number

construct_references(optd)[source]¶

Construct the reference list

Parameters:	optd : dict A dictionary containing AMPLE options
Returns:	str A string containing the references

extract_models(amoptd, sequence=None, single=True, allsame=True)[source]¶

Extract some models

extract_tar(filename, directory, suffixes=[‘.pdb’])[source]¶

extract_zip(filename, directory, suffixes=[‘.pdb’])[source]¶

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:	bool

is_file(fpath)[source]¶

Check if a file exists

Parameters:	fpath : str The path to the file Returns —— bool

make_workdir(run_dir, ccp4i2=False)[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 : str The path to the working directory

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 : dict AMPLE options from saved state

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, 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 : int Subprocess exit code

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

Warning

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

See also

save_amoptd

save_amoptd(amoptd)[source]¶

Save AMPLE options to a PICKLE-formatted file

Parameters:	amoptd : dict AMPLE options from saved state

split_models(dfile, directory)[source]¶

Split a single PDB with multiple models in individual PDB files

Parameters:	dfile : str Single PDB file with multiple model entries directory : str Directory to extract the PDB files to
Returns:	extracted_models : list List of PDB files for all models

split_quark(*args)[source]¶

Split a single PDB with multiple models in individual PDB files

See also

split_models

tmpFileName()[source]¶

Return a filename for a temporary file

Warning

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

See also

tmp_file_name

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