atoms

mdtools.select.atoms(ag, sel, warn_empty=True, verbose=True, **kwargs)

Select Atoms from an MDAnalysis AtomGroup instance based on a selection string.

Parameters:

• ag (MDAnalysis.core.groups.AtomGroup) – MDAnalysis AtomGroup, UpdatingAtomGroup or Universe from which the Atoms will be selected.

• sel (str) – Selection string for selecting Atoms out of ag. See MDAnalysis’ selection syntax for possible choices.

• warn_empty (bool, optional) – If True (default), raise a RuntimeWarning if the created AtomGroup contains no Atoms and is not an UpdatingAtomGroup.

• verbose (bool, optional) – If True, print some basic information about the created MDAnalysis AtomGroup to standard output. In fact, if verbose is False, mdtools.select.atoms() simply calls select_atoms() and returns the resulting AtomGroup.

• kwargs (dict, optional) – Additional keyword arguments to parse to MDAnalysis.core.groups.AtomGroup.select_atoms().

Returns:

selection (MDAnalysis.core.groups.AtomGroup or MDAnalysis.core.groups.UpdatingAtomGroup) – An MDAnalysis AtomGroup or UpdatingAtomGroup (if updating is True) containing the selected Atoms.

Raises:

RuntimeWarning : – warn_empty is True and the created AtomGroup contains no atoms and is not an UpdatingAtomGroup.

See also

MDAnalysis.core.groups.AtomGroup.select_atoms()

Underlying function of this function

mdtools.run_time_info.ag_info_str()

Create a string containing information about an MDAnalysis AtomGroup.

Notes

This function is just a convenient wrapper around MDAnalysis.core.groups.AtomGroup.select_atoms() that can print the information generated by mdtools.run_time_info.ag_info_str() about the created MDAnalysis.core.groups.AtomGroup to standard output.