natms_per_cmp

mdtools.structure.natms_per_cmp(ag, cmp, return_array=False, return_cmp_ix=False, check_contiguous=False)[source]

Get the number of Atoms of each compound in an MDAnalysis AtomGroup.

Parameters:

ag (MDAnalysis.core.groups.AtomGroup) – The MDAnalysis AtomGroup for which to get the number of Atoms per compound.
cmp ({'group', 'segments', 'residues', 'molecules', 'fragments', 'atoms'}) – The compounds of ag for which to get the number of Atoms. If 'atoms', the output will simply be 1 or an array of ones (depending on the value of return_array). Else, the number of Atoms in the entire group or of each Segment, Residue, molecule or fragment in ag is returned. Refer to the MDAnalysis’ user guide for an explanation of these terms. Note that in any case, even if cmp is e.g. 'residues', only the Atoms belonging to ag are taken into account, even if the compound might comprise additional Atoms that are not contained in ag.
return_array (bool, optional) – If True, natms_per_cmp (the output of this function) will always be an array with a length equal to the number of compounds in ag. If False, natms_per_cmp will be an integer if all compounds in ag have the same number of Atoms. However, if this is not the case, natms_per_cmp will be an array even if return_array is False.
return_cmp_ix (bool, optional) – If True, additionally return the unique indices of the compounds as assigned by MDAnalysis. If cmp is e.g. 'residues', this is np.unique(ag.resindices).
check_contiguous (bool, optional) – If True, check if Atoms belonging to the same compound form a contiguous set in the input AtomGroup. This is e.g. important when constructing compound contact matrices from Atom contact matrices with mdtools.structure.cmp_contact_matrix().

Returns:

natms_per_cmp (int or numpy.ndarray) – Number of Atoms of each compound contained in ag. If return_array is False and all compounds in ag have the same number of Atoms, a single integer is returned. If return_array is True or if not all compounds in ag have the same number of Atoms, an array is returned containing the number of Atoms of each single compound in ag.
cmp_ix (array_like) – Unique compound indices as assigned by MDAnalysis. Only returned if return_cmp_ix is True.

See also

mdtools.structure.cmp_attr(): Get attributes of an MDAnalysis AtomGroup compound-wise.
mdtools.structure.cmp_contact_matrix(): Convert an Atom contact matrix to a compound contact matrix
mdtools.structure.cmp_contact_count_matrix(): Take an Atom contact matrix and sum the contacts of all Atoms belonging to the same compound
mdtools.structure.contact_hists(): Bin the number of contacts between reference and selection compounds into histograms

Examples

Create an MDAnalysis Universe from scratch for the following examples.

>>> import MDAnalysis as mda
>>> # Number of segments.
>>> n_seg = 1
>>> # Number of residues per segment.
>>> n_res = [n+2 for n in range(n_seg)]
>>> # Number of atoms per residue.
>>> n_atms = [n+2 for n_r in n_res for n in range(n_r)]
>>> u = mda.Universe.empty(
...     n_atoms=sum(n_atms),
...     n_residues=sum(n_res),
...     n_segments=n_seg,
...     atom_resindex=[
...         ix for ix, n_a in enumerate(n_atms) for _ in range(n_a)
...     ],
...     residue_segindex=[
...         ix for ix, n_r in enumerate(n_res) for _ in range(n_r)
...     ],
...     trajectory=True,
...     velocities=True,
...     forces=True,
... )
>>> bonds = [
...     (sum(n_atms[:i]), j)
...     for i in range(len(n_atms))
...     for j in range(sum(n_atms[:i])+1, sum(n_atms[:i+1]))
... ]
>>> u.add_TopologyAttr("bonds", bonds)
>>> ag = u.atoms

>>> mdt.strc.natms_per_cmp(ag, cmp="group")
5
>>> mdt.strc.natms_per_cmp(ag, cmp="group", return_array=True)
array([5])
>>> mdt.strc.natms_per_cmp(ag, cmp="segments")
5
>>> mdt.strc.natms_per_cmp(ag, cmp="residues")
array([2, 3])
>>> mdt.strc.natms_per_cmp(ag, cmp="residues", return_cmp_ix=True)
(array([2, 3]), array([0, 1]))
>>> mdt.strc.natms_per_cmp(ag, cmp="fragments")
array([2, 3])
>>> mdt.strc.natms_per_cmp(ag, cmp="atoms")
1