cmp_contact_count_matrix

mdtools.structure.cmp_contact_count_matrix(cm, natms_per_refcmp=1, natms_per_selcmp=1, dtype=int)[source]

Take an Atom contact matrix and sum the contacts of all Atoms belonging to the same compound.

A compound is usually a chemically meaningful subgroup of an AtomGroup. This can e.g. be a Segment, Residue, fragment or a single Atom. Refer to the MDAnalysis’ user guide for an explanation of these terms. Note that in any case, only Atoms belonging to the input AtomGroup are taken into account, even if the compound might comprise additional Atoms that are not contained in the input AtomGroup.

Parameters:

cm (array_like) – (Boolean) contact matrix of shape (m, n) as e.g. generated by mdtools.structure.contact_matrix(), where m is the number of reference Atoms and n is the number of selection Atoms.
natms_per_refcmp (int or array_like, optional) – Number of Atoms per reference compound. Can be a single integer or an array of integers. If natms_per_refcmp is a single integer, all reference compounds are assumed to contain the same number of Atoms. In this case, natms_per_refcmp must be an integer divisor of cm.shape[0]. If natms_per_refcmp is an array of integers, it must contain the number of reference Atoms for each single reference compound. In this case, sum(natms_per_refcmp) must be equal to cm.shape[0].
natms_per_selcmp (int or array_like, optional) – Same for selection compounds (natms_per_selcmp is checked against cm.shape[1]).
dtype (dtype, optional) – Data type of the output array.

Returns:

cmp_ccm (numpy.ndarray) – A new (smaller) contact count matrix indicating how many contacts exist between the Atoms of a given reference and selection compound. If both natms_per_refcmp and natms_per_selcmp are 1, the input contact matrix is returned instead with its data type converted to dtype.

See also

mdtools.structure.contact_matrix(): Construct a boolean contact matrix for two MDAnalysis AtomGroups
mdtools.structure.natms_per_cmp(): Get the number of Atoms of each compound in an MDAnalysis AtomGroup
mdtools.structure.cmp_contact_matrix(): Convert an Atom contact matrix to a compound contact matrix
mdtools.structure.contact_hists(): Bin the number of contacts between reference and selection compounds into histograms.
numpy.ufunc.reduceat(): Perform a (local) reduce() with specified slices over a single axis

Notes

Atoms belonging to the same compound must form a contiguous set in the input contact matrix, otherwise the result will be wrong.

If both natms_per_refcmp and natms_per_selcmp are 1, cmp_contact_count_matrix(cm, dtype=dtype) is equivalent to np.asarray(cm, dtype=dtype).

Examples

>>> cm = np.array([[ True,  True, False, False],
...                [ True, False, False,  True],
...                [False, False,  True,  True]])
>>> mdt.strc.cmp_contact_count_matrix(cm, natms_per_refcmp=3)
array([[2, 1, 1, 2]])
>>> mdt.strc.cmp_contact_count_matrix(cm, natms_per_selcmp=2)
array([[2, 0],
       [1, 1],
       [0, 2]])
>>> mdt.strc.cmp_contact_count_matrix(
...     cm, natms_per_refcmp=[1, 2], natms_per_selcmp=[2, 2]
... )
array([[2, 0],
       [1, 3]])
>>> mdt.strc.cmp_contact_count_matrix(
...     cm,
...     natms_per_refcmp=[1, 2],
...     natms_per_selcmp=[2, 2],
...     dtype=np.uint32,
... )
array([[2, 0],
       [1, 3]], dtype=uint32)

If both natms_per_refcmp and natms_per_selcmp are 1, cmp_contact_count_matrix(cm, dtype=dtype) is equivalent to np.asarray(cm, dtype=dtype):

>>> mdt.strc.cmp_contact_count_matrix(cm, dtype=bool) is cm
True
>>> mdt.strc.cmp_contact_count_matrix(cm, dtype=int) is cm
False

Edge cases:

>>> cm = np.array([], dtype=bool).reshape(0, 4)
>>> mdt.strc.cmp_contact_count_matrix(cm, natms_per_refcmp=[])
array([], shape=(0, 4), dtype=int64)
>>> mdt.strc.cmp_contact_count_matrix(cm, natms_per_refcmp=1)
array([], shape=(0, 4), dtype=int64)

>>> cm = np.array([], dtype=bool).reshape(6, 0)
>>> mdt.strc.cmp_contact_count_matrix(
...     cm, natms_per_refcmp=3, natms_per_selcmp=[], dtype=np.uint32
... )
array([], shape=(2, 0), dtype=uint32)