contact_hists

mdtools.structure.contact_hists(cm, natms_per_refcmp=1, natms_per_selcmp=1, minlength=0, dtype=int)[source]

Bin the number of contacts between reference and selection compounds into histograms.

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 original AtomGroup are taken into account, even if the compound might comprise additional Atoms that are not contained in the original 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. Alternatively, cm can already be a compound contact count matrix as e.g. generated by mdtools.structure.cmp_contact_count_matrix(). In this case, you probably want to set natms_per_refcmp and natms_per_selcmp to 1, to keep cm unaltered.

  • 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]).

  • minlength (int, optional) – A minimum number of bins for the output arrays. The output arrays will have at least this number of elements, though they will be longer if necessary. All output arrays will always have the same length.

  • dtype (dtype, optional) – Data type of the output array.

Returns:

  • hist_refcmp_diff_selcmp (numpy.ndarray) – Histogram of the number of contacts that reference compounds establish to different selection compounds. Multiple contacts with the same selection compound are not taken into account.

  • hist_refcmp_same_selcmp (numpy.ndarray) – Histogram of the number of contacts that reference compounds establish to the same selection compound. Different selection compounds that are connected to the same reference compound via the same number of “bonds” (Atom- Atom contacts) are not taken into account.

  • hist_refcmp_selcmp_tot (numpy.ndarray) – Histogram of the total number of contacts that reference compounds establish to selection compounds. All contacts are taken into account.

  • hist_refcmp_selcmp_pair (numpy.ndarray) – Histogram of the number of “bonds” (Atom- Atom contacts) between pairs of reference and selection compounds (refcmp-selcmp pairs). A refcmp-selcmp pair is defined as a reference and selection compound that are connected with each other via at least one “bond”.

See also

contact_hist

MDTools script to calculate contact histograms.

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.contact_hist_refcmp_diff_selcmp()

Bin the number of contacts that reference compounds establish to different selection compounds into a histogram.

mdtools.structure.contact_hist_refcmp_same_selcmp()

Bin the number of contacts that reference compounds establish to the same selection compound into a histogram.

mdtools.structure.contact_hist_refcmp_selcmp_tot()

Bin the total number of contacts that reference compounds establish to selection compounds into a histogram.

mdtools.structure.contact_hist_refcmp_selcmp_pair()

Bin the number of “bonds” (Atom- Atom contacts) between pairs of reference and selection compounds

Notes

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

This function gathers the output of

See there for further details about the returned histograms.

If both natms_per_refcmp and natms_per_selcmp are 1 and cm is a true boolean contact matrix, hist_refcmp_same_selcmp and hist_refcmp_selcmp_pair are rather meaningless and hist_refcmp_diff_selcmp and hist_refcmp_selcmp_tot are equal. Thus, in this case it might be better to call mdtools.structure.contact_hist_refcmp_diff_selcmp() or mdtools.structure.contact_hist_refcmp_selcmp_tot() directly.

Examples

>>> cm = np.tril(np.ones((5,4), dtype=bool), -1)
>>> cm[3, 0] = 0
>>> cm
array([[False, False, False, False],
       [ True, False, False, False],
       [ True,  True, False, False],
       [False,  True,  True, False],
       [ True,  True,  True,  True]])
>>> hists = mdt.strc.contact_hists(cm, minlength=7, dtype=np.uint32)
>>> hists[0]
array([1, 1, 2, 0, 1, 0, 0], dtype=uint32)
>>> hists[1]
array([1, 4, 0, 0, 0, 0, 0], dtype=uint32)
>>> hists[2]
array([1, 1, 2, 0, 1, 0, 0], dtype=uint32)
>>> hists[3]
array([0, 9, 0, 0, 0, 0, 0], dtype=uint32)
>>> np.array_equal(hists[0], hists[2])
True
>>> hists[1][1] == cm.shape[0] - hists[1][0]
True
>>> hists[3][1] == np.count_nonzero(cm)
True

>>> mdt.strc.cmp_contact_count_matrix(
...     cm=cm, natms_per_refcmp=[2, 2, 1], natms_per_selcmp=2
... )
array([[1, 0],
       [3, 1],
       [2, 2]])
>>> hists = mdt.strc.contact_hists(
...     cm=cm, natms_per_refcmp=[2, 2, 1], natms_per_selcmp=2
... )
>>> hists[0]
array([0, 1, 2, 0, 0])
>>> hists[1]
array([0, 2, 1, 1, 0])
>>> hists[2]
array([0, 1, 0, 0, 2])
>>> hists[3]
array([0, 2, 2, 1, 0])

Edge cases:

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

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