structure

Functions to calculate structural properties.

This module can be called from mdtools via the shortcut strc:

import mdtools as mdt
mdt.strc  # insetad of mdt.structure

Functions

cm_fill_missing_cmp_ix	Insert elements in a contact matrix at missing intermediate compound indices.
cm_selix_stats	Get statistics about the indices of selection compounds bound to reference compounds for each reference compound.
cmp_contact_count_matrix	Take an Atom contact matrix and sum the contacts of all Atoms belonging to the same compound.
cmp_contact_matrix	Convert an Atom contact matrix to a compound contact matrix.
cms_n_common_contacts	Get the number of contancts common in all contact matrices.
cms_n_contacts	Get the number of contancts per contact matrix and the number of contacts common in all contact matrices.
com	Calculate the center of mass of (compounds of) a MDAnalysis AtomGroup.
contact_hist_refcmp_diff_selcmp	Bin the number of contacts that reference compounds establish to different selection compounds into a histogram.
contact_hist_refcmp_same_selcmp	Bin the number of contacts that reference compounds establish to the same selection compound into a histogram.
contact_hist_refcmp_selcmp_pair	Bin the number of “bonds” (Atom- Atom contacts) between pairs of reference and selection compounds.
contact_hist_refcmp_selcmp_tot	Bin the total number of contacts that reference compounds establish to selection compounds into a histogram.
contact_hists	Bin the number of contacts between reference and selection compounds into histograms.
contact_matrices	Construct a contact matrix for two MDAnalysis AtomGroups for each frame in a trajectory.
contact_matrix	Construct a contact matrix for two MDAnalysis AtomGroups.
discrete_pos_trj	Create a discrete posotion trajectory.
natms_per_cmp	Get the number of Atoms of each compound in an MDAnalysis AtomGroup.