structure

Functions to calculate structural properties.

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

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

Functions

assign_atoms_to_grid	Assign Atoms to grid points.
center	Calculate different types of centers of (compounds of) an MDAnalysis AtomGroup.
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_attr	Get attributes of an MDAnalysis AtomGroup compound-wise.
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 contacts common in all contact matrices.
cms_n_contacts	Get the number of contacts per contact matrix and the number of contacts common in all contact matrices.
coc	Calculate the center of charge of (compounds of) an MDAnalysis AtomGroup.
cog	Calculate the center of geometry (a.k.a centroid) of (compounds of) an MDAnalysis AtomGroup.
com	Calculate the center of mass of (compounds of) an 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 position trajectory.
natms_per_cmp	Get the number of Atoms of each compound in an MDAnalysis AtomGroup.
rmsd	Calculate the Root Mean Square Deviation (RMSD) between two sets of positions.
wcenter	Calculate the weighted center of (compounds of) an MDAnalysis AtomGroup.
wcenter_pos	Calculate the weighted center of an position array.