contact_hist

Calculate the number of contacts between two MDAnalysis AtomGroups.

Todo

Finish docstring.

Contacts are binned into histograms according to how many different selection Atoms/compounds have contact with a given reference Atom/compound and according to how many contacts exist between a given reference-selection pair.

Options

-f

Trajectory file. See supported coordinate formats of MDAnalysis.

-s

Topology file. See supported topology formats of MDAnalysis.

-o

Output filename.

-b

First frame to read from the trajectory. Frame numbering starts at zero. Default: 0.

-e

Last frame to read from the trajectory. This is exclusive, i.e. the last frame read is actually END - 1. A value of -1 means to read the very last frame. Default: -1.

--every

Read every n-th frame from the trajectory. Default: 1.

--ref

Selection string to select the reference group. See MDAnalysis’ selection syntax for possible choices.

--sel

Selection string to select the selection group. See MDAnalysis’ selection syntax for possible choices.

-c

Cutoff distance in Angstrom. A reference and selection atom are considered to be in contact, if their distance is less than or equal to this cutoff.

--refcmp

{‘segments’, ‘residues’, ‘fragments’}

The compounds of the reference group to use for calculating the contact histograms. Contact histograms are always calculated for single atom contacts, but also for contacts between entire compounds. Specify here, which compounds to use for the reference group. Compounds can be ‘segments’, ‘residues’ or ‘fragments’. Refer to the MDAanalysis user guide for an explanation of these terms. Note that in any case, even if REFCMP is e.g. ‘residues’, only the atoms belonging to the reference group are taken into account, even if the compound might comprise additional atoms that are not contained in the reference group. Default: 'residues'

--selcmp

{‘segments’, ‘residues’, ‘fragments’}

Same for the selection group. Default: 'residues'

--updating-ref

Use an UpdatingAtomGroup for the reference group. Selection expressions of UpdatingAtomGroups are re-evaluated every time step. This is e.g. useful for position-based selections like ‘type Li and prop z <= 2.0’.

--updating-sel

Use an UpdatingAtomGroup for the selection group.