Removing elements and structures#

This page documents view.remove(...).

view.remove(...) removes atoms and/or structures from the molecular system behind the view.

It is a live operation: it updates view.molsys and refreshes the viewer so the change is reflected in the browser.

For more details and additional examples, see the MolSysMT tutorial: Remove.

A practical guideline: whenever you can, prefer removing by selection rather than by hard-coded atom indices. Atom indices can change after removals, and selections are usually more robust.

Elements and structures#

remove supports two complementary operations, and you can use either one depending on what you are trying to do:

Remove atoms (and therefore any higher-level elements that become empty) using selection=....
Remove structures using structure_indices=....

If you need a reminder of the available element levels (atom, group, molecule, …), here is a quick reference:

Element	Meaning
`atom`	Atoms of the molecular system.
`group`	First supra-atomic chemical level: amino acids, waters, ions, lipids, etc.
`component`	A covalently connected set of atoms (a covalent component).
`molecule`	A single molecular instance (one water molecule, one benzene molecule, etc.).
`chain`	An author-defined grouping that can vary across sources; it may represent anything from a polymer chain to a higher-level supra-molecular partition.
`entity`	Molecular nature/type. For example, you can have two entities (water and benzene) and six molecules (four waters and two benzenes).
`system`	The whole molecular system.
`bond`	Covalent connectivity between atoms (may be absent or inferred depending on the input).

Example: remove water#

We start by checking how many atoms we have, and then we remove water molecules.

This is a destructive operation on the loaded system: if you want to undo it, reload the view (or re-create it from the original data).

import molsysviewer as viewer

view = viewer.demo["181L"]
view.show()

view.get(element="system", n_atoms=True, n_waters=True, output_type="dictionary")

{'n_atoms': 1441, 'n_waters': 136}

view.remove(selection='molecule_type=="water"')
view.get(element="system", n_atoms=True, n_waters=True, output_type="dictionary")

{'n_atoms': 1305, 'n_waters': 0}

You have to find something like this in your viewer:

Example: remove structures#

Some systems include multiple structures (for example, a trajectory or multiple coordinate sets). In that case, you can remove structures by index (0-based).

In the demo below, the molecular system includes many structures, and we remove a few of them.

view = viewer.demo["pentalanine"]
view.show()

view.get(element="system", n_structures=True)

view.remove(structure_indices=[0, 1, 2])
view.get(element="system", n_structures=True)

Check your first structure now and the total number of structures in the viewer: