Is a molecular system#

Verifying whether an object defines a single valid molecular system.

A molecular system can be defined using a single item or a list of items. To check whether a given collection defines a valid molecular system, use the function molsysmt.basic.is_a_molecular_system().

What does “valid” mean in this context? It means that all items can be combined into a single system — without internal inconsistencies — by layering their attributes (e.g., topology, coordinates, box) in a compatible way. MolSysMT first classifies the forms: two items that both provide a topology are separate systems. Complementary items, such as a topology and a trajectory, are then checked for matching atom counts. The result is False if that consistency check fails or cannot be completed.

Hint

Visit the section Items and Forms for an introduction to items and forms in MolSysMT.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.basic.is_a_molecular_system().

Basic usage#

Let’s show how this function works using demonstration datasets (pentalanine):

import molsysmt as msm

topology = msm.systems['pentalanine']['pentalanine.prmtop']
structures_A = msm.systems['pentalanine']['pentalanine.inpcrd']
structures_B = msm.systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.dcd']

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

We have a single item — a *.prmtop file — that by itself defines a molecular system with no structure data:

msm.info(topology)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_peptides	n_structures
file:prmtop	5207	1722	1716	1	1716	2	1715	1	None

We also have two items — an “inpcrd” file and a “dcd” trajectory — which can independently define molecular systems without topological attributes.

msm.info(structures_A)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_structures
file:inpcrd	5207	None	None	None	None	None	1

msm.info(structures_B)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_structures
file:dcd	4369	None	None	None	None	None	20

Can the items topology and structures_A be combined to form a valid molecular system?

msm.is_a_molecular_system([topology, structures_A])

True

Tip

All functions in the molsysmt.basic module are also accessible from the top-level namespace of the library. Hence, molsysmt.is_a_molecular_system() is the same function as molsysmt.basic.is_a_molecular_system().

What about combining topology with structures_B?

msm.is_a_molecular_system([topology, structures_B])

False