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 {func}molsysmt.basic.is_a_molecular_system.

But 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.

Hint

What is an item? Visit the section User guide > Introduction > Molecular System in case you are not familiar with the concept of “item” in MolSysMT.

Added in version 1.0.0.

How this function works#

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().

Let’s illustrate how the function works with a simple example:

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']

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	4306	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 method as molsysmt.basic.is_a_molecular_system().

What about combining topology with structures_B?

msm.is_a_molecular_system([topology, structures_B])

False