Contains#

Checking whether a molecular system contains specific elements or attributes

The function molsysmt.basic.contains() can check whether or not a molecular system contains certain elements or attributes without the need to use molsysmt.basic.get().

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.contains().

Let’s illustrate how this function works using the following molecular system:

import molsysmt as msm

molsys = msm.convert('181L')

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_ions	n_small_molecules	n_proteins	n_structures
molsysmt.MolSys	1441	302	141	6	141	5	136	2	2	1	1

Let’s check if the system contains water molecules:

msm.contains(molsys, waters=True)

True

We can also check whether the system includes periodic boundary conditions:

msm.contains(molsys, box=True)

True

Tip

All methods defined in the molsysmt.basic module can be invoked also from the main level of the library. As such, molsysmt.contains() is the same method as molsysmt.basic.contains().

Now let’s verify if the system contains ions, small molecules, and proteins:

msm.contains(molsys, ions=True, small_molecules=True, proteins=True)

True

You can also check for the absence of specific elements or attributes:

msm.contains(molsys, proteins=True, lipids=False)

True

Or check whether the system contains a specific number of molecules:

msm.contains(molsys, small_molecules=2, ions=2)

True

msm.contains(molsys, small_molecules=2, proteins=2)

False

The input argument selection can also be used instead of attributes:

msm.contains(molsys, selection='hydrogens')

False

msm.contains(molsys, selection='molecule_type!="water" and atom_name==["CA", "CB"]')

True

Or combine a selection with additional conditions on elements:

msm.contains(molsys, selection='molecule_type!="water"', small_molecules=2)

True

msm.contains(molsys, selection='molecule_type!="water"', water=True)

False