Contains#

Checking whether a molecular system contains specific elements or attributes.

The function molsysmt.basic.contains() allows to check whether or not a molecular system contains certain elements or attributes without needing to call molsysmt.basic.get() directly.

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.contains().

Basic usage#

Let’s show how this function works using the T4 lysozyme dataset (181l.bcif.gz):

import molsysmt as msm

molsys = msm.convert(msm.systems['T4 lysozyme L99A']['181l.bcif.gz'], to_form='molsysmt.MolSys')

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.

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 (box):

msm.contains(molsys, box=True)

True

Tip

All methods defined in the molsysmt.basic module can also be invoked from the main level of the library. Hence, molsysmt.contains() is the same function 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 by setting their value to False:

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

True

Or check whether the system contains a specific minimum count of molecules by passing an integer threshold:

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

True

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

False

The input argument selection can be used to test whether specific atom selections exist in the system:

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

False

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

True

Finally, you can combine a selection with additional attribute conditions:

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

True

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

False