Is composed of#

Checking whether a molecular system is composed of specific elements.

The function molsysmt.basic.is_composed_of() checks whether a molecular system is made up exclusively of certain types or number of elements.

Hint

Visit the section Elements for a detailed overview of element hierarchy 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_composed_of().

Basic usage#

Let’s show how this function works using a PDB structure (181L):

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

We know in advance that the system includes multiple molecule types: proteins, ions, waters, and small molecules. Therefore, although it contains proteins, it is not composed solely of proteins:

msm.is_composed_of(molsys, proteins=True)

False

Tip

All methods defined in the molsysmt.basic module can also be invoked from the main level of the library. Hence, molsysmt.is_composed_of() is the same function as molsysmt.basic.is_composed_of().

Let’s see now if the molecular system is indeed composed of proteins, waters, small molecules and ions:

msm.is_composed_of(molsys, proteins=True, waters=True, small_molecules=True, ions=True)

True

You can also specify the exact number of each element type using keyword arguments. For example:

msm.is_composed_of(molsys, proteins=1, waters=True, small_molecules=2, ions=True)

True

msm.is_composed_of(molsys, proteins=1, small_molecules=1)

False

Other element types, such as atoms, groups, components or molecules, can also be checked using their respective attribute names:

msm.is_composed_of(molsys, n_atoms=1441, n_groups=302)

True

msm.is_composed_of(molsys, n_components=3, n_molecules=3)

False

Finally, you can apply this function to a selection of elements using the selection argument:

msm.is_composed_of(molsys, selection='molecule_type in ["ion", "water", "small molecule", "protein"]')

True

msm.is_composed_of(molsys, selection='molecule_type not in ["ion", "water", "small molecule"]', proteins=1)

True