Get attributes#

Retrieving the set of available attributes in a molecular system.

Molecular systems have attributes such as the number of atoms, the group ids, the box shape or the water model. The set of attribute values of a system and its elements defines a molecular system, making it different from others. Given that a system can take different forms, the attributes are also limited by each form. Given a molecular system, the function molsysmt.basic.get_attributes() returns a dictionary indicating whether each attribute is present with a non-None value.

Hint

Visit the section Items and Forms or Attributes if you are not familiar with the concepts of “form” or “attribute” 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.get_attributes().

Basic usage#

Let’s show how this function works using an OpenMM Topology converted from PDB 181L:

import molsysmt as msm

molecular_system = msm.convert('181L', to_form='openmm.Topology')
dict_attributes = msm.get_attributes(molecular_system, output_type='dictionary')

Tip

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

Let’s inspect the resultant dictionary:

dict_attributes['box_volume']

True

dict_attributes['forcefield']

False

As mentioned earlier, not all molecular systems have all attributes with non-None values.. If this is the case, the function molsysmt.basic.get_attributes() returns False for these attributes -although they can be contained in the corresponding molecular system’s form-:

msm.set(molecular_system, box=None)

dict_attributes = msm.get_attributes(molecular_system, output_type='dictionary')

dict_attributes['box_volume']

False

Note

Have a look to the function molsysmt.form.has_attribute() if the presence of a specific attribute needs to be checked in a molecular system. However, if instead of the attributes of a molecular system, the attributes of a molecular system’s form need to be checked make use of the functions molsysmt.form.get_attributes() and molsysmt.form.has_attribute().