Has attribute#

Checking whether a molecular system has a specific attribute.

Not all molecular system forms include the same attributes, and not all molecular systems have values for every available attribute. For example, an openmm.Topology system supports a periodic box, but a particular molecular system might not define one. In order to check whether or not a molecular has a specific attribute value, MolSysMT provides a specific function in the basic module: molsysmt.basic.has_attribute().

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.has_attribute().

Let’s illustrate the use of molsysmt.basic.has_attribute() with the following examples.

import molsysmt as msm

molsys = msm.systems['pentalanine']['pentalanine.inpcrd']

msm.has_attribute(molsys, attribute='box')

True

Tip

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

The function confirms that two conditions are met:

the “file:inpcrd” molecular system form has the attribute ‘box’
the molecular system has a value different from None for the attribute ‘box’.

Indeed, we can retrieve the corresponding value:

msm.get(molsys, box=True)

Magnitude	[[[4.29511093 0.0 0.0] [-1.4317035278131303 4.049469460244502 0.0] [-1.4317035278131303 -2.0247344850669022 3.506943565903758]]]
Units	nanometer

A molecular system may support a given attribute, but the value may still be None. In this case the function molsysmt.basic.has_attribute() returns False. Let’s see this case with the following example:

molsys = msm.convert(msm.systems['pentalanine']['pentalanine.prmtop'], to_form='openmm.Topology')

msm.set(molsys, box=None)

msm.has_attribute(molsys, attribute='box')

False

We can check whether a specific form (regardless of system instance) supports an attribute using molsysmt.form.has_attribute().

msm.form.has_attribute('file:prmtop', attribute='box')

True

Finally, let’s see how molsysmt.basic.has_attribute() behaves when the requested attribute is not supported by the molecular system’s form.

molecular_system = msm.systems['pentalanine']['pentalanine.prmtop']

msm.has_attribute(molsys, attribute='coordinates')

False