Compare#

Comparing molecular systems across selected attributes.

The function molsysmt.basic.compare() allows to compare two molecular systems, or specific parts of them, based on selected attributes. The function can return a single boolean or a detailed per-attribute report.

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.compare().

Let’s explore how to compare molecular systems using the following three systems:

import molsysmt as msm

molsys_A = msm.convert('pdb_id:181L', to_form='openmm.Modeller')
molsys_B = msm.convert(molsys_A, to_form='molsysmt.MolSys')
molsys_C = msm.extract(molsys_B, selection='molecule_type=="protein"')

The systems \(A\) and \(B\) are equivalent in content—they only differ in form. System \(C\) is a subset of the same molecular system, using the same form as \(B\).

Let’s make some comparisons between these systems to illustrate how molsysmt.basic.compare() works:

msm.compare(molsys_A, molsys_B)

False

msm.compare(molsys_B, molsys_C)

False

Tip

All methods defined in the molsysmt.basic module can also be invoked from the top level of the library. Therefore, molsysmt.compare() is equivalent to molsysmt.basic.compare().

By default, only the elements are compared. Other attributes as coordinates, box or n_groups can be included explicitly in the comparison:

msm.compare(molsys_A, molsys_B, coordinates=True, box=True, n_groups=True)

True

msm.compare(molsys_B, molsys_C, coordinates=True, box=True, n_groups=True)

False

A detailed report showing the result for each attribute can be obtained by setting the output_type="dictionary" argument:

msm.compare(molsys_B, molsys_C, coordinates=True, box=True, n_groups=True, output_type='dictionary')

{'n_groups': False, 'box': True, 'coordinates': False}

You can also test for the negation of a condition by setting the attribute value to False:

msm.compare(molsys_B, molsys_C, coordinates=False, box=True, n_groups=False, output_type='dictionary')

{'n_groups': True, 'box': True, 'coordinates': True}

Remember, you can restrict the comparison to specific elements or structures using the arguments selection, structure_indices, selection_2 and structure_indices_2:

msm.compare(molsys_B, molsys_C, selection='molecule_type=="protein"', selection_2='all',
            coordinates=True, box=True, n_groups=True, output_type='dictionary')

{'n_groups': True, 'box': True, 'coordinates': True}