DF - Distribution Function

DF is a object-oriented class, which is supposed to reproduce basic features of a single distribution function (e.g. RDF, bond length distribution, angle distribution, intermolecular potential, angle-bending potential, correction to potential, etc.).

The class contains properties and methods, which are common for every function, however, some methods are redefined when necessary to keep function specificity:

Properties:

Name

- Name of the function

Kind

- Kind of the function: 'RDF' or 'POTENTIAL'

Type

- Type of the function: It can be 'NB', 'B' or 'A', for Non-bonded, pairwise bond and angle bond, respectively.

Npoints

- Number of points in a table defining the function.

Min,Max

- Range of distances(Å)/angles(deg) where the function is defined

Resol

- Resolution of the table

g[:, 0:2]

- The table (numpy array) defining the function. g[:,0]-keeps argument (r,angle), g[:,1]-keeps function's value

AtomTypes

- (NB only) Names of the atom/bead types involved in the interaction represented by the function

BondNumber

- (B/A only) Number of the bond represented by the function.

MolTypeName

- (B/A only) Name of the Molecular type the bond function refers to.

AtomGroups

- (B/A only) List of atom pairs/triplets involved in the bond

Methods:

Plot()

- Plot the function, using matplotlib library

Save()

- Write the function in a tabulated format to a text file.

Smooth()

- Smooth values of g[:,1] using Savitzky-Golay 5 points smoothing procedure

Trim(tolerance)

- Cut function's (g[:,1]) left and right tails which have values smaller then tolerance

Examples:
import DF - import the class
RDFref=MagicTools.ReadRDF('dmpc.400ns.v2.rdf') - read a set of RDFs, which is and object of the class DFset, containing a number of DF-objects.
rdfNB=RDFref.DFs[0] - Access the first function of the set. It is an object of class DF representing a non-bonded RDF.
rdfNB.g - Access the table of the function
rdfNB.Plot() - Plot the function
rdfNB.AtomTypes - See what bead/atom types are involved in the function.
rdfB=RDFref.DFs_B[0] - Access the first pairwise bond related function of the set (they are indexed from 0)
rdfB.MolTypeName - See the name of the molecular type the bond function belongs to.