DF: Distribution Function
DF is a base class representing 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 DF
- FullName
- Completely resolved name of the DF, including type and kind of the DF
- x,y
- numpy arrays storing tabulated values of the argument and the function
- Min,Max
- Range of distance/angle values where the function is defined
- Type
- Type of the function: NB, B (pairwise bond), A (angle-bond)
- Kind
- Kind of the function: RDF, Potential
- Npoints
- Number of points in a table defining the function
- Resol
- Resolution of the table defining the function
- 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:
-
- Write()
- Write the function into a file-stream
- Plot()
- Plot the function
- Save()
- Save the function in a tabulated for to a text file.
- Average()
- Make a new DF which is average of given list of DFs
- ExtendRange()
- Extend range of the DF
- ExtendTail()
- Extend the tail range of NB distribution function in to RcutNB
- CutTail()
- Cut the tail of NB RDF/potential
- IsSimilar()
- Check if the DF is similar to given one, based on its Type, Kind, AtomTypes, MolecularType and Bond number
- ChangeResolution()
- Change resolution of the potential. The new points will have an average value between closest neighbors
- Distance()
- Calculate the distance between this and the given DF
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.
