A_SCM_Methods.py

Meow

A_SCM_Methods.py, Geoffrey Weal, 20/11/2018

This script is designed to include all the methods for performing structural recognition task in terms of the Atom-by-Atom Structural Comparison Method.

Organisms.GA.SCM_Scripts.A_SCM_Methods.get_CNA_profile(input_data)

This def will return the CNA profile of a cluster at a range of given values of rCut.

Parameters

  • cluster (Either Cluster or ase.Atoms) – This is the cluster to obtain the CNA profile of.

  • rCuts (float) – The range of values of rCuts to obtain the CNA profile of.

Returns

This resutrn the name of the cluster, and the atomic_CNA_profiles.

Return type

(int, Counter)

Organisms.GA.SCM_Scripts.A_SCM_Methods.get_CNA_similarities(input_data)

Get the full similarity profile of the two clusters.

input_data contains two parameters

Parameters

  • name_1 (int) – Name of the first cluster

  • name_2 (int) – Name of the second cluster

  • cluster_1_CNA_profile ([asap3.analysis.localstructure.FullCNA ,..]) – the full CNA profile of cluster 1 for all values of rCut.

  • cluster_2_CNA_profile ([asap3.analysis.localstructure.FullCNA ,..]) – the full CNA profile of cluster 2 for all values of rCut.

Returns

returns the name of the two clusters, and the similarity profile.

Return type

(int, int, list of float)

Organisms.GA.SCM_Scripts.A_SCM_Methods.get_CNA_similarity(cluster_1_CNA, cluster_2_CNA, total_no_of_atoms)

Get the similarity for the two clusters at a particular value of rCut.

Parameters

  • cluster_1_CNA (asap3.analysis.localstructure.FullCNA) – the CNA profile of cluster 1 at rCut

  • cluster_2_CNA (asap3.analysis.localstructure.FullCNA) – the CNA profile of cluster 2 at rCut

  • total_no_of_atoms (int) – The total number of atoms in the cluster

Organisms.GA.SCM_Scripts.A_SCM_Methods.get_atomic_CNA_profile(input_data)

This method will obtain the Atomic CNA profile

Parameters

input_data ((Organisms.GA.Cluster, float)) – Contains the cluster to perform the CNA on at the rCut value rCut.

Returns

The atomic CNA profile.

Return type

Counter

Organisms.GA.SCM_Scripts.A_SCM_Methods.get_tasks(system, rCuts)

This is a generator that allows many atomic_CNA_profiles to be obtained at many rCut values in parallel

Parameters

  • system (Organisms.GA.Cluster) – This is the cluster to obtain the atomic_CNA_profiles for

  • rCuts (float) – This is the rCut value to to obtain the atomic_CNA_profiles at.

Returns

Yields a tuple of (the cluster, rCut)

Return type

(Organisms.GA.Cluster, float)