T_SCM_Methods.py¶
Meow
T_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 Total Structural Comparison Method.
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Organisms.GA.SCM_Scripts.T_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)
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Organisms.GA.SCM_Scripts.T_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)
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Organisms.GA.SCM_Scripts.T_SCM_Methods.
get_CNA_similarity
(cluster_1_CNA, cluster_2_CNA)¶ 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
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Organisms.GA.SCM_Scripts.T_SCM_Methods.
get_tasks
(system, rCuts)¶ This is a generator that allows many total_CNA_profiles to be obtained at many rCut values in parallel
- Parameters
system (Organisms.GA.Cluster) – This is the cluster to obtain the total_CNA_profiles for
rCuts (float) – This is the rCut value to to obtain the total_CNA_profiles at.
- Returns
Yields a tuple of (the cluster, rCut)
- Return type
(Organisms.GA.Cluster, float)
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Organisms.GA.SCM_Scripts.T_SCM_Methods.
get_total_CNA_profile
(input_data, return_list)¶ This method will obtain the Total 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