ElementEmbeddings 0.3.0__tar.gz → 0.4__tar.gz

{ElementEmbeddings-0.3.0/src/ElementEmbeddings.egg-info → ElementEmbeddings-0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ElementEmbeddings
-Version: 0.3.0
+Version: 0.4
 Summary: Element Embeddings
 Author: Anthony O. Onwuli
 Author-email: anthony.onwuli16@imperial.ac.uk

{ElementEmbeddings-0.3.0 → ElementEmbeddings-0.4}/setup.py

@@ -5,7 +5,7 @@ from setuptools import find_namespace_packages, setup
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
 
-VERSION = "0.3.0"
+VERSION = "0.4"
 DESCRIPTION = "Element Embeddings"
 with open(os.path.join(module_dir, "README.md"), encoding="utf-8") as f:
     LONG_DESCRIPTION = f.read()

{ElementEmbeddings-0.3.0 → ElementEmbeddings-0.4/src/ElementEmbeddings.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ElementEmbeddings
-Version: 0.3.0
+Version: 0.4
 Summary: Element Embeddings
 Author: Anthony O. Onwuli
 Author-email: anthony.onwuli16@imperial.ac.uk

{ElementEmbeddings-0.3.0 → ElementEmbeddings-0.4}/src/ElementEmbeddings.egg-info/SOURCES.txt

@@ -23,6 +23,7 @@ src/elementembeddings/data/element_representations/matscholar-embedding.json
 src/elementembeddings/data/element_representations/megnet16.json
 src/elementembeddings/data/element_representations/mod_petti.json
 src/elementembeddings/data/element_representations/oliynyk.csv
+src/elementembeddings/data/element_representations/oliynyk_preprocessed.csv
 src/elementembeddings/data/element_representations/oliynyk_sc.json
 src/elementembeddings/data/element_representations/random_200.csv
 src/elementembeddings/data/element_representations/random_200_new.csv

{ElementEmbeddings-0.3.0 → ElementEmbeddings-0.4}/src/elementembeddings/composition.py

@@ -354,6 +354,7 @@ def _composition_distance(
 
 def composition_featuriser(
     data: Union[pd.DataFrame, pd.Series, CompositionalEmbedding, list],
+    formula_column: str = "formula",
     embedding: Union[Embedding, str] = "magpie",
     stats: Union[str, list] = "mean",
     inplace: bool = False,
@@ -385,13 +386,14 @@ def composition_featuriser(
     if isinstance(data, pd.DataFrame):
         if not inplace:
             data = data.copy()
-        if "formula" not in data.columns:
+        if formula_column not in data.columns:
             raise ValueError(
-                "The data must contain a column named 'formula' to featurise."
+                f"The data must contain a column named {formula_column}  to featurise."
             )
         print("Featurising compositions...")
         comps = [
-            CompositionalEmbedding(x, embedding) for x in tqdm(data["formula"].tolist())
+            CompositionalEmbedding(x, embedding)
+            for x in tqdm(data[formula_column].tolist())
         ]
         print("Computing feature vectors...")
         fvs = [x.feature_vector(stats) for x in tqdm(comps)]

{ElementEmbeddings-0.3.0 → ElementEmbeddings-0.4}/src/elementembeddings/core.py

@@ -64,11 +64,6 @@ class Embedding:
         self.embedding_name = embedding_name
         self.feature_labels = feature_labels
         if not self._is_standardised():
-            warnings.warn(
-                "Embedding is not standardised. "
-                "It is recommended that you standardise your embeddings before use. "
-                "Use the standardise() method to standardise your embeddings."
-            )
             self.is_standardised = False
         else:
             self.is_standardised = True
@@ -159,7 +154,7 @@ class Embedding:
             "matscholar": "matscholar-embedding.json",
             "megnet16": "megnet16.json",
             "mod_petti": "mod_petti.json",
-            "oliynyk": "oliynyk.csv",
+            "oliynyk": "oliynyk_preprocessed.csv",
             "oliynyk_sc": "oliynyk_sc.json",
             "random_200": "random_200_new.csv",
             "skipatom": "skipatom_20201009_induced.csv",

ElementEmbeddings-0.4/src/elementembeddings/data/element_representations/oliynyk_preprocessed.csv

@@ -0,0 +1,86 @@
+element,Atomic_Number,Atomic_Weight,Period,group,families,Metal,Nonmetal,Metalliod,Mendeleev_Number,l_quantum_number,Atomic_Radius,Miracle_Radius_[pm],Covalent_Radius,Zunger_radii_sum,ionic_radius,crystal_radius,Pauling_Electronegativity,MB_electonegativity,Gordy_electonegativity,Mulliken_EN,Allred-Rockow_electronegativity,metallic_valence,number_of_valence_electrons,gilmor_number_of_valence_electron,valence_s,valence_p,valence_d,valence_f,Number_of_unfilled_s_valence_electrons,Number_of_unfilled_p_valence_electrons,Number_of_unfilled_d_valence_electrons,Number_of_unfilled_f_valence_electrons,outer_shell_electrons,1st_ionization_potential_(kJ/mol),polarizability(A^3),Melting_point_(K),Boiling_Point_(K),Density_(g/mL),specific_heat_(J/g_K)_,heat_of_fusion_(kJ/mol)_,heat_of_vaporization_(kJ/mol)_,thermal_conductivity_(W/(m_K))_,heat_atomization(kJ/mol),Cohesive_energy
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+He,2.0,4.002602,1.0,18.0,9.0,0.0,1.0,0.0,98.0,0.0,0.31,98.6,0.32,0.0,0.31,0.0,0.0,0.0,12.0486,0.0,4.16,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.0,6.0,10.0,14.0,0.0,2372.0,0.198,0.95,4.25,0.000179,5.193,0.02,0.0845,0.152,0.0,0.0
+Li,3.0,6.941,2.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,1.67,152.0,1.34,1.61,1.45,0.9,0.98,0.9,3.2223,3.01,0.912,1.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,6.0,10.0,14.0,1.0,520.0,24.3,453.65,1615.15,0.543,3.6,3.0,145.92,84.7,161.0,1.63
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+B,5.0,10.811,2.0,13.0,6.0,0.0,0.0,1.0,72.0,1.0,0.87,88.0,0.82,0.795,0.85,0.25,2.04,1.9,4.5951,4.29,2.051,3.0,3.0,3.0,2.0,1.0,0.0,0.0,0.0,5.0,10.0,14.0,3.0,801.0,3.0,2352.15,4275.0,2.34,1.02,50.2,489.7,27.0,573.0,5.81
+C,6.0,12.011,2.0,14.0,7.0,0.0,1.0,0.0,77.0,1.0,0.67,77.0,0.77,0.64,0.7,0.29,2.55,2.37,5.6246,6.27,2.544,4.0,4.0,4.0,2.0,2.0,0.0,0.0,0.0,4.0,10.0,14.0,4.0,1086.0,1.8,3640.15,5100.15,2.25,0.71,105.0,355.8,129.0,717.0,7.37
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