Finalize plots for paper

Fixes #13
RECETOX · Nov 13, 2023 · c978dad · c978dad
1 parent adf8208
commit c978dad
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Showing 8 changed files with 756 additions and 351 deletions.
diff --git a/analysis/Python_scripts/chemical_composition_boxplot.ipynb b/analysis/Python_scripts/chemical_composition_boxplot.ipynb
diff --git a/analysis/Python_scripts/chemical_composition_boxplot.png b/analysis/Python_scripts/chemical_composition_boxplot.png
diff --git a/analysis/Python_scripts/chemical_composition_boxplot2.png b/analysis/Python_scripts/chemical_composition_boxplot2.png
diff --git a/analysis/Python_scripts/chemical_composition_boxplot2_N.png b/analysis/Python_scripts/chemical_composition_boxplot2_N.png
diff --git a/analysis/Python_scripts/chemical_composition_boxplot_N.png b/analysis/Python_scripts/chemical_composition_boxplot_N.png
diff --git a/analysis/Python_scripts/scatter_plot.png b/analysis/Python_scripts/scatter_plot.png
diff --git a/analysis/Python_scripts/scatterplot.ipynb b/analysis/Python_scripts/scatterplot.ipynb
diff --git a/analysis/Python_scripts/utils.py b/analysis/Python_scripts/utils.py
@@ -26,7 +26,7 @@ def has_atom(mol, atom):
 def has_organic_atoms(mol):
     # Check if the molecule contains any halogen atoms
     for atom in mol.GetAtoms():
-        if atom.GetSymbol() in ['C', 'O', 'N', 'H']:
+        if atom.GetSymbol() in ['C', 'O', 'H']:
             return True
 
     return False
@@ -47,7 +47,7 @@ def append_classes(df, left_on):
         "S": [has_atom(m, 'S') for m in molecules],
         "P": [has_atom(m, 'P') for m in molecules],
         "Si": [has_atom(m, 'Si') for m in molecules],
-        "C,O,N,H": [has_organic_atoms(m) for m in molecules],
+        "C,O,N,H": [has_organic_atoms(m) or has_atom(m, 'N') for m in molecules],
         "N": [has_atom(m, 'N') for m in molecules],
     })
     merged_df = pd.merge(df, class_names, left_on=left_on, right_on='molname')