Merge pull request grimme-lab#100 from lmseidler/main

Element composition dict with str and mixed keys

CHANGELOG.md

@@ -5,6 +5,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Changed
+- to set the elemental composition it is now possible to use dicts with not only int but also the element symbols (str)
+- dict keys for elemental compositions will now always be checked for validity
 
 ## [0.5.0] - 2024-12-16
 ### Changed

README.md

@@ -133,6 +133,8 @@ def main():
     config.generate.max_num_atoms = 15
     config.generate.element_composition = "Ce:1-1"
     # alternatively as a dictionary: config.generate.element_composition = {39:(1,1)}
+    # or: config.generate.element_composition = {"Ce":(1,1)"}
+    # or as mixed-key dict, e.g. for Ce and O: {"Ce":(1,1), 7:(2,2)}
     config.generate.forbidden_elements = "21-30,39-48,57-80"
     # alternatively as a list: config.generate.forbidden_elements = [20,21,22,23] # 24,25,26...
 

src/mindlessgen/prog/config.py

@@ -12,6 +12,8 @@
 import numpy as np
 import toml
 
+from mindlessgen.molecules.molecule import PSE_SYMBOLS
+
 from ..molecules import PSE_NUMBERS
 
 
@@ -290,18 +292,19 @@ def element_composition(self):
 
     @element_composition.setter
     def element_composition(
-        self, composition: None | str | dict[int, tuple[int | None, int | None]]
+        self, composition: None | str | dict[int | str, tuple[int | None, int | None]]
     ) -> None:
         """
-        If composition_str: str, it should be a string with the format:
+        If composition: str:
             Parses the element_composition string and stores the parsed data
             in the _element_composition dictionary.
             Format: "C:2-10, H:10-20, O:1-5, N:1-*"
-        If composition_str: dict, it should be a dictionary with integer keys and tuple values. Will be stored as is.
+        If composition: dict:
+            Should be a dictionary with integer/string keys and tuple values. Will be stored as is.
 
         Arguments:
             composition_str (str): String with the element composition
-            composition_str (dict): Dictionary with integer keys and tuple values
+            composition_str (dict): Dictionary with integer/str keys and tuple values
         Raises:
             TypeError: If composition_str is not a string or a dictionary
             AttributeError: If the element is not found in the periodic table
@@ -312,25 +315,50 @@ def element_composition(
 
         if not composition:
             return
+
+        # Will return if composition dict does not contain either int or str keys and tuple[int | None, int | None] values
+        # Will also return if dict is valid after setting property
         if isinstance(composition, dict):
+            tmp = {}
+
+            # Check validity and also convert str keys into atomic numbers
             for key, value in composition.items():
                 if (
-                    not isinstance(key, int)
+                    not (isinstance(key, int) or isinstance(key, str))
                     or not isinstance(value, tuple)
                     or len(value) != 2
                     or not all(isinstance(val, int) or val is None for val in value)
                 ):
                     raise TypeError(
-                        "Element composition dictionary should be a dictionary with integer keys and tuple values (int, int)."
+                        "Element composition dictionary should be a dictionary with either integer or string keys and tuple values (int, int)."
                     )
-            self._element_composition = composition
+
+                # Convert str keys
+                if isinstance(key, str):
+                    element_number = PSE_NUMBERS.get(key.lower(), None)
+                    if element_number is None:
+                        raise KeyError(
+                            f"Element {key} not found in the periodic table."
+                        )
+                    tmp[element_number - 1] = composition[key]
+                # Check int keys
+                else:
+                    if key + 1 in PSE_SYMBOLS:
+                        tmp[key] = composition[key]
+                    else:
+                        raise KeyError(
+                            f"Element with atomic number {key+1} (provided key: {key}) not found in the periodic table."
+                        )
+            self._element_composition = tmp
             return
+
         if not isinstance(composition, str):
             raise TypeError(
                 "Element composition should be a string (will be parsed) or "
-                + "a dictionary with integer keys and tuple values."
+                + "a dictionary with integer/string keys and tuple values."
             )
 
+        # Parsing composition string
         element_dict: dict[int, tuple[int | None, int | None]] = {}
         elements = composition.split(",")
         # remove leading and trailing whitespaces
@@ -537,9 +565,11 @@ def check_config(self, verbosity: int = 1) -> None:
             if (
                 np.sum(
                     [
-                        self.element_composition.get(i, (0, 0))[0]
-                        if self.element_composition.get(i, (0, 0))[0] is not None
-                        else 0
+                        (
+                            self.element_composition.get(i, (0, 0))[0]
+                            if self.element_composition.get(i, (0, 0))[0] is not None
+                            else 0
+                        )
                         for i in self.element_composition
                     ]
                 )

test/test_generate/test_generate_molecule.py

@@ -41,9 +41,9 @@ def test_generate_atom_list(min_atoms, max_atoms, default_generate_config):
     assert np.sum(atom_list) <= max_atoms
 
 
-# Test the element composition property of the GenerateConfig class
-def test_generate_config_element_composition(default_generate_config):
-    """Test the element composition property of the GenerateConfig class."""
+# Test the element composition property of the GenerateConfig class with a composition string
+def test_generate_config_element_composition_string(default_generate_config):
+    """Test the element composition property of the GenerateConfig class with a composition string."""
     default_generate_config.min_num_atoms = 10
     default_generate_config.max_num_atoms = 15
     default_generate_config.element_composition = "C:2-2, N:3-3, O:1-1"
@@ -55,6 +55,60 @@ def test_generate_config_element_composition(default_generate_config):
     assert atom_list[7] == 1
 
 
+# Test the element composition property of the GenerateConfig class with an int key composition dict
+def test_generate_config_element_composition_dict_int(default_generate_config):
+    """Test the element composition property of the GenerateConfig class with an int key composition dict."""
+
+    # Pure int keys
+    default_generate_config.min_num_atoms = 10
+    default_generate_config.max_num_atoms = 15
+    default_generate_config.element_composition = {
+        5: (2, 2),
+        6: (3, 3),
+        7: (1, 1),
+    }  # NOTE: mind 0-based indexing for atomic numbers
+    atom_list = generate_atom_list(default_generate_config, verbosity=1)
+
+    # Check that the atom list contains the correct number of atoms for each element
+    assert atom_list[5] == 2
+    assert atom_list[6] == 3
+    assert atom_list[7] == 1
+
+
+# Test the element composition property of the GenerateConfig class with an int key composition dict
+def test_generate_config_element_composition_dict_string(default_generate_config):
+    """Test the element composition property of the GenerateConfig class with a str key composition dict."""
+
+    default_generate_config.min_num_atoms = 10
+    default_generate_config.max_num_atoms = 15
+    default_generate_config.element_composition = {
+        "C": (2, 2),
+        "N": (3, 3),
+        "O": (1, 1),
+    }
+    atom_list = generate_atom_list(default_generate_config, verbosity=1)
+
+    # Check that the atom list contains the correct number of atoms for each element
+    assert atom_list[5] == 2
+    assert atom_list[6] == 3
+    assert atom_list[7] == 1
+
+
+# Test the element composition property of the GenerateConfig class with an int key composition dict
+def test_generate_config_element_composition_dict_mixed(default_generate_config):
+    """Test the element composition property of the GenerateConfig class with a str key composition dict."""
+
+    default_generate_config.min_num_atoms = 10
+    default_generate_config.max_num_atoms = 15
+    default_generate_config.element_composition = {5: (2, 2), "N": (3, 3), "O": (1, 1)}
+    atom_list = generate_atom_list(default_generate_config, verbosity=1)
+
+    # Check that the atom list contains the correct number of atoms for each element
+    assert atom_list[5] == 2
+    assert atom_list[6] == 3
+    assert atom_list[7] == 1
+
+
 # Test the forbidden_elements property of the GenerateConfig class
 def test_generate_config_forbidden_elements(default_generate_config):
     """Test the forbidden_elements property of the GenerateConfig class."""