Merge branch 'main' of https://github.com/lamalab-org/xtal2txt into a…

…nalysis

pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
     "transformers>=4.37.2",
     "pyshtools==4.10",
     "pyxtal==0.5.7",
+    "keras==2.15.0"
 ]
 requires-python = ">=3.9,<3.11"
 readme = "README.md"

src/xtal2txt/core.py

@@ -571,6 +571,34 @@ def cif_string_matcher_sym(self, input: str, ltol = 0.2, stol = 0.5, angle_tol =
         return StructureMatcher(ltol, stol, angle_tol, primitive_cell, scale, allow_subset, attempt_supercell).fit(output_struct, original_struct)
 
 
+    def get_atoms_params_rep(self, lattice_params: bool = False, decimal_places: int = 2) -> str:
+        """
+        Generating a string with the elements of composition inside the crystal lattice with the option to
+        get the lattice parameters as angles (int) and lengths (float) in a string with a space
+        between them
+
+        Params:
+            lattice_params: boolean, optional 
+                To specify whether use lattice parameters in generating crystal structure.
+                Defaults to False
+            decimal_places : int, optional, 
+                to specify the rounding digit for float numbers.
+                Defaults to 2
+        
+        Returns:
+            output: str
+                An oneline string.
+        """
+
+        output = [site.specie.element.symbol for site in self.structure.sites]
+        if lattice_params:
+            params = self.get_lattice_parameters(decimal_places=decimal_places)
+            params[3:] = [str(int(float(i))) for i in params[3:]]
+            output.extend(params)
+
+        return " ".join(output)
+
+
     def get_all_text_reps(self, decimal_places: int = 2):
         """
         Returns all the Text representations of the crystal structure in a dictionary.

tests/test_get_atom_params.py

@@ -0,0 +1,16 @@
+from xtal2txt.core import TextRep
+import os
+
+THIS_DIR = os.path.dirname(os.path.abspath(__file__))
+
+srtio3_p1 = TextRep.from_input(os.path.join(THIS_DIR, "data", "SrTiO3_p1.cif"))
+tiCrSe_p1 = TextRep.from_input(os.path.join(THIS_DIR, "data", "TlCr5Se8_p1.cif"))
+
+
+def test_get_atom_params() -> None: 
+    expected_wo_params = "Sr Ti O O O"
+    expected_w_params = "Sr Ti O O O 3.91 3.91 3.91 90 90 90"
+    expected_tiCrSe_p1 = "Tl Tl Cr Cr Cr Cr Cr Cr Cr Cr Cr Cr Se Se Se Se Se Se Se Se Se Se Se Se Se Se Se Se"
+    assert srtio3_p1.get_atoms_params_rep() == expected_wo_params
+    assert tiCrSe_p1.get_atoms_params_rep() == expected_tiCrSe_p1
+    assert srtio3_p1.get_atoms_params_rep(lattice_params=True) == expected_w_params