Apply suggestions from code review

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Co-authored-by: James <144615809+JamesOBrien2@users.noreply.github.com>

Author: JamesOBrien2

docs/source/xyzgraph_adapter.rst

@@ -2,7 +2,7 @@ xyzgraph Adapter
 ================
 
 ``spyrmsd`` can use `xyzgraph <https://github.com/aligfellow/xyzgraph>`_ as an
-optional adjacency builder for molecular graph construction.
+optional adjacency matrix builder for molecular graph construction.
 
 Install the optional dependency with:
 
@@ -36,5 +36,5 @@ Example
    )
 
 .. note::
-   The default graph builder remains the built-in ``simple`` path. The
-   ``xyzgraph`` adapter is opt-in.
+   The default graph builder remains the built-in ``simple`` one,
+   based on distance and VdW radii. The ``xyzgraph`` adapter is opt-in.

spyrmsd/__main__.py

@@ -32,8 +32,8 @@ def build_parser() -> ap.ArgumentParser:
     parser.add_argument(
         "--graph-builder",
         dest="graph_builder",
-        choices=("xyzgraph",),
-        default=None,
+        choices=("simple","xyzgraph"),
+        default="simple",
         help="Use optional adjacency builder (xyzgraph: Molecular Graph Construction from Cartesian Coordinates)",
     )
     parser.add_argument(
@@ -53,7 +53,7 @@ def build_parser() -> ap.ArgumentParser:
     return parser
 
 
-def main(argv: Optional[Sequence[str]] = None) -> int:
+def main() -> int:
     parser = build_parser()
     args = parser.parse_args(argv)
     graph._set_graph_builder("simple")
@@ -117,8 +117,8 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
         strip=not args.hydrogens,
     )
 
-    for value in rmsd_list:
-        print(f"{value:.5f}")
+    for rmsd in rmsd_list:
+        print(f"{rmsd:.5f}")
 
     return 0
 

spyrmsd/adapters/simple.py

@@ -1,5 +1,5 @@
 """
-Simple built-in adjacency builder.
+Simple built-in adjacency matrix builder.
 """
 
 import numpy as np
@@ -11,7 +11,7 @@ def adjacency_matrix_from_atomic_coordinates(
     aprops: np.ndarray, coordinates: np.ndarray
 ) -> np.ndarray:
     """
-    Compute an adjacency matrix with the built-in distance heuristic.
+    Compute an adjacency matrix with a distance heuristic.
     """
 
     n = len(aprops)

spyrmsd/constants.py

@@ -15,126 +15,22 @@
 
 _anum_to_symbol_data = (
     "",
-    "H",
-    "He",
-    "Li",
-    "Be",
-    "B",
-    "C",
-    "N",
-    "O",
-    "F",
-    "Ne",
-    "Na",
-    "Mg",
-    "Al",
-    "Si",
-    "P",
-    "S",
-    "Cl",
-    "Ar",
-    "K",
-    "Ca",
-    "Sc",
-    "Ti",
-    "V",
-    "Cr",
-    "Mn",
-    "Fe",
-    "Co",
-    "Ni",
-    "Cu",
-    "Zn",
-    "Ga",
-    "Ge",
-    "As",
-    "Se",
-    "Br",
-    "Kr",
-    "Rb",
-    "Sr",
-    "Y",
-    "Zr",
-    "Nb",
-    "Mo",
-    "Tc",
-    "Ru",
-    "Rh",
-    "Pd",
-    "Ag",
-    "Cd",
-    "In",
-    "Sn",
-    "Sb",
-    "Te",
-    "I",
-    "Xe",
-    "Cs",
-    "Ba",
-    "La",
-    "Ce",
-    "Pr",
-    "Nd",
-    "Pm",
-    "Sm",
-    "Eu",
-    "Gd",
-    "Tb",
-    "Dy",
-    "Ho",
-    "Er",
-    "Tm",
-    "Yb",
-    "Lu",
-    "Hf",
-    "Ta",
-    "W",
-    "Re",
-    "Os",
-    "Ir",
-    "Pt",
-    "Au",
-    "Hg",
-    "Tl",
-    "Pb",
-    "Bi",
-    "Po",
-    "At",
-    "Rn",
-    "Fr",
-    "Ra",
-    "Ac",
-    "Th",
-    "Pa",
-    "U",
-    "Np",
-    "Pu",
-    "Am",
-    "Cm",
-    "Bk",
-    "Cf",
-    "Es",
-    "Fm",
-    "Md",
-    "No",
-    "Lr",
-    "Rf",
-    "Db",
-    "Sg",
-    "Bh",
-    "Hs",
-    "Mt",
-    "Ds",
-    "Rg",
-    "Cn",
-    "Nh",
-    "Fl",
-    "Mc",
-    "Lv",
-    "Ts",
-    "Og",
+    "H", "He",
+    "Li", "Be", "B", "C", "N", "O", "F", "Ne",
+    "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar",
+    "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
+    "Ga", "Ge", "As", "Se", "Br", "Kr",
+    "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd",
+    "In", "Sn", "Sb", "Te", "I", "Xe",
+    "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy",
+    "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt",
+    "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn",
+    "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf",
+    "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds",
+    "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og",
 )
 
+
 anum_to_symbol: Dict = {
     anum: symbol for anum, symbol in enumerate(_anum_to_symbol_data) if anum > 0
 }

spyrmsd/graph.py

@@ -196,7 +196,7 @@ def _validate_graph_builder(graph_builder):
     return graph_builder
 
 
-def _set_graph_builder(graph_builder):
+def set_graph_builder(graph_builder):
     """
     Set graph builder used for adjacency construction.
     """
@@ -210,7 +210,7 @@ def _set_graph_builder(graph_builder):
     _current_graph_builder = graph_builder
 
 
-def _get_graph_builder():
+def get_graph_builder():
     """
     Get the current graph builder.
     """