Use symbols on --print (#121)

* Use symbols on --print, instead of integers

.github/workflows/test.yml

@@ -19,6 +19,7 @@ jobs:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
+      - run: sudo apt-get install libopenblas-dev gcc
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:

requirements.txt

@@ -3,12 +3,10 @@ matplotlib
 monkeytype
 mypy
 numpy
-numpy
 pre-commit
 pylint
 pytest
 pytest-cov
 qmllib
 scipy
-scipy
 twine

rmsd/calculate_rmsd.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+
 __doc__ = """
 Calculate Root-mean-square deviation (RMSD) between structure A and B, in XYZ
 or PDB format, using transformation and rotation.
@@ -1567,7 +1568,7 @@ def _parse_pdb_atom_line(line: str) -> Optional[str]:
     return None
 
 
-def _parse_pdb_coord_line(line: str):
+def _parse_pdb_coord_line(line: str) -> Optional[ndarray]:
     """
     Try my best to coordinates from a PDB ATOM or HETATOM line
 
@@ -2227,8 +2228,9 @@ def main(args: Optional[List[str]] = None) -> str:
         if settings.print_only_rmsd_atoms or not use_view:
             q_coord_sub = np.dot(q_coord_sub, U)
             q_coord_sub += p_cent_sub
+            _atoms = np.asarray([str_atom(atom) for atom in q_atoms_sub])
             return set_coordinates(
-                q_atoms_sub,
+                _atoms,
                 q_coord_sub,
                 title=f"Rotated '{settings.structure_b}' to match '{settings.structure_a}', with a RMSD of {result_rmsd:.8f}",
             )
@@ -2244,8 +2246,9 @@ def main(args: Optional[List[str]] = None) -> str:
 
         q_coord = np.dot(q_coord, U)
         q_coord += p_cent_sub
+        _atoms = np.asarray([str_atom(atom) for atom in q_atoms])
         return set_coordinates(
-            q_atoms,
+            _atoms,
             q_coord,
             title=f"Rotated {settings.structure_b} to match {settings.structure_a}, with RMSD of {result_rmsd:.8f}",
         )

tests/test_reorder.py

@@ -1,6 +1,7 @@
 import copy
 
 import numpy as np
+from numpy import ndarray
 
 import rmsd as rmsdlib
 
@@ -9,9 +10,9 @@ def test_reorder_distance() -> None:
 
     N = 5
     atoms = np.array(["H"] * N)
-    p_coord = np.arange(N * 3)
+    p_coord: ndarray = np.arange(N * 3)
     p_coord = p_coord.reshape((5, 3))
-    q_coord = copy.deepcopy(p_coord)
+    q_coord = np.array(p_coord, copy=True)
 
     np.random.seed(6)
     np.random.shuffle(q_coord)
@@ -24,9 +25,9 @@ def test_reorder_distance() -> None:
 def test_reorder_brute() -> None:
     N = 5
     atoms = np.array(["H"] * N)
-    p_coord = np.arange(N * 3)
+    p_coord: ndarray = np.arange(N * 3)
     p_coord = p_coord.reshape((N, 3))
-    q_coord = copy.deepcopy(p_coord)
+    q_coord = np.array(p_coord, copy=True)
 
     np.random.seed(6)
     np.random.shuffle(q_coord)
@@ -41,7 +42,7 @@ def test_reorder_brute_ch() -> None:
     p_atoms_str = ["C"] * 3 + ["H"] * 3
     p_atoms_int = [rmsdlib.int_atom(atom) for atom in p_atoms_str]
     p_atoms = np.array(p_atoms_int)
-    p_coord = np.arange(N * 3)
+    p_coord: ndarray = np.arange(N * 3)
     p_coord = p_coord.reshape((N, 3))
 
     # random index
@@ -65,7 +66,7 @@ def test_reorder_hungarian() -> None:
 
     N = 5
     atoms = np.array(["H"] * N)
-    p_coord = np.arange(N * 3)
+    p_coord: ndarray = np.arange(N * 3)
     p_coord = p_coord.reshape((5, 3))
     q_coord = copy.deepcopy(p_coord)