From d8be3a273cdbb5943555d67515f529a97a793827 Mon Sep 17 00:00:00 2001
From: Patrick Kunzmann <padix.key@gmail.com>
Date: Tue, 15 Oct 2024 17:50:29 +0200
Subject: [PATCH] fixup! Add 3Di substitution matrix

---
 src/biotite/sequence/align/matrix.py | 44 ++++++++++++++++------------
 tests/sequence/align/test_matrix.py  | 15 ++++++++++
 2 files changed, 41 insertions(+), 18 deletions(-)

diff --git a/src/biotite/sequence/align/matrix.py b/src/biotite/sequence/align/matrix.py
index bfdbc52a7..6afee019f 100644
--- a/src/biotite/sequence/align/matrix.py
+++ b/src/biotite/sequence/align/matrix.py
@@ -2,14 +2,17 @@
 # under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
 # information.
 
+__all__ = ["SubstitutionMatrix"]
 __name__ = "biotite.sequence.align"
 __author__ = "Patrick Kunzmann"
 
-import os
+import functools
+from pathlib import Path
 import numpy as np
 from biotite.sequence.seqtypes import NucleotideSequence, ProteinSequence
 
-__all__ = ["SubstitutionMatrix"]
+# Directory of matrix files
+_DB_DIR = Path(__file__).parent / "matrix_data"
 
 
 class SubstitutionMatrix(object):
@@ -128,9 +131,6 @@ class SubstitutionMatrix(object):
     >>> matrix = SubstitutionMatrix(alph, alph, "BLOSUM50")
     """
 
-    # Directory of matrix files
-    _db_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "matrix_data")
-
     def __init__(self, alphabet1, alphabet2, score_matrix):
         self._alph1 = alphabet1
         self._alph2 = alphabet2
@@ -354,7 +354,7 @@ def dict_from_db(matrix_name):
         matrix_dict : dict
             A dictionary representing the substitution matrix.
         """
-        filename = SubstitutionMatrix._db_dir + os.sep + matrix_name + ".mat"
+        filename = _DB_DIR / f"{matrix_name}.mat"
         with open(filename, "r") as f:
             return SubstitutionMatrix.dict_from_str(f.read())
 
@@ -368,11 +368,10 @@ def list_db():
         db_list : list
             List of matrix names in the internal database.
         """
-        files = os.listdir(SubstitutionMatrix._db_dir)
-        # Remove '.mat' from files
-        return [file[:-4] for file in sorted(files)]
+        return [path.stem for path in _DB_DIR.glob("*.mat")]
 
     @staticmethod
+    @functools.cache
     def std_protein_matrix():
         """
         Get the default :class:`SubstitutionMatrix` for protein sequence
@@ -383,9 +382,10 @@ def std_protein_matrix():
         matrix : SubstitutionMatrix
             Default matrix.
         """
-        return _matrix_blosum62
+        return ProteinSequence.alphabet, ProteinSequence.alphabet, "BLOSUM62"
 
     @staticmethod
+    @functools.cache
     def std_nucleotide_matrix():
         """
         Get the default :class:`SubstitutionMatrix` for DNA sequence
@@ -396,13 +396,21 @@ def std_nucleotide_matrix():
         matrix : SubstitutionMatrix
             Default matrix.
         """
-        return _matrix_nuc
+        return NucleotideSequence.alphabet_amb, NucleotideSequence.alphabet_amb, "NUC"
+
+    @staticmethod
+    @functools.cache
+    def std_3di_matrix():
+        """
+        Get the default :class:`SubstitutionMatrix` for 3Di sequence
+        alignments.
 
+        Returns
+        -------
+        matrix : SubstitutionMatrix
+            Default matrix.
+        """
+        # Import inside function to avoid circular import
+        from biotite.structure.alphabet.i3d import I3DSequence
 
-# Preformatted BLOSUM62 and NUC substitution matrix from NCBI
-_matrix_blosum62 = SubstitutionMatrix(
-    ProteinSequence.alphabet, ProteinSequence.alphabet, "BLOSUM62"
-)
-_matrix_nuc = SubstitutionMatrix(
-    NucleotideSequence.alphabet_amb, NucleotideSequence.alphabet_amb, "NUC"
-)
+        return I3DSequence.alphabet, I3DSequence.alphabet, "3Di"
diff --git a/tests/sequence/align/test_matrix.py b/tests/sequence/align/test_matrix.py
index 05bb18acf..9455a1650 100644
--- a/tests/sequence/align/test_matrix.py
+++ b/tests/sequence/align/test_matrix.py
@@ -39,6 +39,21 @@ def test_structural_alphabet_matrices(matrix_name, alphabet):
     align.SubstitutionMatrix(alphabet, alphabet, matrix_name)
 
 
+@pytest.mark.parametrize(
+    "method_name",
+    [
+        "std_protein_matrix",
+        "std_nucleotide_matrix",
+        "std_3di_matrix",
+    ],
+)
+def test_default_matrices(method_name):
+    """
+    Test for exceptions when using the static methods for getting default matrices.
+    """
+    getattr(align.SubstitutionMatrix, method_name)()
+
+
 def test_matrix_str():
     """
     Test conversion of substitution matrix to string via a small