Add CLePAPS structural alphabet

doc/apidoc.json

@@ -465,11 +465,13 @@
     "biotite.structure.alphabet" : {
         "Structural alphabets": [
             "I3DSequence",
-            "ProteinBlocksSequence"
+            "ProteinBlocksSequence",
+            "ClepapsSequence"
         ],
         "Conversion Function": [
             "to_3di",
-            "to_protein_blocks"
+            "to_protein_blocks",
+            "to_clepaps"
         ]
     }
 }

doc/references.bib

@@ -917,6 +917,21 @@ @article{Varadi2024
   doi = {10.1093/nar/gkad1011}
 }
 
+@article{Wang2008,
+  title = {{{CLePAPS}}: {{FAST PAIR ALIGNMENT OF PROTEIN STRUCTURES BASED ON CONFORMATIONAL LETTERS}}},
+  shorttitle = {{{CLePAPS}}},
+  author = {Wang, Sheng and Zheng, Wei-Mou},
+  year = {2008},
+  month = apr,
+  journal = {Journal of Bioinformatics and Computational Biology},
+  volume = {06},
+  number = {02},
+  pages = {347--366},
+  publisher = {World Scientific Publishing Co.},
+  issn = {0219-7200},
+  doi = {10.1142/S0219720008003461}
+}
+
 @article{Westbrook2015,
   title = {The Chemical Component Dictionary: Complete Descriptions of Constituent Molecules in Experimentally Determined {{3D}} Macromolecules in the {{Protein Data Bank}}},
   shorttitle = {The Chemical Component Dictionary},

src/biotite/sequence/align/matrix.py

@@ -76,6 +76,7 @@ class SubstitutionMatrix(Generic[S1, S2]):
 
             - **3Di** - For 3Di alphabet from ``foldseek`` :footcite:`VanKempen2024`
             - **PB** - For Protein Blocks alphabet from *PBexplore* :footcite:`Barnoud2017`
+            - **CLESUM** - For CLePAPS alphabet :footcite:`Wang2008`
 
     A list of all available matrix names is returned by
     :meth:`list_db()`.
@@ -630,6 +631,50 @@ def std_protein_blocks_matrix(
             matrix_dict,
         )
 
+    @staticmethod
+    @functools.cache
+    def std_clepaps_matrix(
+        unknown_match: int = 200, unknown_mismatch: int = -200
+    ) -> SubstitutionMatrix[str, str]:
+        """
+        Get the *CLESUM* substitution matrix for *CLePAPS* sequence.
+        :footcite:`Wang2008`
+
+        Parameters
+        ----------
+        unknown_match, unknown_mismatch : int, optional
+            The match and mismatch score for the unknown symbol.
+            The default values were chosen arbitrarily, but are in the order of
+            magnitude of the other score values.
+
+        Returns
+        -------
+        matrix : SubstitutionMatrix
+            Default matrix.
+
+        References
+        ----------
+
+        .. footbibliography::
+        """
+        from biotite.structure.alphabet.clepaps import ClepapsSequence
+
+        alphabet = ClepapsSequence.alphabet
+        unknown_symbol = ClepapsSequence.unknown_symbol
+        matrix_dict = SubstitutionMatrix.dict_from_db("CLESUM")
+        # Add match/mismatch scores for the unknown symbol
+        for symbol in alphabet:
+            if symbol == unknown_symbol:
+                continue
+            matrix_dict[symbol, unknown_symbol] = unknown_mismatch
+            matrix_dict[unknown_symbol, symbol] = unknown_mismatch
+        matrix_dict[unknown_symbol, unknown_symbol] = unknown_match
+        return SubstitutionMatrix(
+            alphabet,
+            alphabet,
+            matrix_dict,
+        )
+
     def _fill_with_matrix_dict(self, matrix_dict: dict[tuple[Any, Any], int]) -> None:
         self._matrix = np.zeros((len(self._alph1), len(self._alph2)), dtype=np.int32)
         for i in range(len(self._alph1)):

src/biotite/sequence/align/matrix_data/CLESUM.mat

@@ -0,0 +1,19 @@
+# CLESUM: The conformation letter substitution matrix from the CLePAPS paper
+      A    B    C    D    E    F    G    H    I    J    K    L    M    N    O    P    Q
+A    73   20   13  -17  -25  -20   -6  -45  -31  -23  -19  -11   -2   10   25   35   16
+B    20   51    7   13   15    7   13  -96  -74  -57  -50  -12  -13  -11  -12   42   12
+C    13    7   53   21    3   20   -4  -77  -56  -43  -33    0  -12   -5    3    4   29
+D   -17   13   21   52   22   21  -31 -124 -105  -88  -81  -22  -49  -44  -42  -10   14
+E   -25   15    3   22   36   26  -22 -127 -108  -93  -84  -21  -47  -43  -48   -5   -6
+F   -20    7   20   21   26   50   -5 -107  -88  -73  -69  -16  -33  -32  -30    0    3
+G    -6   13   -4  -31  -22   -5   69  -51  -34  -21  -13   29   21   -8   -1    5    8
+H   -45  -96  -77 -124 -127 -107  -51   23   18   13    5  -62   -4  -34  -55  -60  -87
+I   -31  -74  -56 -105 -108  -88  -34   18   23   16   21  -41    1  -11  -34  -49  -62
+J   -23  -57  -43  -88  -93  -73  -21   13   16   37   13  -32   16   -2  -24  -34  -44
+K   -19  -50  -33  -81  -84  -69  -13    5   21   13   49   -1   12   28    5  -36  -24
+L   -11  -12    0  -22  -21  -16   29  -62  -41  -32   -1   74    5    8   -4  -12   26
+M    -2  -13  -12  -49  -47  -33   21   -4    1   16   12    5   61    7    5    8   -7
+N    10  -11   -5  -44  -43  -32   -8  -34  -11   -2   28    8    7   90   15   -3   32
+O    25  -12    3  -42  -48  -30   -1  -55  -34  -24    5   -4    5   15  104    4  -13
+P    35   42    4  -10   -5    0    5  -60  -49  -34  -36  -12    8   -3    4   66    7
+Q    16   12   29   14   -6    3    8  -87  -62  -44  -24   26   -7   32  -13    7   90

src/biotite/structure/alphabet/__init__.py

@@ -21,5 +21,6 @@
 __name__ = "biotite.structure.alphabet"
 __author__ = "Martin Larralde, Patrick Kunzmann"
 
+from .clepaps import *
 from .i3d import *
 from .pb import *