Add data, methods, and descriptions for Atchley factors (#5)

* Add data, methods, and descriptions for Atchley factors * Add Atchley factors to `Peptide` descriptors index * Fix outdated doctest in `Peptide.descriptors` --------- Co-authored-by: Martin Larralde <[email protected]>
althonos · Sep 9, 2024 · a4b0948 · a4b0948
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diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ versions (3.6+).
 A non-exhaustive list of available features:
 
 - Peptide statistics: amino acid counts and frequencies.
-- **QSAR** descriptors: BLOSUM indices, Cruciani properties, FASGAI vectors, Kidera factors, MS-WHIM scores, PCP descriptors, ProtFP descriptors, Sneath vectors, ST-scales, T-scales, VHSE-scales, Z-scales.
+- **QSAR** descriptors: BLOSUM indices, Cruciani properties, FASGAI vectors, Kidera factors, Atchley factors, MS-WHIM scores, PCP descriptors, ProtFP descriptors, Sneath vectors, ST-scales, T-scales, VHSE-scales, Z-scales.
 - Sequence profiles: hydrophobicity, hydrophobic moment, membrane position.
 - Physicochemical properties: aliphatic index, instability index, theoretical net charge, isoelectric point, molecular weight (with isotope labelling support).
 - Biological properties: structural class prediction.

diff --git a/docs/api/descriptors.rst b/docs/api/descriptors.rst
@@ -11,6 +11,8 @@ Descriptors
 
 .. autoclass:: peptides.KideraFactors(typing.NamedTuple)
 
+.. autoclass:: peptides.AtchleyFactors(typing.NamedTuple)
+
 .. autoclass:: peptides.MSWHIMScores(typing.NamedTuple)
 
 .. autoclass:: peptides.PhysicalDescriptors(typing.NamedTuple)

diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -27,6 +27,7 @@ Descriptors
    CrucianiProperties
    FasgaiVectors
    KideraFactors
+   AtchleyFactors
    MSWHIMScores
    PhysicalDescriptors
    PCPDescriptors

diff --git a/docs/index.rst b/docs/index.rst
@@ -81,6 +81,7 @@ A non-exhaustive list of available features:
   - `Cruciani properties <https://doi.org/10.1002/cem.856>`_
   - `FASGAI vectors <https://doi.org/10.1111/j.1747-0285.2008.00641.x>`_
   - `Kidera factors <https://doi.org/10.1007/BF01025492>`_
+  - `Atchley factors <https://doi.org/10.1073/pnas.0408677102>`_
   - `MS-WHIM scores <https://doi.org/10.1021/ci980211b>`_
   - `PCP descriptors <https://doi.org/10.1007/s00894-001-0058-5>`_
   - `ProtFP descriptors <https://doi.org/10.1186/1758-2946-5-41>`_

diff --git a/peptides/__init__.py b/peptides/__init__.py
@@ -144,6 +144,34 @@ class KideraFactors(typing.NamedTuple):
     kf10: float
 
 
+class AtchleyFactors(typing.NamedTuple):
+    """The Atchley factors of a peptide.
+
+    The Atchley Factors were originally derived by applying multivariate
+    analysis to 494 physical properties of the 20 amino acids and using
+    dimension reduction techniques.
+
+    Attributes:
+        af1 (`float`): A factor modeling polarity, accessibility, and hydrophobicity.
+        af2 (`float`): A factor modeling propensity for secondary structure.
+        af3 (`float`): A factor modeling molecular size.
+        af4 (`float`): A factor modeling codon composition.
+        af5 (`float`): A factor modeling electrostatic charge.
+
+    References:
+        - Atchley, W. R., Zhao, J., Fernandes, A. D., Drüke, T.
+          *Solving the protein sequence metric problem*.
+          Proceedings of the National Academy of Sciences.
+          Apr 2005;102(18):6395-6400. :doi:`10.1073/pnas.040867710`.
+
+    """
+    af1: float
+    af2: float
+    af3: float
+    af4: float
+    af5: float
+
+
 class MSWHIMScores(typing.NamedTuple):
     """The MS-WHIM scores of a peptide.
 
@@ -648,7 +676,7 @@ def descriptors(self) -> typing.Dict[str, float]:
         Example:
             >>> peptide = Peptide("SDKEVDEVDAALSDLEITLE")
             >>> sorted(peptide.descriptors().keys())
-            ['BLOSUM1', ..., 'F1', ..., 'KF1', ..., 'MSWHIM1', ..., 'PP1', ...]
+            ['AF1', ..., 'F1', ..., 'KF1', ..., 'MSWHIM1', ..., 'PP1', ...]
 
         Hint:
             Use this method to create a `~pandas.DataFrame` containing the
@@ -2115,6 +2143,32 @@ def kidera_factors(self) -> KideraFactors:
             out.append(_sum(p) / len(self))
         return KideraFactors(*out)
 
+    def atchley_factors(self) -> AtchleyFactors:
+        """Compute the Atchley factors of the peptide.
+
+        See `~peptides.AtchleyFactors` for more information.
+
+        Returns:
+            `peptides.AtchleyFactors`: The computed average Atchley factors
+            for all the amino acids in the peptide.
+
+        Example:
+            >>> peptide = Peptide("KLKLLLLLKLK")
+            >>> for i, kf in enumerate(peptide.atchley_factors()):
+            ...     print(f"AF{i+1:<3} {kf: .4f}")
+            AF1    0.0176
+            AF2   -0.8321
+            AF3   -0.7636
+            AF4    0.7048
+            AF5    0.0189
+
+        """
+        out = []
+        for i in range(len(tables.ATCHLEY)):
+            p = self.profile(tables.ATCHLEY[f"AF{i+1}"])
+            out.append(_sum(p) / len(self))
+        return AtchleyFactors(*out)
+
     def ms_whim_scores(self) -> MSWHIMScores:
         """Compute the MS-WHIM scores of the peptide.
 
@@ -2407,6 +2461,7 @@ def z_scales(self) -> ZScales:
         return ZScales(*out)
 
     __DESCRIPTORS = {
+        "AF": atchley_factors,
         "BLOSUM": blosum_indices,
         "PP": cruciani_properties,
         "F": fasgai_vectors,

diff --git a/peptides/tables/atchley/AF1.csv b/peptides/tables/atchley/AF1.csv
@@ -0,0 +1,20 @@
+A,-0.59145974
+R,1.53754853
+N,0.94535614
+D,1.05015062
+C,-1.34267179
+Q,0.93056541
+E,1.35733226
+G,-0.38387987
+H,0.33616543
+I,-1.23936304
+L,-1.01895162
+K,1.83146558
+M,-0.66312569
+F,-1.00610084
+P,0.18862522
+S,-0.22788299
+T,-0.03181782
+W,-0.59533918
+Y,0.25999617
+V,-1.33661279
diff --git a/peptides/tables/atchley/AF2.csv b/peptides/tables/atchley/AF2.csv
@@ -0,0 +1,20 @@
+A,-1.30209266
+R,-0.05472897
+N,0.82846219
+D,0.30242411
+C,0.465423
+Q,-0.17926549
+E,-1.45275578
+G,1.65201497
+H,-0.4166278
+I,-0.54652238
+L,-0.98693471
+K,-0.56109831
+M,-1.52353917
+F,-0.59046634
+P,2.08084151
+S,1.39869991
+T,0.32571153
+W,0.0090776
+Y,0.82992312
+V,-0.27854634
diff --git a/peptides/tables/atchley/AF3.csv b/peptides/tables/atchley/AF3.csv
@@ -0,0 +1,20 @@
+A,-0.7330651
+R,1.5021086
+N,1.2991286
+D,-3.6559147
+C,-0.8620345
+Q,-3.0048731
+E,1.476661
+G,1.3301017
+H,-1.673369
+I,2.1314349
+L,-1.5046185
+K,0.5332237
+M,2.2194787
+F,1.8909687
+P,-1.6283286
+S,-4.7596375
+T,2.2134612
+W,0.6719274
+Y,3.0973596
+V,-0.5440132
diff --git a/peptides/tables/atchley/AF4.csv b/peptides/tables/atchley/AF4.csv
@@ -0,0 +1,20 @@
+A,1.5703918
+R,0.4403185
+N,-0.1688162
+D,-0.2590236
+C,-1.0200786
+Q,-0.502591
+E,0.1129444
+G,1.0449765
+H,-1.4738898
+I,0.3931618
+L,1.2658296
+K,-0.2771101
+M,-1.0047207
+F,-0.3966186
+P,0.4207004
+S,0.6701745
+T,0.9078985
+W,-2.1275244
+Y,-0.8380164
+V,1.2419935
diff --git a/peptides/tables/atchley/AF5.csv b/peptides/tables/atchley/AF5.csv
@@ -0,0 +1,20 @@
+A,-0.14550842
+R,2.89744417
+N,0.93339498
+D,-3.24176791
+C,-0.25516894
+Q,-1.85303476
+E,-0.83715681
+G,2.06385566
+H,-0.07772917
+I,0.81630366
+L,-0.91181195
+K,1.64762794
+M,1.21181214
+F,0.41194139
+P,-1.39177378
+S,-2.64747356
+T,1.31337035
+W,-0.18358096
+Y,1.51150958
+V,-1.26225362