Revert "Made requested changes"

This reverts commit c14c0bb.

Author: satvshr

pyaptamer/pseaac/_features.py

@@ -13,52 +13,39 @@ class PSeAAC:
     selected physicochemical properties and sequence-order correlations as described in
     the PseAAC model by Chou.
 
-    The PSeAAC algorithm uses normalized physicochemical (NP) properties of amino
-    acids, which we load from a predefined matrix using `aa_props`. These properties
-    can be grouped using one of the following options:
-
-
-    - `prop_indices`: A list of property indices (0-based) to use (e.g.,
-    `prop_indices=[3, 4, 8]` uses property groups [Polarity, Molecular Weight,
-    Bulkiness] (refer table below)).
-    - If `group_props` is an integer, the selected properties are grouped into chunks of
-    that size (e.g., `group_props=3` groups into sets of 3). If `group_props` is None,
-    then each property is treated as its own group.
-    - If `custom_groups` is provided, it overrides all other logic. It must be a list of
-    lists, where each sublist contains indices (0-based) of properties to group
-    together. (e.g., `prop_indices=[[3, 4], [8]]` groups Polarity and Molecular Weight
-    together, and Bulkiness is its own group).
+    The PSeAAC algorith uses 21 normalized physiochemical (NP) properties of amino
+    acids, which we load from a predefined matrix using `aa_props`.These 21 properties
+    are grouped into 7 distinct property groups, with each group containing
+    3 consecutive properties. Specifically, the groups are arranged in order as follows:
+    Group 1 includes properties 1–3, Group 2 includes properties 4–6, and so on, up to
+    Group 7, which includes properties 19–21.
 
 
     The properties in order are:
-
-
-    0. Hydrophobicity
-    1. Hydrophilicity
-    2. Side-chain Mass
-    3. Polarity
-    4. Molecular Weight
-    5. Melting Point
-    6. Transfer Free Energy
-    7. Buriability
-    8. Bulkiness
-    9. Solvation Free Energy
-    10. Relative Mutability
-    11. Residue Volume
-    12. Volume
-    13. Amino Acid Distribution
-    14. Hydration Number
-    15. Isoelectric Point
-    16. Compressibility
-    17. Chromatographic Index
-    18. Unfolding Entropy Change
-    19. Unfolding Enthalpy Change
-    20. Unfolding Gibbs Free Energy Change
+    1. Hydrophobicity
+    2. Hydrophilicity
+    3. Side-chain Mass
+    4. Polarity
+    5. Molecular Weight
+    6. Melting Point
+    7. Transfer Free Energy
+    8. Buriability
+    9. Bulkiness
+    10. Solvation Free Energy
+    11. Relative Mutability
+    12. Residue Volume
+    13. Volume
+    14. Amino Acid Distribution
+    15. Hydration Number
+    16. Isoelectric Point
+    17. Compressibility
+    18. Chromatographic Index
+    19. Unfolding Entropy Change
+    20. Unfolding Enthalpy Change
+    21. Unfolding Gibbs Free Energy Change
 
 
     Each feature vector consists of:
-
-
     - 20 normalized amino acid composition features (frequency of each standard
     amino acid)
     - 30 sequence-order correlation features based on physicochemical similarity between
@@ -67,7 +54,6 @@ class PSeAAC:
     resulting in a final vector of length 50 × number of property groups.
     For example, if there are 7 groups, the output length is 350 ((20 + 30) * 7 = 350).
 
-
     References
     ----------
     Shen HB, Chou KC. PseAAC: a flexible web server for generating various kinds of