version small peptides

Author: RobbinBouwmeester

CHANGELOG.md

@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.1.8] - 2025-02-21
+
+### Changed
+
+- Allow for much smaller peptides in feature calculation
+
 ## [3.1.7] - 2025-02-03
 
 ### Changed

deeplc/feat_extractor.py

@@ -412,7 +412,11 @@ def rolling_sum(a, n=2):
                         )
 
             for p in positions_pos:
-                aa = seq[p]
+                try:
+                    aa = seq[p]
+                except:
+                    warn_once(f"Unable to get the following position: {p}")
+                    continue
                 for atom, val in mass.std_aa_comp[aa].items():
                     try:
                         matrix_pos[p, dict_index_pos[atom]] = val
@@ -422,7 +426,11 @@ def rolling_sum(a, n=2):
                         warn_once(f"Could not add the following atom: {p} {atom} {val}")
 
             for pn in positions_neg:
-                aa = seq[seq_len + pn]
+                try:
+                    aa = seq[seq_len + pn]
+                except:
+                    warn_once(f"Unable to get the following position: {p}")
+                    continue
                 for atom, val in mass.std_aa_comp[aa].items():
                     try:
                         matrix_pos[pn, dict_index_pos[atom]] = val

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "deeplc"
-version = "3.1.7"
+version = "3.1.8"
 description = "DeepLC: Retention time prediction for (modified) peptides using Deep Learning."
 readme = "README.md"
 license = { file = "LICENSE" }