From 9e1ff60fa026465b57fd308738a81185e7e951da Mon Sep 17 00:00:00 2001
From: Alex Morehead <acmwhb@missouri.edu>
Date: Sat, 1 Jun 2024 21:26:52 -0500
Subject: [PATCH] Handle for missing relaxed NeuralPLexer structures n some
 dataset contexts

---
 src/analysis/complex_alignment.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/analysis/complex_alignment.py b/src/analysis/complex_alignment.py
index b705a4db..46ae728e 100644
--- a/src/analysis/complex_alignment.py
+++ b/src/analysis/complex_alignment.py
@@ -370,7 +370,18 @@ def main(cfg: DictConfig):
             raise ValueError(f"Invalid method: {cfg.method}")
 
         if len(output_ligand_files) < len(output_protein_files):
-            if cfg.method == "rfaa":
+            if cfg.method == "neuralplexer":
+                output_protein_files = sorted(
+                    [
+                        file
+                        for file in list(output_dir.rglob(f"prot_rank{cfg.rank_to_align}_*.pdb"))
+                        if "_aligned" not in file.stem
+                        and any(
+                            [file.parent.stem in item.parent.stem for item in output_ligand_files]
+                        )
+                    ]
+                )
+            elif cfg.method == "rfaa":
                 output_protein_files = sorted(
                     [
                         item