From 2ad9afdd82746c6223a76dbf3a14060d4f5736d0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 15 Dec 2025 20:16:23 +0000
Subject: [PATCH 1/3] Initial plan


From cfa8e632930a51548636bd397fedb375a6f119ea Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 15 Dec 2025 20:21:46 +0000
Subject: [PATCH 2/3] Fix AttributeError in calcHydrophobic by removing
 redundant select() call

Co-authored-by: AnthonyBogetti <34397256+AnthonyBogetti@users.noreply.github.com>
---
 prody/proteins/interactions.py |   2 +-
 test_3o21_disu.npy             | Bin 0 -> 970 bytes
 2 files changed, 1 insertion(+), 1 deletion(-)
 create mode 100644 test_3o21_disu.npy

diff --git a/prody/proteins/interactions.py b/prody/proteins/interactions.py
index dfca7a1d3..4d4123ee8 100644
--- a/prody/proteins/interactions.py
+++ b/prody/proteins/interactions.py
@@ -1505,7 +1505,7 @@ def calcHydrophobic(atoms, **kwargs):
                     sele2_filter = sele2_filter.select('all and not (resname TYR PHE TRP or resid '+str(i[0])+' and chain '+i[1]+')')
                 elif sele1_name[0] not in aromatic and i in sele2_nr:
                     # don't include same residue interactions but don't worry about double counting pi stacking
-                    sele2_filter = sele2_filter.select(sele2.select('all and not (resid '+str(i[0])+' and chain '+i[1]+')'))
+                    sele2_filter = sele2_filter.select('all and not (resid '+str(i[0])+' and chain '+i[1]+')')
 
                 if sele2_filter != None:
                     listOfAtomToCompare = cleanNumbers(findNeighbors(sele1, distA, sele2_filter))
diff --git a/test_3o21_disu.npy b/test_3o21_disu.npy
new file mode 100644
index 0000000000000000000000000000000000000000..8388b84f69608679ed3619381a6c3c11ce30ac1c
GIT binary patch
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g`{24E?pv?=q<Nk%iu<aY^?jB#1wq`G3QP!k05noP;{X5v

literal 0
HcmV?d00001


From bdec243251d935c8ee7a873bd0d1ccb3f2d10f6e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 15 Dec 2025 20:22:12 +0000
Subject: [PATCH 3/3] Remove accidentally committed test file and add .npy to
 gitignore

Co-authored-by: AnthonyBogetti <34397256+AnthonyBogetti@users.noreply.github.com>
---
 .gitignore         |   1 +
 test_3o21_disu.npy | Bin 970 -> 0 bytes
 2 files changed, 1 insertion(+)
 delete mode 100644 test_3o21_disu.npy

diff --git a/.gitignore b/.gitignore
index 927eb99f1..5d8d73671 100644
--- a/.gitignore
+++ b/.gitignore
@@ -54,3 +54,4 @@ Documentation/*
 *log
 *BAK
 *.sublime*
+*.npy
diff --git a/test_3o21_disu.npy b/test_3o21_disu.npy
deleted file mode 100644
index 8388b84f69608679ed3619381a6c3c11ce30ac1c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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