From 65919f2688378c3972e96a502022fc3164045ea7 Mon Sep 17 00:00:00 2001
From: James Krieger <jamesmkrieger@gmail.com>
Date: Fri, 12 Apr 2024 13:54:22 +0200
Subject: [PATCH] fix consideredAtoms errors

---
 prody/proteins/waterbridges.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/prody/proteins/waterbridges.py b/prody/proteins/waterbridges.py
index e1f9e51e8..a13da5971 100644
--- a/prody/proteins/waterbridges.py
+++ b/prody/proteins/waterbridges.py
@@ -385,9 +385,17 @@ def calcWaterBridges(atoms, **kwargs):
     if outputType not in ['info', 'atomic', 'indices']:
         raise TypeError('Output can be info, atomic or indices.')
 
+    water = atoms.select('water')
+    if water is None:
+        raise ValueError('atoms has no water so cannot be analysed with WatFinder')
+
     relations = RelationList(len(atoms))
-    consideredAtoms = ~atoms.select(
+    tooFarAtoms = atoms.select(
         f'water and not within {distWR} of protein')
+    if tooFarAtoms is None:
+        consideredAtoms = atoms
+    else:
+        consideredAtoms = ~tooFarAtoms
 
     waterHydrogens = consideredAtoms.select('water and hydrogen') or []
     waterOxygens = consideredAtoms.select('water and oxygen')