From e29779bee06135133c7ea69b147454d97a252098 Mon Sep 17 00:00:00 2001
From: Sean Colby <seanmcolby@gmail.com>
Date: Fri, 24 Jan 2025 15:54:30 -0800
Subject: [PATCH] Fix attribute referencing for conformational ensemble

---
 isicle/conformers.py | 19 +++++++------------
 isicle/geometry.py   | 15 ---------------
 isicle/parse.py      |  3 +--
 3 files changed, 8 insertions(+), 29 deletions(-)

diff --git a/isicle/conformers.py b/isicle/conformers.py
index ea9e428..6aa7357 100644
--- a/isicle/conformers.py
+++ b/isicle/conformers.py
@@ -398,13 +398,10 @@ def _check_attributes(self, attr):
             If all members do not have `attr`.
 
         '''
-
-        value = [x.get___dict__() for x in self]
-        for key in safelist(attr):
-            if not all(key in x for x in value):
-                raise AttributeError('"{}" not found for all conformational '
-                                     'ensemble members.'.format(attr))
-            value = [x.get(key) for x in value]
+        
+        if not all(hasattr(x, attr) for x in self):
+            raise AttributeError('"{}" not found for all conformational '
+                                    'ensemble members.'.format(attr))
 
     def reduce(self, attr, func='boltzmann', **kwargs):
         '''
@@ -438,9 +435,7 @@ def reduce(self, attr, func='boltzmann', **kwargs):
             self._check_attributes('energy')
 
         # Extract (possibly nested) value attribute
-        value = [x.get___dict__() for x in self]
-        for key in safelist(attr):
-            value = [x.get(key) for x in value]
+        value = [getattr(x, attr) for x in self]
 
         # Check nested values
         if isinstance(value[0], dict):
@@ -463,7 +458,7 @@ def reduce(self, attr, func='boltzmann', **kwargs):
                 value = np.array([x['mean'] for x in value]).flatten()
 
             else:
-                value = np.array([x[attr] for x in value]).flatten()
+                value = np.array([getattr(x, attr) for x in value]).flatten()
 
         # Not nested
         else:
@@ -474,7 +469,7 @@ def reduce(self, attr, func='boltzmann', **kwargs):
         # Extract energy attribute
         if _energy_based(f):
             energy = np.array(
-                [np.repeat(x.get___dict__()['energy'], pad) for x in self])
+                [np.repeat(getattr(x, 'energy'), pad) for x in self])
             energy = energy.flatten()
 
             # Exectue energy-based method
diff --git a/isicle/geometry.py b/isicle/geometry.py
index a394aff..8907c00 100644
--- a/isicle/geometry.py
+++ b/isicle/geometry.py
@@ -27,7 +27,6 @@ class Geometry(GeometryInterface):
         "_connectivity",
         "_formal_charge",
         "_ccs",
-        "_ccs_std"
         ]
     _default_value = None
 
@@ -171,20 +170,6 @@ def ccs(self):
 
         return self._ccs
 
-    @property
-    def ccs_std(self):
-        """
-        Get standard deviation of CCS prediction of the molecule.
-
-        Returns
-        -------
-        float
-            Standard deviation of collision cross section.
-
-        """
-
-        return self._ccs_std
-
     def view(self):
         """
         View internal rdkit mol object representation.
diff --git a/isicle/parse.py b/isicle/parse.py
index 05cd747..f6f85a6 100644
--- a/isicle/parse.py
+++ b/isicle/parse.py
@@ -835,8 +835,7 @@ def parse(self):
             elif "standard deviation (percent)" in line:
                 done = True
         if done is True:
-            self.result["ccs"] = ccs_mn
-            self.result["ccs_std"] = ccs_std
+            self.result["ccs"] = {"mean": ccs_mn, "std": ccs_std}
         
         self.result["geometry"] = self.data["geometry"]