From 744874f425d48e86c8a6687df6006e1b7fe4594c Mon Sep 17 00:00:00 2001
From: Pablo Martinez Bulit <pbulit@ccdc.cam.ac.uk>
Date: Thu, 1 May 2025 15:17:30 +0100
Subject: [PATCH 1/2] Added filter for chirality NO_JIRA

---
 .../entry_property_calculator.py              | 38 +++++++++++++++++++
 .../refcodes_with_properties.py               |  4 +-
 2 files changed, 40 insertions(+), 2 deletions(-)

diff --git a/scripts/refcodes_with_properties/entry_property_calculator.py b/scripts/refcodes_with_properties/entry_property_calculator.py
index 588a17e..8300cbf 100644
--- a/scripts/refcodes_with_properties/entry_property_calculator.py
+++ b/scripts/refcodes_with_properties/entry_property_calculator.py
@@ -85,6 +85,20 @@ def __call__(self, theobject):
         return value >= self.minimum and value <= self.maximum
 
 
+class _ValueFilter(_Filter):
+    def __init__(self, args):
+        values = [p for p in args.split()]
+        #To do: add option for two values?
+        self.expected_value = values[0]
+
+    def value(self, theobject):
+        raise NotImplementedError  # override this
+
+    def __call__(self, theobject):
+        value = self.value(theobject)
+        return value == self.expected_value
+
+
 class AllowedAtomicNumbersFilter(_Filter):
     def __init__(self, args):
         self.allowed_atomic_numbers = [int(atomic_number) for atomic_number in args.strip().split()]
@@ -413,6 +427,30 @@ def value(self, entry):
 register(SpacegroupNumberFilter)
 
 
+class ChiralityFilter(_ValueFilter):
+    def __init__(self, args):
+        super().__init__(args)
+
+    @staticmethod
+    def name():
+        return "chirality"
+
+    @staticmethod
+    def helptext():
+        return "specify the chirality value to be used as filter"
+
+    def value(self, entry):
+        try:
+            molecule = entry.crystal.molecule
+            chirality = next((atom.chirality for atom in molecule.atoms if atom.is_chiral), None)
+            return chirality
+        except TypeError:
+            return 0
+
+
+register(ChiralityFilter)
+
+
 class FilterEvaluation(object):
     def __init__(self):
         self._methods = []
diff --git a/scripts/refcodes_with_properties/refcodes_with_properties.py b/scripts/refcodes_with_properties/refcodes_with_properties.py
index e98b7ea..df92dd6 100644
--- a/scripts/refcodes_with_properties/refcodes_with_properties.py
+++ b/scripts/refcodes_with_properties/refcodes_with_properties.py
@@ -46,7 +46,7 @@
 
     outfile = sys.stdout
     if args.output_file is not None:
-        outfile = open(args.output_file, 'wb')
+        outfile = open(args.output_file, 'w', encoding='utf-8')
 
     filterer = entry_property_calculator.parse_control_file(open(control_file, "r").readlines())
 
@@ -73,4 +73,4 @@
     else:
         for entry in reader:
             if filterer.evaluate(entry):
-                outfile.write(entry.identifier + "\n")
+                outfile.write(entry.identifier + "\n")
\ No newline at end of file

From 6c174d51b768e5a1158a63420d2b2ee0167861d5 Mon Sep 17 00:00:00 2001
From: Pablo Martinez Bulit <pbulit@ccdc.cam.ac.uk>
Date: Fri, 2 May 2025 10:42:53 +0100
Subject: [PATCH 2/2] Added filter 3D structures and fixed SG bug NO_JIRA

---
 .../entry_property_calculator.py              | 28 +++++++++++++++++--
 .../refcodes_with_properties.py               |  2 +-
 2 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/scripts/refcodes_with_properties/entry_property_calculator.py b/scripts/refcodes_with_properties/entry_property_calculator.py
index 8300cbf..aa1ee9f 100644
--- a/scripts/refcodes_with_properties/entry_property_calculator.py
+++ b/scripts/refcodes_with_properties/entry_property_calculator.py
@@ -89,7 +89,10 @@ class _ValueFilter(_Filter):
     def __init__(self, args):
         values = [p for p in args.split()]
         #To do: add option for two values?
-        self.expected_value = values[0]
+        if values[0] == 'None':
+            self.expected_value = None
+        else:
+            self.expected_value = values[0]
 
     def value(self, theobject):
         raise NotImplementedError  # override this
@@ -214,6 +217,25 @@ def value(self, entry):
 register(AllHaveSitesFilter)
 
 
+class Has3DStructure(_ComparativeFilter):
+    def __init__(self, args):
+        super().__init__(args)
+
+    @staticmethod
+    def name():
+        return "has 3D structure"
+
+    @staticmethod
+    def helptext():
+        return "whether 3D coordinates have been determined for the structure"
+
+    def value(self, entry):
+        return entry.has_3d_structure
+
+
+register(Has3DStructure)
+
+
 class DisorderedFilter(_ComparativeFilter):
     def __init__(self, args):
         super().__init__(args)
@@ -445,7 +467,7 @@ def value(self, entry):
             chirality = next((atom.chirality for atom in molecule.atoms if atom.is_chiral), None)
             return chirality
         except TypeError:
-            return 0
+            return None
 
 
 register(ChiralityFilter)
@@ -463,7 +485,7 @@ def evaluate(self, entry):
             try:
                 if not method(entry):
                     return False
-            except TypeError:
+            except (TypeError, RuntimeError):
                 return False
 
         return True
diff --git a/scripts/refcodes_with_properties/refcodes_with_properties.py b/scripts/refcodes_with_properties/refcodes_with_properties.py
index df92dd6..474fc68 100644
--- a/scripts/refcodes_with_properties/refcodes_with_properties.py
+++ b/scripts/refcodes_with_properties/refcodes_with_properties.py
@@ -73,4 +73,4 @@
     else:
         for entry in reader:
             if filterer.evaluate(entry):
-                outfile.write(entry.identifier + "\n")
\ No newline at end of file
+                outfile.write(entry.identifier + "\n")