From 13f2867b56c5ceddab4b777fe50f6f00495177d5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=80lex=20Sol=C3=A9?= <jaume.alexandre.sole@upc.edu>
Date: Fri, 24 Jan 2025 15:53:57 +0100
Subject: [PATCH] updated enviroment

---
 README.md                   | 11 +++++++++--
 dataset/extract_csd_data.py | 20 +++++++++++---------
 environment_2.yml           |  2 +-
 3 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 062ab80..9c03b03 100644
--- a/README.md
+++ b/README.md
@@ -49,16 +49,19 @@ Instructions to set up the environment:
 git clone https://github.com/imatge-upc/CartNet.git
 cd CartNet
 
-# Create a Conda environment
+# Create a Conda environment (original env)
 conda env create -f environment.yml
 
+# or alternatively, if you want to use torch 2.4.0
+conda env create -f environment_2.yml
+
 # Activate the environment
 conda activate CartNet
 ```
 
 ## Dependencies
 
-The environment relies on these dependencies:
+The environment used for the results reported in the paper relies on these dependencies:
 
 ```sh
 pytorch==1.13.1
@@ -79,6 +82,10 @@ csd-python-api==3.3.1
 
 These dependencies are automatically installed when you create the Conda environment using the `environment.yml` file.
 
+### Update
+
+We have updated our dependencies to torch 2.4.0 to facilitate further research. This can be installed via the “environment_2.yml” file.
+
 
 ## Dataset
 
diff --git a/dataset/extract_csd_data.py b/dataset/extract_csd_data.py
index cfd88a7..01b7c67 100644
--- a/dataset/extract_csd_data.py
+++ b/dataset/extract_csd_data.py
@@ -47,13 +47,13 @@ def refcsd2graph(refcode, output_folder):
         entry = csd_reader.entry(refcode)
 
         if entry.pressure is not None:
-            return None
+            return refcode
         
         if entry.remarks is not None:
-            return None
+            return refcode
         
         if entry.crystal.has_disorder:
-            return None
+            return refcode
         
         if entry.temperature is None:
             doc = cif.read_string(entry.to_string(format='cif'))
@@ -67,7 +67,7 @@ def refcsd2graph(refcode, output_folder):
                 assert(temperature[0] is not None)
                 temperature = float(temperature[0])
             except Exception as e:
-                return None
+                return refcode
         else:
             temperature = entry.temperature
             
@@ -75,7 +75,7 @@ def refcsd2graph(refcode, output_folder):
             try:
                 assert(len(temp)==1)
             except:
-                return None
+                return refcode
             
             temperature = float(temp[0])
         
@@ -94,7 +94,7 @@ def refcsd2graph(refcode, output_folder):
                     continue
                 elif atom.atomic_number != 1:
                     print("istrotropic")
-                    return
+                    return refcode
             
             if atom.displacement_parameters.type == "Isotropic" and atom.atomic_number == 1:
                 adp.append(torch.eye(3).unsqueeze(0)*atom.displacement_parameters.isotropic_equivalent)
@@ -192,6 +192,8 @@ def target(error_flag):
     data_df = pd.read_csv('./csv/all_dataset.csv', header=None)
     
     res = [refcsd2graph(refcode, output_folder) for refcode in tqdm(data_df[0].tolist())]
-    res = [r for r in res if r is None]
-    with open("errors.txt", "w") as f:
-        f.write("\n".join(res))
\ No newline at end of file
+    res = [r for r in res if r is not None]
+    
+    if len(res) > 0:
+        with open("errors.txt", "w") as f:
+            f.write("\n".join(res))
\ No newline at end of file
diff --git a/environment_2.yml b/environment_2.yml
index 3fa961b..38d7f2e 100644
--- a/environment_2.yml
+++ b/environment_2.yml
@@ -1,4 +1,4 @@
-name: CartNet_paper
+name: CartNet_paper_2.4.0
 channels:
   - pytorch
   - pyg