hotfix for fingerprint calculation (when SMILES is invalid)

README.md

@@ -15,14 +15,14 @@ The goal of model-based optimization is to find an input **x** that maximizes an
 Design-Bench can be installed with the complete set of benchmarks via our pip package.
 
 ```bash
-pip install design-bench[all]==2.0.15
+pip install design-bench[all]==2.0.16
 pip install morphing-agents==1.5.1
 ```
 
 Alternatively, if you do not have MuJoCo, you may opt for a minimal install.
 
 ```bash
-pip install design-bench==2.0.15
+pip install design-bench==2.0.16
 ```
 
 ## Available Tasks

design_bench/oracles/feature_extractors/morgan_fingerprint_features.py

@@ -101,12 +101,12 @@ def dataset_to_oracle_x(self, x_batch, dataset):
             tokens = xi[1:stop_tokens[0] if stop_tokens.size > 0 else xi[1:]]
 
             # apply morgan fingerprint featurization using rdkit
-            value = self.featurizer.featurize(
-                self.tokenizer.decode(tokens).replace(" ", ""))[0]
+            token_string = self.tokenizer.decode(tokens).replace(" ", "")
+            value = self.featurizer.featurize(token_string)[0]
 
             # collate all results into a single numpy array
-            x_out.append(np.zeros([2048], dtype=self.dtype)
-                         if value is None
+            x_out.append(np.zeros([self.size], dtype=self.dtype)
+                         if value.size != self.size
                          else np.array(value, dtype=self.dtype))
 
         return np.asarray(x_out)

example_iteration_script.py

@@ -1,11 +1,12 @@
 import pickle as pkl
 import design_bench as db
 import numpy as np
+from design_bench.oracles.feature_extractors.morgan_fingerprint_features import MorganFingerprintFeatures
 
 
 if __name__ == "__main__":
 
-    with open("type_assay_pairs.pkl", "wb") as f:
+    with open("type_assay_pairs.pkl", "rb") as f:
         type_assay_pairs = pkl.load(f)
 
     all_rank_corr = []

setup.py

@@ -7,7 +7,7 @@
     LONG_DESCRIPTION = readme.read()
 
 
-setup(name='design-bench', version='2.0.15', license='MIT',
+setup(name='design-bench', version='2.0.16', license='MIT',
       packages=find_packages(include=['design_bench', 'design_bench.*']),
       description='Design-Bench: Benchmarks for '
                   'Data-Driven Offline Model-Based Optimization',
@@ -17,7 +17,7 @@
       author_email='brandon@btrabucco.com',
       url='https://github.com/brandontrabucco/design-bench',
       download_url='https://github.com/'
-                   'brandontrabucco/design-bench/archive/v2_0_15.tar.gz',
+                   'brandontrabucco/design-bench/archive/v2_0_16.tar.gz',
       keywords=['Deep Learning', 'Neural Networks',
                 'Benchmark', 'Model-Based Optimization'],
       extras_require={'all': ['gym[mujoco]'], 'cma': ['cma']},