added Curie-Generate BETA

1 files changed, 44 insertions, 0 deletions

diff --git a/lstm_chem/generator.py b/lstm_chem/generator.py
new file mode 100755
index 0000000..498f864
--- /dev/null
+++ b/lstm_chem/generator.py
@@ -0,0 +1,44 @@
+from tqdm import tqdm
+import numpy as np
+from lstm_chem.utils.smiles_tokenizer import SmilesTokenizer
+
+
+class LSTMChemGenerator(object):
+    def __init__(self, modeler):
+        self.session = modeler.session
+        self.model = modeler.model
+        self.config = modeler.config
+        self.st = SmilesTokenizer()
+
+    def _generate(self, sequence):
+        while (sequence[-1] != 'E') and (len(self.st.tokenize(sequence)) <=
+                                         self.config.smiles_max_length):
+            x = self.st.one_hot_encode(self.st.tokenize(sequence))
+            preds = self.model.predict_on_batch(x)[0][-1]
+            next_idx = self.sample_with_temp(preds)
+            sequence += self.st.table[next_idx]
+
+        sequence = sequence[1:].rstrip('E')
+        return sequence
+
+    def sample_with_temp(self, preds):
+        streched = np.log(preds) / self.config.sampling_temp
+        streched_probs = np.exp(streched) / np.sum(np.exp(streched))
+        return np.random.choice(range(len(streched)), p=streched_probs)
+
+    def sample(self, num=1, start='G'):
+        sampled = []
+        if self.session == 'generate':
+            for _ in tqdm(range(num)):
+                sampled.append(self._generate(start))
+            return sampled
+        else:
+            from rdkit import Chem, RDLogger
+            RDLogger.DisableLog('rdApp.*')
+            while len(sampled) < num:
+                sequence = self._generate(start)
+                mol = Chem.MolFromSmiles(sequence)
+                if mol is not None:
+                    canon_smiles = Chem.MolToSmiles(mol)
+                    sampled.append(canon_smiles)
+            return sampled