Merge pull request #107 from PaddlePaddle/demo

comments

Author: luohongyu

pahelix/model_zoo/sd_vae_model.py

@@ -35,9 +35,7 @@
 
 
 class StateDecoder(nn.Layer):
-    """
-    Description:
-        encoder
+    """encoder
 
     Args:
         max_len: the maximun length of input sequemce
@@ -79,9 +77,7 @@ def forward(self, z, n_steps=None):
 
 
 class PerpCalculator(nn.Layer):
-    """
-    Description:
-        loss type
+    """loss type
 
     Args:
         true_binary: one-hot, with size=time_steps x bsize x DECISION_DIM
@@ -93,7 +89,7 @@ def __init__(self):
 
     def forward(self, true_binary, rule_masks, raw_logits):
         """
-        tbd
+        forward
         """
         if cmd_args.loss_type == 'binary':
             exp_pred = paddle.exp(raw_logits) * rule_masks
@@ -124,9 +120,7 @@ def forward(self, true_binary, rule_masks, raw_logits):
 
 
 class MyPerpLoss(nn.Layer):
-    """
-    Description:
-        perplexity loss
+    """perplexity loss
     """
     def __init__(self):
         super(MyPerpLoss, self).__init__()
@@ -154,9 +148,7 @@ def forward(self, true_binary, rule_masks, input_logits):
 
 
 class CNNEncoder(nn.Layer):
-    """
-    Description:
-        the encoder
+    """the encoder
 
     Args:
         max_len: the maximum length of input 
@@ -215,9 +207,7 @@ def get_encoder(model_config):
 
 
 class MolVAE(nn.Layer):
-    """
-    Description:
-        The Mol VAE model
+    """The Mol VAE model
 
     Args:
         model_config: the model parameters

pahelix/model_zoo/seq_vae_model.py

@@ -28,9 +28,7 @@
 
 
 class VAE(nn.Layer):
-    """
-    Description:
-        The sequence VAE model
+    """The sequence VAE model
 
     Args:
         vocab: the vocab object.
@@ -148,15 +146,13 @@ def forward_decoder(self, x, z):
         return recon_loss
 
     def sample_z_prior(self, n_batch):
-        """
-        Description:
-            Sampling z ~ p(z) = N(0, I)
+        """Sampling z ~ p(z) = N(0, I)
 
         Args:
             n_batch: number of batches
-        
-        Returns:
-            (n_batch, d_z) of floats, sample of latent z.
+
+        Returns: 
+        (n_batch, d_z) of floats, sample of latent z
         """
         return paddle.randn([n_batch, self.q_mu.weight.shape[1]])
 
@@ -170,9 +166,7 @@ def tensor2string(self, tensor):
         return string
 
     def sample(self, n_batch, max_len=100, z=None, temp=1.0):
-        """
-        Description:
-            Generating n_batch samples in eval mode (`z` could be
+        """Generating n_batch samples in eval mode (`z` could be
             not on same device)
 
         Args:

pahelix/utils/metrics/molecular_generation/metrics_.py

@@ -47,10 +47,10 @@ def get_all_metrics(gen, k=None, n_jobs=1,
                     test=None, test_scaffolds=None,
                     ptest=None, ptest_scaffolds=None,
                     train=None):
-    """
-    Description:
-        Computes all available metrics between test (scaffold test)
+    """Computes all available metrics between test (scaffold test)
         and generated sets of SMILES.
+
+    Description:
         Available metrics:
             * %valid
             * %unique@k
@@ -167,9 +167,7 @@ def get_all_metrics(gen, k=None, n_jobs=1,
 
 def compute_intermediate_statistics(smiles, n_jobs=1, device='cpu',
                                     batch_size=512, pool=None):
-    """
-    Description:
-        The function precomputes statistics such as mean and variance for FCD, etc.
+    """ The function precomputes statistics such as mean and variance for FCD, etc.
         It is useful to compute the statistics for test and scaffold test sets to
             speedup metrics calculation.
     """
@@ -198,9 +196,7 @@ def compute_intermediate_statistics(smiles, n_jobs=1, device='cpu',
 
 
 def fraction_passes_filters(gen, n_jobs=1):
-    """
-    Description:
-        Computes the fraction of molecules that pass filters:
+    """Computes the fraction of molecules that pass filters:
         * MCF
         * PAINS
         * Only allowed atoms ('C','N','S','O','F','Cl','Br','H')
@@ -212,9 +208,7 @@ def fraction_passes_filters(gen, n_jobs=1):
 
 def internal_diversity(gen, n_jobs=1, device='cpu', fp_type='morgan',
                        gen_fps=None, p=1):
-    """
-    Description:
-        Computes internal diversity as:
+    """Computes internal diversity as:
         1/|A|^2 sum_{x, y in AxA} (1-tanimoto(x, y))
     """
     if gen_fps is None:
@@ -224,9 +218,7 @@ def internal_diversity(gen, n_jobs=1, device='cpu', fp_type='morgan',
 
 
 def fraction_unique(gen, k=None, n_jobs=1, check_validity=True):
-    """
-    Description:
-        Computes a number of unique molecules
+    """Computes a number of unique molecules
 
     Args:
         gen: list of SMILES
@@ -248,9 +240,7 @@ def fraction_unique(gen, k=None, n_jobs=1, check_validity=True):
 
 
 def fraction_valid(gen, n_jobs=1):
-    """
-    Description:
-        Computes a number of valid molecules
+    """Computes a number of valid molecules
 
     Args:
         gen: list of SMILES