remove pyc

wengong-jin · Jan 28, 2019 · e25a4e2 · e25a4e2
1 parent 4ed4755
commit e25a4e2
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Showing 25 changed files with 10,512 additions and 37,288 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1 +1,2 @@
 smiles/
+*.pyc
diff --git a/diff_vae_gan/drd2/ste-h300s8b1.0/LOG b/diff_vae_gan/drd2/ste-h300s8b1.0/LOG
diff --git a/diff_vae_gan/drd2/ste-h300s8b1.0/gan.iter-23 → diff_vae_gan/drd2/ste-h300s8b1.0/gan.iter-20 b/diff_vae_gan/drd2/ste-h300s8b1.0/gan.iter-23 → diff_vae_gan/drd2/ste-h300s8b1.0/gan.iter-20
diff --git a/...vae_gan/drd2/ste-h300s8b1.0/model.iter-23 → ...vae_gan/drd2/ste-h300s8b1.0/model.iter-20 b/...vae_gan/drd2/ste-h300s8b1.0/model.iter-23 → ...vae_gan/drd2/ste-h300s8b1.0/model.iter-20
diff --git a/diff_vae_gan/drd2/ste-h300s8b1.0/summary.txt b/diff_vae_gan/drd2/ste-h300s8b1.0/summary.txt
diff --git a/diff_vae_gan/results.drd2 b/diff_vae_gan/results.drd2
diff --git a/diff_vae_gan/results.qed b/diff_vae_gan/results.qed
diff --git a/diff_vae_gan/results/results.drd2 b/diff_vae_gan/results/results.drd2
diff --git a/fast_jtnn/__init__.pyc b/fast_jtnn/__init__.pyc
diff --git a/fast_jtnn/chemutils.pyc b/fast_jtnn/chemutils.pyc
diff --git a/fast_jtnn/datautils.pyc b/fast_jtnn/datautils.pyc
diff --git a/fast_jtnn/diff_vae.pyc b/fast_jtnn/diff_vae.pyc
diff --git a/fast_jtnn/jtmpn.pyc b/fast_jtnn/jtmpn.pyc
diff --git a/fast_jtnn/jtnn_dec.pyc b/fast_jtnn/jtnn_dec.pyc
diff --git a/fast_jtnn/jtnn_enc.pyc b/fast_jtnn/jtnn_enc.pyc
diff --git a/fast_jtnn/mol_tree.pyc b/fast_jtnn/mol_tree.pyc
diff --git a/fast_jtnn/mpn.pyc b/fast_jtnn/mpn.pyc
diff --git a/fast_jtnn/nnutils.pyc b/fast_jtnn/nnutils.pyc
diff --git a/fast_jtnn/scaff_gan.pyc b/fast_jtnn/scaff_gan.pyc
diff --git a/props/__init__.pyc b/props/__init__.pyc
diff --git a/props/drd2_scorer.pyc b/props/drd2_scorer.pyc
diff --git a/props/properties.pyc b/props/properties.pyc
diff --git a/props/sascorer.pyc b/props/sascorer.pyc
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,4 @@
+rdkit
+scikit-learn
+torch
+numpy
diff --git a/scripts/preprocess.py b/scripts/preprocess.py
@@ -3,8 +3,8 @@
 from multiprocessing import Pool
 
 import math, random, sys
-from optparse import OptionParser
 import cPickle as pickle
+import argparse
 
 from fast_jtnn import *
 import rdkit
@@ -34,21 +34,21 @@ def tensorize_pair(smiles_pair):
     lg = rdkit.RDLogger.logger() 
     lg.setLevel(rdkit.RDLogger.CRITICAL)
 
-    parser = OptionParser()
-    parser.add_option("-t", "--train", dest="train_path")
-    parser.add_option("-n", "--split", dest="nsplits")
-    parser.add_option("-m", "--mode", dest="mode")
-    opts,args = parser.parse_args()
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--train', required=True)
+    parser.add_argument('--mode', type=str, default='pair')
+    parser.add_argument('--ncpu', type=int, default=4)
+    args = parser.parse_args()
 
-    pool = Pool(12)
-    num_splits = int(opts.nsplits)
+    pool = Pool(args.ncpu)
 
-    if opts.mode == 'pair':
+    if args.mode == 'pair':
         #dataset contains molecule pairs
-        with open(opts.train_path) as f:
+        with open(args.train) as f:
             data = [line.strip("\r\n ").split()[:2] for line in f]
 
         all_data = pool.map(tensorize_pair, data)
+        num_splits = len(data) / 10000
 
         le = (len(all_data) + num_splits - 1) / num_splits
 
@@ -59,12 +59,13 @@ def tensorize_pair(smiles_pair):
             with open('tensors-%d.pkl' % split_id, 'wb') as f:
                 pickle.dump(sub_data, f, pickle.HIGHEST_PROTOCOL)
 
-    elif opts.mode == 'single':
+    elif args.mode == 'single':
         #dataset contains single molecules
-        with open(opts.train_path) as f:
+        with open(args.train) as f:
             data = [line.strip("\r\n ").split()[0] for line in f]
 
         all_data = pool.map(tensorize, data)
+        num_splits = len(data) / 10000
 
         le = (len(all_data) + num_splits - 1) / num_splits