Updates

Representation/scr.py

@@ -10,6 +10,7 @@ import re
 import os
 import sys
 from os import path, remove
+import glob
 
 sys.path.insert(1, '../lib/')
 import tools as tl
@@ -178,13 +179,21 @@ def rimcoresup(rsa_rec,rsa_lig,rsa_complex):
     return rim, core, support
 
 def get_scr(rec, lig, com, name):
-    #print('rec', path.basename(rec.replace('pdb', 'rsa')))
-    cmdcompl=tl.NACCESS_PATH + ' ' + com
-    os.system(cmdcompl) 
-    cmdrec=tl.NACCESS_PATH + ' ' + rec
-    os.system(cmdrec) 
-    cmdlig=tl.NACCESS_PATH + ' ' + lig
-    os.system(cmdlig)
+    
+    if tl.USE_FREESASA:
+        cmdcompl=tl.NACCESS_PATH + ' --format=rsa ' + com + ' > ' + path.basename(com.replace('pdb', 'rsa'))
+        os.system(cmdcompl) 
+        cmdrec=tl.NACCESS_PATH + ' --format=rsa ' + rec + ' > ' + path.basename(rec.replace('pdb', 'rsa'))
+        os.system(cmdrec) 
+        cmdlig=tl.NACCESS_PATH + ' --format=rsa ' + lig + ' > ' + path.basename(lig.replace('pdb', 'rsa'))
+        os.system(cmdlig)    
+    else:
+        cmdcompl=tl.NACCESS_PATH + ' ' + com
+        os.system(cmdcompl) 
+        cmdrec=tl.NACCESS_PATH + ' ' + rec
+        os.system(cmdrec) 
+        cmdlig=tl.NACCESS_PATH + ' ' + lig
+        os.system(cmdlig)
  
     # ('GLN', 'B', '44', '55.7', 'receptor')
     rim,core,support = rimcoresup(path.basename(rec.replace('pdb', 'rsa')), path.basename(lig.replace('pdb', 'rsa')), path.basename(com.replace('pdb', 'rsa')))
@@ -198,15 +207,32 @@ def get_scr(rec, lig, com, name):
         outprimcoresup.write(str((' '.join(map(str,elementsup)))+" S")+"\n") #Support
 
     outprimcoresup.close()
-    remove(path.basename(rec.replace('pdb', 'rsa')))
-    remove(path.basename(rec.replace('pdb', 'asa')))
-    remove(path.basename(rec.replace('pdb', 'log')))
     
-    remove(path.basename(lig.replace('pdb', 'rsa')))
-    remove(path.basename(lig.replace('pdb', 'asa')))
-    remove(path.basename(lig.replace('pdb', 'log')))
+    for f in glob.glob("*.rsa"):
+        try:
+            remove(f)
+        except:
+            continue
+        
+    for f in glob.glob("*.asa"):
+        try:
+            remove(f)
+        except:
+            continue
     
+    """
+    remove(path.basename(rec.replace('pdb', 'rsa')))    
+    remove(path.basename(lig.replace('pdb', 'rsa')))
     remove(path.basename(com.replace('pdb', 'rsa')))
+    remove(path.basename(rec.replace('pdb', 'asa')))
+    remove(path.basename(lig.replace('pdb', 'asa')))
     remove(path.basename(com.replace('pdb', 'asa')))
-    remove(path.basename(com.replace('pdb', 'log')))
+    """
+    
+    try:
+        remove(path.basename(rec.replace('pdb', 'log')))
+        remove(path.basename(lig.replace('pdb', 'log')))
+        remove(path.basename(com.replace('pdb', 'log')))
+    except:
+        pass
 ########################
\ No newline at end of file

Test/test.py

@@ -39,23 +39,26 @@ from sklearn.metrics import mean_squared_error, accuracy_score, roc_auc_score, r
 from sklearn.preprocessing import MinMaxScaler
 import pickle
 
+sys.path.insert(1, '../lib/')
+import tools as tl
+
 print('Your python version: {}'.format(sys.version_info.major))
 USE_TENSORFLOW_AS_BACKEND = True
-# IF YOU *DO* HAVE AN Nvidia GPU on your computer, or execute on Google COLAB, then change below to False!
-FORCE_CPU = False #False 
+ 
 if USE_TENSORFLOW_AS_BACKEND:
     os.environ['KERAS_BACKEND'] = 'tensorflow'
 else:
     os.environ['KERAS_BACKEND'] = 'theano'
-if FORCE_CPU:
+if tl.FORCE_CPU:
     os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"   # see issue #152
     os.environ["CUDA_VISIBLE_DEVICES"] = ""
 if USE_TENSORFLOW_AS_BACKEND == True:
     import tensorflow as tf
     print('Your tensorflow version: {}'.format(tf.__version__))
-    print("GPU : "+tf.test.gpu_device_name())
-    physical_devices = tf.config.experimental.list_physical_devices('GPU')
-    tf.config.experimental.set_memory_growth(physical_devices[0], True)
+    if not tl.FORCE_CPU:
+        print("GPU : "+tf.test.gpu_device_name())
+        physical_devices = tf.config.experimental.list_physical_devices('GPU')
+        tf.config.experimental.set_memory_growth(physical_devices[0], True)
 else:
     import theano
     print('Your theano version: {}'.format(theano.__version__))
@@ -67,6 +70,7 @@ logging.Logger
 seed(int(np.round(np.random.random()*10)))
 #################################################################################################
 
+"""
 def save_obj(obj, name):
     with open(name + '.pkl', 'wb') as f:
         pickle.dump(obj, f, pickle.HIGHEST_PROTOCOL)
@@ -74,6 +78,7 @@ def save_obj(obj, name):
 def load_obj(name):
     with open(name + '.pkl', 'rb') as f:
         return pickle.load(f)
+"""
 
 v_dim = 24
 
@@ -93,7 +98,7 @@ def load_map(sample_path):
             sample_path
         ],
         stdout=sys.stdout)
-    X_train, y_train, reg_type, res_pos,_,info = load_obj(sample_path.replace('.pkl.lz4',''))
+    X_train, y_train, reg_type, res_pos,_,info = tl.load_obj(sample_path.replace('.pkl.lz4',''))
     remove(sample_path.replace('.lz4',''))
     return X_train, y_train, reg_type, res_pos, info
 

lib/tools.py

@@ -24,8 +24,10 @@ import sys
 import gzip
 
 #========================================================
-#NACCESS
+FORCE_CPU = False # IF YOU *DO* HAVE AN Nvidia GPU on your computer, or execute on Google COLAB, then change this option to False!
+USE_FREESASA = True
 NACCESS_PATH='naccess'
+FreeSASA_PATH='freesasa'
 #========================================================