add sys.stdout.flush for printing

Author: Truman-Xu

sampledock/SnD/__init__.py

@@ -1,2 +1,3 @@
 from .docking import dock, sort_pose, save_pose
-from .pocket_prepare import prep_prm
+from .pocket_prepare import prep_prm
+from .sampler_util import hyperparam_loader, create_wd, smiles_to_sdfile

sampledock/SnD/docking.py

@@ -2,11 +2,13 @@
 from rdkit import Chem
 from rdkit.Chem import AllChem
 import os
+import sys
 import subprocess
 
 def dock(ligs, dock_dir, prmfile, docking_prm, npose, prefix = 'docked'):
     # ligs must be a list of file path
     print('Docking in Progress\t', end = '\r')
+    sys.stdout.flush()
     procs = []
     for i,lig in enumerate(ligs):
         output = os.path.join(dock_dir,prefix+str(i))
@@ -20,6 +22,7 @@ def dock(ligs, dock_dir, prmfile, docking_prm, npose, prefix = 'docked'):
         # makes sure the docking has completed before sorting the score
         proc.wait()
     print('Docking Complete!  \t', end = '\r')
+    sys.stdout.flush()
 
 def sort_pose(dock_dir, sort_by, prefix = None):
     # list all pose_docked.sd files
@@ -44,6 +47,7 @@ def sort_pose(dock_dir, sort_by, prefix = None):
         best_pose = sorted_poses[0]
         best_poses.append((float(best_pose.GetProp(sort_by)),best_pose.GetProp('Name'),best_pose))
     print('Docked Poses Sorted       \t', end = '\r')
+    sys.stdout.flush()
     # return the sorted tuple (ranked design based on the score of the best pose)
     return sorted(best_poses)
 

sampledock/SnD/pocket_prepare.py

@@ -1,5 +1,6 @@
 # Prepare pocket_docking.prm file for rDock
 import subprocess
+import sys
 import os
 
 def mk_dir(parent='.',target='NewTarget'):
@@ -45,6 +46,7 @@ def wrt_prm(parameter,filename='pocket_docking.prm'):
         f.writelines(line for line in parameter)
     f.close()
     print('\nDocking Parameters File Saved at: \n'+filename+'\n')
+    sys.stdout.flush()
 
 def prep_prm(receptor,ligand,recep_name,target_dir):
 

sampledock/SnD/sampler_util.py

@@ -36,6 +36,7 @@ def __init__(self,filename=None):
         FILE.close()
         print('\n'+'#'*50+'\n')
         self.vocab = [x.strip("\r\n ") for x in open(self.vocab_loc)]
+        sys.stdout.flush()
 
 def create_wd(parent_dir,target_name):
 
@@ -50,6 +51,7 @@ def create_wd(parent_dir,target_name):
     directory = os.path.abspath(directory)
     os.makedirs(directory)
     print("\nNew Directory Made:"+directory)
+    sys.stdout.flush()
     return directory
 
 def smiles_to_sdfile(smiles_list, dsgn_dir):

sampledock/__init__.py

@@ -0,0 +1,5 @@
+from .SnD.docking import dock, sort_pose, save_pose
+from .SnD.pocket_prepare import prep_prm
+from .SnD.sampler_util import hyperparam_loader, create_wd, smiles_to_sdfile
+from .jtvae.mol_tree import Vocab
+from .jtvae.jtnn_vae import JTNNVAE

sampledock/__main__.py

@@ -14,6 +14,7 @@
 
 import torch
 import os
+import sys
 import subprocess
 
 from rdkit import rdBase
@@ -83,6 +84,7 @@
         design_list = []
         try:
             print('[INFO]: Generating new designs \t', end = '\r')
+            sys.stdout.flush()
             design_list = jtvae.smiles_gen(smi, p.ndesign)
         # go to the second best candidate if the best does not give any return
         except KeyError as err: