command option changed to rxdock by default

Author: Truman-Xu

sampledock/SnD/docking.py

@@ -19,7 +19,7 @@ def dock(ligs, dock_dir, prmfile, docking_prm, npose, prefix = 'docked'):
         procs.append(proc)
 
     for proc in procs:
-        # makes sure the docking has completed before sorting the score
+        # makes sure the docking has completed before this function ends
         proc.wait()
     print('Docking Complete!  \t', end = '\r')
     sys.stdout.flush()

sampledock/SnD/sampler_util.py

@@ -18,14 +18,14 @@ def __init__(self,filename=None):
         FILE = open(filename)
         print('\n'+'#'*11+' Parameters Loaded as Below '+'#'*11+'\n')
         for i, line in enumerate(FILE):
-            if line.strip('\r\n ').startswith("#") or line.isspace(): pass
+            if line.strip().startswith("#") or line.isspace(): pass
             else: 
                 try:
                     if "#" in line: 
                         line = line.split("#",1)[0]
                     name, value = line.split("=",1)
-                    name = name.strip("\r\n ")
-                    value = value.strip("\r\n ")
+                    name = name.strip()
+                    value = value.strip()
                     if value.isdigit(): value = int(value)
                     setattr(self,name,value)
                     print(name,":",value)

sampledock/__main__.py

@@ -87,8 +87,8 @@
             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:
-            print('[KeyError]',err,'is not part of the vocabulary')
+        except KeyError as key:
+            print('[KeyError]',key,'is not part of the vocabulary')
             continue
 
         if len(design_list) != 0: 

test_hyper.param

@@ -9,7 +9,7 @@ ndesign = 10                                       # number of designs to be gen
 seed_smi = C1=CC=CC=C1                             # initial seeding SMILES for the first cycle, default to benzene
 
 ############### Parameters for rDock ###################
-cavity_protocol = rbcavity -was -d -r              # cmd and option for creating pocket
+cavity_protocol = rbcavity -W -d -r                # cmd and option for creating pocket
 docking_prm = dock.prm                             # docking protocol (-p), no solvation term by default 
 npose = 10                                         # number of poses generated (-n)
 prefix = pose_docked_                              # prefix of the output files from rDock