Merge pull request #19 from MobleyLab/runtime-improve

Runtime improve

Author: megosato

make_absolute_top_solvent.py

@@ -1,6 +1,6 @@
 import parmed as pmd
-from SeparatedTopologies import ligand_files as lf
-from SeparatedTopologies import rot_bonds as rotbond
+import ligand_files as lf
+import rot_bonds as rotbond
 import mdtraj as md
 import numpy as np
 

make_septop.py

@@ -42,27 +42,45 @@ def combine_ligands_top(top_A, top_B, septop, ligand='LIG'):
 
     return
 
-def make_section_dictionary(text):
+def make_section_dictionaries(text):
     # Create dictionary of different section of the topology file
 
+    diclist = []
+
     dic = {}
     start_section = False
 
-    for index, line in enumerate(text):
+    index=0
+    while index < len(text):
+        line = text[index]
+
         # '[ ' marks the start of a section
         if '[ ' in line:
-            if not start_section and index == 0:
+            if not start_section: #and index == 0:
                 start_section = True
                 key = line
                 dic[key] = []
+                index+=1
+
+            # reset for next section dictionary
             else:
                 # break if already next section
-                break
+                diclist.append(dic)
+                dic = {}
+                start_section=False
+
         elif start_section:
             # append all the lines that belong to that section
             dic[key].append(line)
+            index+=1
+
+        else:
+            index+=1
+
+    # append the last section to the diclist
+    diclist.append(dic)
 
-    return dic
+    return diclist
 
 
 def create_A_and_B_state_ligand(line, A_B_state='vdwq_q', lig = 1):
@@ -239,9 +257,18 @@ def create_top(in_top, out_top, gamma, A_B_state_ligA, A_B_state_ligB, in_top_A,
     count = 0
     outtext = []
     section = 0
-    while count < end_text:
-        # Create dictionary of different sections
-        dic = make_section_dictionary(text[count:])
+
+
+    # print text does print out the proper file
+    #print(text)
+
+    diclist = make_section_dictionaries(text)
+
+    for dic in diclist:
+    # Create dictionary of different sections
+        #dic = make_section_dictionary(text[count:])
+
+        #print(dic)
 
         count += 1
 

prep_SepTop_complex.py

@@ -1,6 +1,6 @@
-from SeparatedTopologies import make_septop as ms
-from SeparatedTopologies import boresch_restraints as br
-from SeparatedTopologies import combine_coordinates as ac
+import make_septop as ms
+import boresch_restraints as br
+import combine_coordinates as ac
 import os
 import parmed as pmd
 

prep_SepTop_solvent.py

@@ -1,7 +1,7 @@
-from SeparatedTopologies import make_septop as ms
-from SeparatedTopologies import boresch_restraints as br
-from SeparatedTopologies import combine_coordinates as ac
-from SeparatedTopologies import distance_solvent as ds
+import make_septop as ms
+import boresch_restraints as br
+import combine_coordinates as ac
+import distance_solvent as ds
 import os
 import parmed as pmd
 

prep_solvent_absolute.py

@@ -1,5 +1,5 @@
 import parmed as pmd
-from SeparatedTopologies import solvent as so
+import make_absolute_top_solvent as so
 
 #Name of project directory
 dir = ''