Merge pull request #9 from FlorianvdEnt/master

Small fixes

IO.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 import functions as f
-import src.settings as s
+import settings as s
 
 ## Some useful objects TO DO add GLH etc.
 charged_res = {'HIS': {'HD1' : 'HID',

protprep.py

@@ -451,7 +451,7 @@ def write_qprep(self):
                         outfile.write(outline)            
 
     def run_qprep(self):
-        qprep = s.Q_DIR[self.preplocation] + 'qprep'
+        qprep = s.LOCAL['QPREP']
         options = ' < qprep.inp > qprep.out'
         # Somehow Q is very annoying with this < > input style so had to implement
         # another function that just calls os.system instead of using the preferred

scripts/generate_opls.py

@@ -3,11 +3,13 @@
 import shlex
 import os
 
-curdir = os.getcwd()
-os.chdir(curdir)
-opls2Q = '../opls2Q.py'
-generate = 'python3 ' + opls2Q
+cur_dir = os.getcwd()
+script_dir = os.path.dirname(os.path.dirname(__file__))
+
+os.chdir(cur_dir)
+opls2Q = f'{script_dir}/opls2Q.py'
 
+generate = 'python3 ' + opls2Q
 
 for pdb in glob.glob('*.pdb'):
     name = pdb.split('.')[0]

tutorials/1.QligFEP_CDK2/3.setupFEP/setup.py

@@ -5,7 +5,7 @@
 systems = ['protein', 'water']
 cnt = 0
 # Change this to where you installed QligFEP
-setupFEP = 'python $QligFEPDIR/QligFEP.py'
+setupFEP = 'python $qligfep/QligFEP.py'
 cysbond = ' '
 
 for system in systems: