From bce7ae3e66859063b38d6f7bcf200012816ea53e Mon Sep 17 00:00:00 2001
From: Jonathan Barnoud <jonathan@barnoud.net>
Date: Tue, 10 May 2016 18:54:21 +0200
Subject: [PATCH] Remove duplicates in MDP files

A user can provide a MDP file with the `-x` option. Yet, that MDP file
cannot overwrite options that are defined in the default MDP template.
Indeed, the option would the appear twice in the resulting MDP file,
which would cause Gromacs to crash.

This commit introduces option deduplication for MDP files. When an
option is defined several time, only the last definition is kept. Note
that the deduplication does not conserve the order, the comments, not
the empty lines.
---
 molmaker.py | 33 ++++++++++++++++++++++++++++-----
 1 file changed, 28 insertions(+), 5 deletions(-)

diff --git a/molmaker.py b/molmaker.py
index 0174ba1..36c0110 100755
--- a/molmaker.py
+++ b/molmaker.py
@@ -86,6 +86,29 @@ def find_exec(name, error='error', extra=""):
         return False
 
 
+def deduplicate_mdp(mdp_string):
+    """Only keep the last definition of each option.
+
+    Take the MDP file as a string, and returns the new MDP file as a string.
+    Only the last definition of each option is kept. Comments and empty lines
+    are lost in the process.
+    """
+    # Save the options in a dictionary
+    mdp_dict = {}
+    for line in mdp_string.split('\n'):
+        equal_pos = line.find('=')
+        if equal_pos != -1 and not line.lstrip().startswith(';'):
+            key = line[:equal_pos].strip()
+            value = line[equal_pos + 1:].strip()
+            mdp_dict[key] = value
+    # Format the options back to MDP format
+    key_length = max(len(key) for key in mdp_dict.keys())
+    template = '{key:<{length}} = {value}'
+    lines = (template.format(key=key, value=value, length=key_length)
+             for key, value in mdp_dict.items())
+    return '\n'.join(lines)
+
+
 # Classes
 ##########
 
@@ -213,11 +236,11 @@ def createmdp(self):
         if self.gmx: #GMX >= 5.0
             template += mdp_template_gmx5
         self.mdp = "%s.mdp" % (self.basename)
-        mdp = open (self.mdp,"w")
-        mdp.write(template)
-        if self.values.xmdp:
-            mdp.write("".join(open(self.values.xmdp).readlines()))
-        mdp.close()
+        with open (self.mdp,"w") as mdp:
+            if self.values.xmdp:
+                template += "".join(open(self.values.xmdp).readlines())
+            template = deduplicate_mdp(template)
+            mdp.write(template)
 
     def minimize(self):
         self.tpr = "%s.tpr" % (self.basename)