Added script(s) for making mixmaster's flux graphs prettier.

mixmaster.py just loads Mixmaster
pretty.bat is a batch/shell script you can set in mixmaster as the command used to draw graphs
prettyDot.py is the script that reads an ugly rxnpath.dot and makes a prettier rxnpath2.dot

You'll need a folder of pics/*.png alongside wherever you run dot.

Author: rwest

mixmaster.py

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+from MixMaster import MixMaster
+o =  MixMaster()
+

pretty.bat

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+python prettydot.py
+dot -T gif rxnpath2.dot > rxnpath.gif

prettyDot.py

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+# this version updated by RHW in November 2008
+"""
+make the dot file prettier
+"""
+import os, sys, re
+
+StripLineLabels=False
+if StripLineLabels:
+    print "stripping edge (line) labels"
+
+infile=file('rxnpath.dot')
+outfile=file('rxnpath2.dot','w')
+
+# replace this:
+#  s10 [ fontname="Helvetica", label="C11H23J"];
+# with this:
+#  s10 [ shapefile="mols/C11H23J.png" label="" width="1" height="1" imagescale=true fixedsize=true color="white" ];
+ 
+reSize=re.compile('size=\"5,6\"\;page=\"5,6\"')
+reNode=re.compile('(?P<node>s\d+)\ \[\ fontname=\"Helvetica\",\ label=\"(?P<label>[^\"]*)\"\]\;')
+
+for line in infile:
+    (line,changedSize)=reSize.subn('size="12,12";page="12,12"',line)
+    match=reNode.search(line)
+    if match:
+        if os.path.isfile("pics/%s.png"%match.group('label')):
+            line='%s [ image="pics/%s.png" label="" width="0.5" height="0.5" imagescale=false fixedsize=false color="none" ];\n'%(match.group('node'),match.group('label'))
+
+    # rankdir="LR" to make graph go left>right instead of top>bottom
+
+    if StripLineLabels:
+        line=re.sub('label\s*=\s*\"\s*[\d.]+\"','label=""',line)
+        
+    # change colours
+    line=re.sub('color="0.7,\ (.*?),\ 0.9"',r'color="1.0, \1, 0.7*\1"',line)
+        
+    outfile.write(line)
+
+outfile.close()
+infile.close()
+        
+print "now try:\n dot -O -Tpdf rxnpath2.dot"