Fixed bug in dealing with mda syntax

Author: Gareth Aneurin Tribello

PlumedToHTML/PlumedFormatter.py

@@ -166,6 +166,7 @@ def format(self, tokensource, outfile):
                         outfile.write('</div>')
                       # Deal with atom selections
                       elif "@" in inp :
+                        tooltip, link = "", ""
                         # Deal with residue
                         if "-" in inp : 
                             select, defs, residue = "", inp.split("-"), "" 
@@ -178,9 +179,9 @@ def format(self, tokensource, outfile):
                             else : tooltip, link = self.keyword_dict["groups"][select]["description"] + " " + residue, self.keyword_dict["groups"][select]["link"]
                         else : 
                             select = inp.strip()
-                            if select not in self.keyword_dict["groups"] : raise Exception("special group " + select + " not in special group dictionary")
-                            tooltip, link = self.keyword_dict["groups"][select]["description"], self.keyword_dict["groups"][select]["link"]
-                        outfile.write('<div class="tooltip">' + inp + '<div class="right">' + tooltip + '. <a href="' + link + '">Click here</a> for more information. <i></i></div></div>') 
+                            if select in self.keyword_dict["groups"] : tooltip, link = self.keyword_dict["groups"][select]["description"], self.keyword_dict["groups"][select]["link"]
+                        if len(tooltip)>0 : outfile.write('<div class="tooltip">' + inp + '<div class="right">' + tooltip + '. <a href="' + link + '">Click here</a> for more information. <i></i></div></div>') 
+                        else : outfile.write( html.escape(inp) )
                       else : outfile.write( html.escape(inp) )
                       nocomma = False 
             elif ttype==String or ttype==String.Double :

setup.py

@@ -6,7 +6,7 @@
 
 setuptools.setup(
      name='PlumedToHTML',  
-     version='0.96',
+     version='0.97',
      author="Gareth Tribello",
      author_email="[email protected]",
      description="A package for creating pretified HTML for PLUMED files",

tdata/groups.dat

@@ -0,0 +1,20 @@
+groupa: GROUP ...
+  ATOMS={
+    10
+    50
+    60
+    70
+    80
+    120
+  }
+...
+groupb: GROUP ...
+  ATOMS={
+    11
+    51
+    61
+    71
+    81
+    121
+  }
+...

tdata/tests.json

@@ -158,9 +158,16 @@
        "tooltips": ["DEBUG", "logRequestedAtoms", "STRIDE"],
        "badges": ["pass"]
       },
+      {
+       "input": "INCLUDE FILE=tdata/groups.dat",
+       "index": 25,
+       "actions": ["INCLUDE", "GROUP"], 
+       "tooltips": ["INCLUDE", "FILE", "GROUP", "ATOMS", "GROUP", "ATOMS"],
+       "badges": ["pass"]
+      },
       {
        "input": "#SETTINGS NREPLICAS=2\n t: TORSION ATOMS=1,2,3,4\n INCLUDE FILE=tdata/other.inc",
-       "index": 24,
+       "index": 25,
        "actions": ["TORSION", "INCLUDE", "RESTRAINT", "RESTRAINT"],
        "tooltips": ["TORSION", "ATOMS", "INCLUDE", "FILE", "RESTRAINT", "ARG", "AT", "KAPPA", "RESTRAINT", "ARG", "AT", "KAPPA"],
        "badges": ["pass"]