Adding restriction_uri info.

parser/parser-charmm/CHARMMDictionary.py

@@ -784,6 +784,49 @@ def get_updateDictionary(self, defname):
             ),
         }
 
+    # Info for section_restricted_uri
+    restrictions = {
+        'number_of_restricted_uri_files' : MetaInfoMap(startpage,
+            value=int(1),
+            #autoSections=True,
+            activeInfo=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_files' : MetaInfoMap(startpage,
+            #autoSections=True,
+            activeInfo=True,
+            activeSections=['section_restricted_uri'],
+            subfunction={ 
+                'function' : self.parameter_file_name,
+                'supportDict' : self.fileDict,
+                },
+            ),
+        'restricted_uri_license' : MetaInfoMap(startpage,
+            value='CHARMM License',
+            #autoSections=True,
+            activeInfo=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_restriction' : MetaInfoMap(startpage,
+            value='any access',
+            #autoSections=True,
+            activeInfo=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_reason' : MetaInfoMap(startpage,
+            value='propriety license',
+            #autoSections=True,
+            activeInfo=True,
+            activeSections=['section_restricted_uri']
+            ),
+        'restricted_uri_issue_authority' : MetaInfoMap(startpage,
+            value='CHARMM',
+            #autoSections=True,
+            activeInfo=True,
+            activeSections=['section_restricted_uri']
+            ),
+        }
+
     # ------------------------------------------
     #   Definitions for section_frame_sequence
     # ------------------------------------------
@@ -1503,6 +1546,8 @@ def get_updateDictionary(self, defname):
         dictionary = topology
     elif defname == 'singleconfcalc':
         dictionary = singleconfcalc
+    elif defname == 'restrictions':
+        dictionary = restrictions
     elif defname == 'frameseq':
         dictionary = frameseq
     elif defname == 'frameseqend':

parser/parser-charmm/CHARMMParser.py

@@ -66,6 +66,8 @@ class CHARMMParser(SmartParser.ParserBase):
         set_Dictionaries(self)
         self.metaInfoEnv = get_metaInfo(self)
         self.secGIndexDict = {}
+        #self.metaStorageRestrict = mStore.Container('section_restricted_uri')
+        #self.metaStorageRestrict.build(jsonmetadata, 'section_restricted_uri', {})
 
         self.cachingLevelForMetaName = {
                                PARSERTAG + '_trajectory_file_detect': CachingLevel.Cache,
@@ -256,8 +258,25 @@ class CHARMMParser(SmartParser.ParserBase):
         #self.initialize_values()
         self.secRunOpen = False
         self.metaStorage.reset({'startSection' : [['section_run']]})
+        self.metaStorageRestrict.reset({'startSection' : [['section_restricted_uri']]})
         self.reset_values()
 
+    def parameter_file_name(self, filedict, itemdict):
+        """ Function to generate data for parameter files list
+        """
+        working_dir_name = os.path.dirname(os.path.normpath(os.path.abspath(self.fName)))
+        parmmeta = isMetaStrInDict("prm_file",self.fileDict)
+        filename = []
+        if parmmeta is not None:
+            if self.fileDict[parmmeta].value is not None:
+                fname = self.fileDict[parmmeta].value
+                filename.append(fname.replace(working_dir_name, '.'+os.path.sep))
+        if filename:
+            return False, filename, itemdict
+        else:
+            return False, None, itemdict
+
+
     def findUnitFileInIODict(self, theUnit):
         theUnitList=[]
         for secRun, secList in self.inputOutputCards.items():
@@ -565,7 +584,7 @@ class CHARMMParser(SmartParser.ParserBase):
                             if self.fileDict[fKey+'stream'].value is None:
                                 self.fileDict[fKey+'stream'].value = 'input coor card'
                             else:
-                                self.fileDict[fKey+'stream'].value = elf.fileDict[
+                                self.fileDict[fKey+'stream'].value = self.fileDict[
                                         fKey+'stream'].value + ', input coor card'
                             if self.fileDict[fKey+'stream'].strDict is None:
                                 self.fileDict[fKey+'stream'].strDict = self.latestTopoFile['topoStrDict']
@@ -1096,6 +1115,38 @@ class CHARMMParser(SmartParser.ParserBase):
         #self.stepcontrolDict.update({"follow" : followsteps})
         self.onOpen_section_sampling_method(backend, None, None)
         self.onClose_section_sampling_method(backend, None, None)
+        if self.topology:
+            if self.newTopo:
+                section_file_Dict = {}
+                section_file_Dict.update(self.fileDict)
+                updateDict = {
+                        'startSection' : [[PARSERTAG+'_section_control_parameters']],
+                        'dictionary'   : section_file_Dict
+                        }
+                self.metaStorage.update(updateDict)
+                self.metaStorage.updateBackend(backend.superBackend, 
+                        startsection=[PARSERTAG+'_section_control_parameters'],
+                        autoopenclose=False)
+                #updateDict = {
+                #        'startSection'   : [[PARSERTAG+'_section_input_output_files']],
+                #        'dictionary' : self.sectionInoutDict
+                #        }
+                #self.metaStorage.update(updateDict)
+                #self.metaStorage.updateBackend(backend.superBackend, 
+                #        startsection=[PARSERTAG+'_section_input_output_files'],
+                #        autoopenclose=False)
+
+                self.secRestrictGIndex = backend.superBackend.openSection("section_restricted_uri")
+                restrictionsDict = get_updateDictionary(self, 'restrictions')
+                updateDict = {
+                        'startSection' : [['section_restricted_uri']],
+                        'dictionary' : restrictionsDict
+                        }
+                self.metaStorageRestrict.update(updateDict)
+                self.metaStorageRestrict.updateBackend(backend.superBackend, 
+                        startsection=['section_restricted_uri'],
+                        autoopenclose=False)
+                backend.superBackend.closeSection("section_restricted_uri", self.secRestrictGIndex)
 
     def onOpen_section_method(self, backend, gIndex, section):
         # keep track of the latest method section
@@ -2610,7 +2661,6 @@ class CHARMMParser(SmartParser.ParserBase):
 
         cntrlNameList=getList_MetaStrInDict(self.metaDicts['cntrl'])
         filecntrlNameList=getList_MetaStrInDict(self.metaDicts['filecntrl'])
-        fileNameList=getList_MetaStrInDict(self.metaDicts['file'])
         extraNameList=getList_MetaStrInDict(self.metaDicts['extra'])
 
         self.enerOutputSubParsers = [