missing files

Author: jjtapia

compartmentTree.py

@@ -0,0 +1,55 @@
+import treelib3
+
+def getCompartmentHierarchy(compartmentList):
+    '''
+    constructs a tree structure containing the 
+    compartment hierarchy excluding 2D compartments
+    @param:compartmentList
+    '''
+    def removeMembranes(tree,nodeID):
+        node = tree.get_node(nodeID)
+        if node.data == 2:
+            parent = tree.get_node(nodeID).bpointer
+            if parent == None:
+                #accounting for the case where the topmost node is a membrane
+                newRoot = tree.get_node(nodeID).fpointer[0]
+                tree.root = newRoot
+                node = tree.get_node(newRoot)
+            else:
+                tree.link_past_node(nodeID)
+                nodeID = parent
+                node = tree.get_node(nodeID)
+        for element in node.fpointer:
+            removeMembranes(tree,element)
+        
+    from copy import deepcopy
+    tree = treelib3.Tree()
+    c2 = deepcopy(compartmentList)
+    while len(c2) > 0:
+        removeList = []
+        for element in c2:
+            if c2[element][2] in ['', None]:
+                try:
+                    tree.create_node(element,element,data=c2[element][0])
+                except treelib3.tree.MultipleRootError:
+                    #there's more than one top level element
+                    tree2 = treelib3.Tree()
+                    tree2.create_node('dummyRoot','dummyRoot',data=3)
+                    tree2.paste('dummyRoot',tree)
+                    tree2.create_node(element,element,parent='dummyRoot',data=c2[element][0])
+                    tree = tree2
+                removeList.append(element)
+            elif tree.contains(c2[element][2]):
+                tree.create_node(element,element,parent=c2[element][2],data=c2[element][0])
+                removeList.append(element)
+        for element in removeList:
+            c2.pop(element)
+    removeMembranes(tree,tree.root)
+    return tree
+
+
+def getOutsideInsideCompartment(compartmentList,compartment):
+    outside = compartmentList[compartment][2]
+    for comp in compartmentList:
+        if compartmentList[comp][2] == compartment:
+            return outside, comp

grammarTester.py

@@ -0,0 +1,17 @@
+import grammarDefinition as g
+
+if __name__ == "__main__":
+    s= g.hashed_observable_section.parseString('''#REACTION_DATA_OUTPUT
+{
+   STEP = 1e-6
+    Species    Clusters  R(l!0).L(r!0,r!1).R(l!1)  // Any species with crosslinked receptors
+    Molecules  LRmotif   L(r!0).R(l!0)
+    Molecules  Lfreesite L(r)
+    Molecules  Rfreesite R(l)
+    Species    Lmonomer  L(r,r,r)
+    Species    Rmonomer  R(l,l)
+    Molecules  Ltot      L()    
+    Molecules  Rtot      R() 
+}
+''')
+    print s

nfsimClient.py

@@ -0,0 +1,26 @@
+import xmlrpclib
+import splitBNGXML
+
+
+def getCannonicalLabels(seeds):
+    pass
+
+seed, _ = splitBNGXML.extractSeedBNG('example.mdlr.xml')
+#print seed
+
+
+
+
+proxy = xmlrpclib.ServerProxy("http://localhost:8080/RPC2")
+proxy.nfsim.reset()
+#print seed
+
+initMap = {"c:a~NO_STATE!4!2,c:l~NO_STATE!3,c:l~NO_STATE!3!0,m:Lig!2!1,m:Rec!0,":1}
+proxy.nfsim.initNauty(initMap)
+#proxy.nfsim.step()
+#proxy.nfsim.init(seed)
+print '---'
+print proxy.nfsim.query(2)
+print '---'
+print proxy.nfsim.query(1)
+print proxy.nfsim.printInfo("complex")

test.py

@@ -0,0 +1,37 @@
+from pyparsing import *
+
+identifier = Word(alphas, alphanums + "_")
+plusorminus = Literal('+') | Literal('-')
+point = Literal('.')
+equal = Suppress("=")
+statement = Group(identifier + equal + (quotedString | restOfLine))
+e = CaselessLiteral('E')
+number = Word(nums)
+integer = Combine(Optional(plusorminus) + number)
+real = Combine(integer +
+               Optional(point + Optional(number)) +
+               Optional(e + integer))
+
+section_enclosure_ = Forward()
+nestedParens = nestedExpr('(', ')', content=section_enclosure_) 
+nestedBrackets = nestedExpr('[', ']', content=section_enclosure_) 
+nestedCurlies = nestedExpr('{', '}', content=section_enclosure_) 
+section_enclosure_ << (statement | Group(identifier + ZeroOrMore(identifier) + nestedCurlies) |  Group(identifier + '@' + restOfLine) | Word(alphas, alphanums + "_[]") | identifier | Suppress(',') | '@' | real)
+
+
+
+data = '''
+VIZ_OUTPUT {
+   MODE = CELLBLENDER
+   FILENAME = "./viz_data/rec_dim"
+   MOLECULES
+   {
+      NAME_LIST {ALL_MOLECULES}
+      ITERATION_NUMBERS {
+      ALL_DATA @ [1, 100, [200 TO 100000 STEP 100]]
+      }
+   }
+} '''
+
+
+print section_enclosure_.parseString(data)