refactored addFluxBound 2X speedup using fbexists

Author: bgoli

src/CBModel.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBModel.py 690 2019-07-09 20:00:41Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBModel.py 691 2019-07-26 12:09:03Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -1020,6 +1020,17 @@ def addFluxBound(self, fluxbound, fbexists=None):
         Add an instantiated FluxBound object to the FBA model
 
         - *fluxbound* an instance of the FluxBound class
+        - *fbexists* [default=None] this is a list of strings which contains fluxbounds that have been added to the model, see sample code below.
+        The format of the string is 'reactionid_boundtype'
+
+        ```python
+        fbexists = []
+        for fluxbound in list_of_fluxbounds:
+            model.addFluxBound(c_, fbexists=fbexists)
+            fbexists.append("{}_{}".format(fluxbound.getReactionId(), fluxbound.getType()))
+        ```
+
+        Using the fbexists list drastically reduces the time it takes to add fluxbounds
 
         """
         assert type(fluxbound) == FluxBound, '\nERROR: requires a FluxBound object, not something of type {}'.format(type(fluxbound))
@@ -1046,7 +1057,7 @@ def addFluxBound(self, fluxbound, fbexists=None):
             else:
                 print('\"{}\" FluxBound for reaction {} exists, skipping'.format(fluxbound.is_bound, fluxbound.reaction))
         else:
-            if not (fluxbound.getReactionId(), fluxbound.getType()) in fbexists:
+            if "{}_{}".format(fluxbound.getReactionId(), fluxbound.getType()) not in fbexists:
                 fluxbound.__objref__ = weakref.ref(self)
                 self.flux_bounds.append(fluxbound)
             else:

src/CBXML.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBXML.py 685 2019-06-17 15:54:33Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBXML.py 691 2019-07-26 12:09:03Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -3662,6 +3662,7 @@ def __init__(self, pid):
                 ubcntr += 1
                 # print 'Added new upper bound', newId
     elif HAVE_FBC and FBCver == 2:
+        timeFBV2 = time.time()
         for bnd in FB_data:
             FB = CBModel.FluxBound(bnd['id'], bnd['reaction'], bnd['operation'], bnd['value'])
             FB.annotation = bnd['annotation']
@@ -3672,6 +3673,7 @@ def __init__(self, pid):
             if FB.name == None or FB.name == '':
                 FB.name = bnd['parameter']
             CONSTR.append(FB)
+        print('FluxBounds process1: {}'.format(round(time.time() - timeFBV2, 3)))
 
     if DEBUG: print('FluxBounds process: {}'.format(round(time.time() - time0, 3)))
     time0 = time.time()
@@ -3801,9 +3803,11 @@ def __init__(self, pid):
     if DEBUG: print('Reaction build: {}'.format(round(time.time() - time0, 3)))
     time0 = time.time()
     fbexists = []
+    timeFBV2 = time.time()
     for c_ in CONSTR:
         fm.addFluxBound(c_, fbexists=fbexists)
-        fbexists.append((c_.getReactionId(), c_.getType()))
+        fbexists.append("{}_{}".format(c_.getReactionId(), c_.getType()))
+    print('FluxBounds process2: {}'.format(round(time.time() - timeFBV2, 3)))
     del fbexists
     if DEBUG: print('FluxBound build: {}'.format(round(time.time() - time0, 3)))
     time0 = time.time()