Made neighborhood for bead model backmapping dynamically increase if needed

beadModel.py

@@ -690,20 +690,27 @@ class beadModel():
             helixCutoff = dsDnaHelixNeighborDist if b.type[0] == 'd' else ssDnaHelixNeighborDist
             allCutoff = dsDnaAllNeighborDist if b.type[0] == 'd' else ssDnaAllNeighborDist
 
+            def positionsAreLinear(pos):
+                if len(pos) == 0: return False
+                center = np.mean(pos,axis=0)
+                cPos = pos-center
+                return np.sum( np.abs( np.linalg.eig( cPos.T.dot(cPos) )[0] ) > 1e-3 ) == 3
+
             ids = []
             attempts = 0
-            while len(ids) <= 3:
+            posOld = []
+            while len(ids) <= 3 or not positionsAreLinear(posOld):
                 if attempts > 15: raise Exception("Too many attempts to find a neighborhood for backmaping bead %d" % b.idx)
                 ids = simplerModel._getNeighborhoodIds(b, simplerModelCoords, helixCutoff, allCutoff)
+                posOld = np.array( [simplerModel.particles[i][0].initialPosition for i in ids] )
                 allCutoff *= 1.2
                 attempts+=1
-            posOld = np.array( [simplerModel.particles[i][0].initialPosition for i in ids] )
+
+            if attempts > 1:
+                print("Warning, increased allCutoff to",allCutoff)
+
             posNew = np.array( [simplerModelCoords[i] for i in ids] )
-            try:
-                trans[b.idx] = minimizeRmsd( posOld, posNew )
-            except:
-                raise Error("Crapola")
-                # print("ugly")
+            trans[b.idx] = minimizeRmsd( posOld, posNew )
 
         ## Optionally smooth orientations
             

beadModelTwist.py

@@ -762,20 +762,27 @@ class beadModelTwist():
             helixCutoff = dsDnaHelixNeighborDist if b.type[0] in ('d','O') else ssDnaHelixNeighborDist
             allCutoff = dsDnaAllNeighborDist if  b.type[0] in ('d','O') else ssDnaAllNeighborDist
 
+            def positionsAreLinear(pos):
+                if len(pos) == 0: return False
+                center = np.mean(pos,axis=0)
+                cPos = pos-center
+                return np.sum( np.abs( np.linalg.eig( cPos.T.dot(cPos) )[0] ) > 1e-3 ) == 3
+
             ids = []
             attempts = 0
-            while len(ids) <= 3:
+            posOld = []
+            while len(ids) <= 3 or not positionsAreLinear(posOld):
                 if attempts > 15: raise Exception("Too many attempts to find a neighborhood for backmaping bead %d" % b.idx)
                 ids = simplerModel._getNeighborhoodIds(b, simplerModelCoords, helixCutoff, allCutoff)
+                posOld = np.array( [simplerModel.particles[i][0].initialPosition for i in ids] )
                 allCutoff *= 1.2
                 attempts+=1
-            posOld = np.array( [simplerModel.particles[i][0].initialPosition for i in ids] )
+
+            if attempts > 1:
+                print("Warning, increased allCutoff to",allCutoff)
+
             posNew = np.array( [simplerModelCoords[i] for i in ids] )
-            try:
-                trans[b.idx] = minimizeRmsd( posOld, posNew )
-            except:
-                raise Exception("Failed to find orientation of atom %d in the coarser model" % b.idx)
-                # print("ugly")
+            trans[b.idx] = minimizeRmsd( posOld, posNew )
 
         ## Optionally smooth orientations