Merge branch 'hotfix-1.0.2'

CMakeLists.txt

@@ -15,7 +15,7 @@ include(PROMOD3)
 
 set(PROMOD3_VERSION_MAJOR 1)
 set(PROMOD3_VERSION_MINOR 0)
-set(PROMOD3_VERSION_PATCH 1)
+set(PROMOD3_VERSION_PATCH 2)
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
 

modelling/pymod/_closegaps.py

@@ -14,7 +14,10 @@ import sys
 ###############################################################################
 # helper functions
 def _GetGapExtender(mhandle, actual_gap, use_scoring_extender,
-                    use_full_extender=True, max_length=-1):
+                    use_full_extender, max_length=-1):
+    # DO NOT USE full ext. with max_len = -1 as this can use LOTS of memory
+    if use_full_extender and max_length < 0:
+        raise RuntimeError("Cannot use neg. max_length with full extender!")
     # return appropriate gap extender
     actual_chain_idx = actual_gap.GetChainIndex()
     if use_scoring_extender:
@@ -32,9 +35,7 @@ def _GetGapExtender(mhandle, actual_gap, use_scoring_extender,
                                       mhandle.seqres[actual_chain_idx],
                                       max_length)
         else:
-            return ScoringGapExtender(actual_gap, 0.8,
-                                      extender_penalties,
-                                      mhandle.seqres[actual_chain_idx])
+            raise RuntimeError("Cannot use ScoringGapExtender w/o max_length.")
     else:
         if use_full_extender:
             return FullGapExtender(actual_gap,
@@ -753,9 +754,12 @@ def FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler, max_loops_to_search=
         found_loops = 0
         # currently extended gap and gap-extender
         actual_gap = gap_orig.Copy()
+        # each extension can make it at most 1 longer...
+        max_loop_len = gap_orig.length + max_extension
         actual_extender = _GetGapExtender(mhandle, actual_gap,
                                           use_scoring_extender,
-                                          use_full_extender)
+                                          use_full_extender,
+                                          max_loop_len)
         actual_chain_idx = actual_gap.GetChainIndex()
         # iteratively extend actual_gap
         ext_step = 0