minor fixes

modelling/doc/index.rst

@@ -87,6 +87,10 @@ Modelling Pipeline
   alignment handle or an alignment handle list. Every list item is treated as a
   single chain in the final raw model.
 
+  Each alignment handle must contain exactly two sequences and the second
+  sequence is considered the template sequence, which must have a 
+  :class:`~ost.mol.EntityView` attached.
+
   This is a basic protein core modelling algorithm that copies backbone
   coordinates based on the sequence alignment. For matching residues, the
   side chain coordinates are also copied. Gaps are ignored. Hydrogen an
@@ -109,6 +113,7 @@ Modelling Pipeline
 
   :param alignment: Single alignment handle for raw model.
   :type alignment:  :class:`~ost.seq.AlignmentHandle`
+
   :param alignments: List of alignment handles for raw model with multiple chains.
   :type alignments:  :class:`~ost.seq.AlignmentList`
 
@@ -195,6 +200,7 @@ Modelling Handle class
     List of gaps in the model that could not be copied from the template. These
     gaps may be the result of insertions/deletions in the alignment or due to
     missing or incomplete backbone coordinates in the template structure.
+    Gaps of different chains are appended one after another.
 
     :type: :class:`StructuralGapList`
 

modelling/pymod/_closegaps.py

@@ -645,11 +645,9 @@ def FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler, max_loops_to_search=
 
                 mc_cooler = loop.ExponentialCooler(200,100,0.9)
             except:
-                # could throw an exception upon construction when the neighbouring
-                # residues of the stem residues are invalid
+                # something went terribly wrong...
                 ost.LogError('Failed to set up MC components')
-                # TODO - ignore for now...??
-                continue
+                raise
 
             # try to get candidates for the current loop
             try:

modelling/pymod/_pipeline.py

@@ -183,12 +183,12 @@ def BuildFromRawModel(mhandle, fragment_db=None, structure_db=None,
 
     # step 3: close remaining gaps by Monte Carlo
     if len(mhandle.gaps) > 0:
-        ost.LogInfo("Trying to fill %d gap(s) by database." % len(mhandle.gaps))
+        ost.LogInfo("Trying to fill %d gap(s) by Monte Carlo." % len(mhandle.gaps))
         _closegaps.FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler)
 
     # check if we succeeded
     if len(mhandle.gaps) > 0:
-        ost.LogWarning("Failed to close %d gaps. Returning incomplete model!" % \
+        ost.LogWarning("Failed to close %d gap(s). Returning incomplete model!" % \
                             len(mhandle.gaps))
 
     # step 4: build sidechains