Don't update model while outputting

Updating model while getting outputs results in redundant unecessary and
potentially expensive updates. Instead, assume that model is updated
externally before writing outputs. Fixes #239

pyext/src/io/__init__.py

@@ -582,7 +582,6 @@ def __init__(self,ps,label,init_coords=None):
             self.init_coords = init_coords
         self.label = label
     def get_output(self):
-        self.mdl.update()
         output = {}
         coords = [IMP.core.XYZ(p).get_coordinates() for p in self.ps]
         rmsd = IMP.algebra.get_rmsd(coords,self.init_coords)
@@ -595,7 +594,6 @@ def __init__(self,mdl):
         self.mdl = mdl
         self.rs = IMP.pmi.tools.get_restraint_set(self.mdl)
     def get_output(self):
-        self.mdl.update()
         score = self.rs.evaluate(False)
         output = {}
         output["Total_Score"] = str(score)

pyext/src/macros.py

@@ -398,6 +398,11 @@ def execute_macro(self):
         output = IMP.pmi.output.Output(atomistic=self.vars["atomistic"])
         low_temp_stat_file = globaldir + \
             self.vars["stat_file_name_suffix"] + "." + str(myindex) + ".out"
+
+        # Ensure model is updated before saving init files
+        if not self.test_mode:
+            self.model.update()
+
         if not self.test_mode:
             if self.output_objects is not None:
                 output.init_stat2(low_temp_stat_file,
@@ -526,6 +531,10 @@ def execute_macro(self):
                 score_perc=mpivs.get_percentile("score")
                 save_frame=(score_perc*100.0<=75.0)
 
+            # Ensure model is updated before saving output files
+            if save_frame or not self.test_mode:
+                self.model.update()
+
             if save_frame:
                 print("--- frame %s score %s " % (str(i), str(score)))
 
@@ -1406,6 +1415,7 @@ def set_coordinates(self,hier_name,xyz_tuple):
     def save_rmf(self,rmfname):
 
         o=IMP.pmi.output.Output()
+        self.simo.m.update()
         o.init_rmf(rmfname,[self.simo.prot])
         o.write_rmf(rmfname)
         o.close_rmf(rmfname)
@@ -1907,6 +1917,7 @@ def clustering(self,
                             IMP.core.transform(rb,transformation)
 
                     o=IMP.pmi.output.Output()
+                    self.model.update()
                     out_pdb_fn=os.path.join(dircluster,str(cnt)+"."+str(self.rank)+".pdb")
                     out_rmf_fn=os.path.join(dircluster,str(cnt)+"."+str(self.rank)+".rmf3")
                     o.init_pdb(out_pdb_fn,prot)
@@ -2112,6 +2123,7 @@ def clustering(self,
 
                     # pdb writing should be optimized!
                     o = IMP.pmi.output.Output()
+                    self.model.update()
                     o.init_pdb(dircluster + str(k) + ".pdb", prot)
                     o.write_pdb(dircluster + str(k) + ".pdb")
 
@@ -2396,6 +2408,7 @@ def save_coordinates(self,cluster,rmf_name=None,reference="Absolute", prefix="./
             rmf_name=prefix+'/'+str(cluster.cluster_id)+".rmf3"
 
         d1=self.stath1[cluster.members[0]]
+        self.model.update()
         o.init_rmf(rmf_name, [self.stath1])
         for n1 in cluster.members:
             d1=self.stath1[n1]

pyext/src/output.py

@@ -63,7 +63,10 @@ def _flatten(seq):
     return l
 
 class Output(object):
-    """Class for easy writing of PDBs, RMFs, and stat files"""
+    """Class for easy writing of PDBs, RMFs, and stat files
+
+    \note Model should be updated prior to writing outputs.
+    """
     def __init__(self, ascii=True,atomistic=False):
         self.dictionary_pdbs = {}
         self.dictionary_rmfs = {}

pyext/src/restraints/__init__.py

@@ -100,7 +100,6 @@ def get_particles_to_sample(self):
     def get_output(self):
         """Get outputs to write to stat files."""
         output = {}
-        self.m.update()
         score = self.evaluate()
         output["_TotalScore"] = str(score)
 

pyext/src/restraints/basic.py

@@ -206,7 +206,6 @@ def add_to_model(self):
         IMP.pmi.tools.add_restraint_to_model(self.m, self)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -282,7 +281,6 @@ def add_to_model(self):
         IMP.pmi.tools.add_restraint_to_model(self.m, self)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)

pyext/src/restraints/crosslinking.py

@@ -1180,8 +1180,6 @@ def set_weight(self, weight):
     def get_output(self):
         # content of the crosslink database pairs
         # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
-        self.m.update()
-
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -1406,8 +1404,6 @@ def plot_restraint(self, radius1, radius2, maxdist=50, npoints=10):
     def get_output(self):
         # content of the crosslink database pairs
         # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
-        self.m.update()
-
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -1633,8 +1629,6 @@ def plot_restraint(self, radius1, radius2, maxdist=50, npoints=10):
     def get_output(self):
         # content of the crosslink database pairs
         # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
-        self.m.update()
-
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -2114,8 +2108,6 @@ def write_db(self,filename):
     def get_output(self):
         # content of the crosslink database pairs
         # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
-        self.m.update()
-
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -2399,7 +2391,6 @@ def get_sigma(self):
         return self.sigma
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)

pyext/src/restraints/crosslinking_new.py

@@ -159,8 +159,6 @@ def create_psi(self, name):
 
 
     def get_output(self):
-        self.m.update()
-
         output = {}
         score = self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)

pyext/src/restraints/em.py

@@ -369,7 +369,6 @@ def get_restraint_set(self):
         return self.rs
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         ccc = self.gaussianEM_restraint.get_cross_correlation_coefficient()
@@ -458,7 +457,6 @@ def get_restraint_set(self):
         return self.rs
 
     def get_output(self):
-        self.mdl.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -506,7 +504,6 @@ def set_weight(self,weight):
         self.rs.set_weigth(self.weight)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight*self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)

pyext/src/restraints/em2d.py

@@ -115,7 +115,6 @@ def set_weight(self,weight):
         self.rs.set_weight(self.weight)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight*self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -236,7 +235,6 @@ def set_weight(self,weight):
         self.rs.set_weight(self.weight)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight*self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)

pyext/src/restraints/proteomics.py

@@ -84,7 +84,6 @@ def set_weight(self, weight):
         self.rs.set_weight(weight)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -163,7 +162,6 @@ def add_to_model(self):
         IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -351,8 +349,6 @@ def set_weight(self, weight):
     def get_output(self):
         # content of the crosslink database pairs
         # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
-        self.m.update()
-
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -519,8 +515,6 @@ def set_output_level(self, level="low"):
     def get_output(self):
         # content of the crosslink database pairs
         # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
-        self.m.update()
-
         output = {}
         score = self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -623,7 +617,6 @@ def set_weight(self, weight):
         self.rs.set_weight(weight)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -954,7 +947,6 @@ def get_movers(self):
 
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)

pyext/src/restraints/stereochemistry.py

@@ -147,7 +147,6 @@ def set_weight(self, weight):
         self.rs.set_weight(weight)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -278,7 +277,6 @@ def set_weight(self, weight):
         self.rs.set_weight(weight)
 
     def get_output(self):
-        self.mdl.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -347,7 +345,6 @@ def evaluate(self):
         return self.weight * self.rs.unprotected_evaluate(None)
 
     def get_output(self):
-        self.mdl.update()
         output = {}
         score = self.evaluate()
         output["_TotalScore"] = str(score)
@@ -434,7 +431,6 @@ def get_excluded_pairs(self):
         return self.pairslist
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -513,7 +509,6 @@ def get_excluded_pairs(self):
         return self.pairslist
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -614,7 +609,6 @@ def get_excluded_pairs(self):
         return self.pairslist
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -834,7 +828,6 @@ def get_distance_restraint(self, p0, p1, d0, kappa):
 
     def get_output(self):
         output = {}
-        self.m.update()
         score_angle = self.anglrs.unprotected_evaluate(None)
         score_dihers = self.dihers.unprotected_evaluate(None)
         score_bondrs = self.bondrs.unprotected_evaluate(None)
@@ -926,7 +919,6 @@ def get_excluded_pairs(self):
         return self.pairslist
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -1045,7 +1037,6 @@ def set_weight(self, weight):
         self.rs.set_weight(weight)
 
     def get_output(self):
-        self.mdl.update()
         output = {}
         bonds_score = self.weight * self.bonds_rs.unprotected_evaluate(None)
         nonbonded_score = self.weight * self.nonbonded_rs.unprotected_evaluate(None)
@@ -1193,7 +1184,6 @@ def get_excluded_pairs(self):
         return self.pairslist
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)
@@ -1263,7 +1253,6 @@ def get_excluded_pairs(self):
         return self.pairslist
 
     def get_output(self):
-        self.mdl.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["SymmetryRestraint_" + self.label] = str(score)
@@ -1338,7 +1327,6 @@ def set_weight(self, weight):
         self.rs.set_weight(weight)
 
     def get_output(self):
-        self.m.update()
         output = {}
         score = self.weight * self.rs.unprotected_evaluate(None)
         output["_TotalScore"] = str(score)