Metadata restoration that was preventing tests finishing - removed for now

Author: Rob-Welch

README.md

@@ -9,6 +9,8 @@ A utility to automatically prepare structures from the PDB for molecular dynamic
 * [X] Automatically add missing atoms and fix non-standard residues with pdbfixer
 * [X] Automatically propagate metadata through to finalised structure files
 * [X] Automatically resolve steric clashes and minimise structures
+* [X] Run simple MD simulations for testing, validation and minimisation
+* [ ] Create 'morph' trajectories with metadynamics
 * [ ] AIIDA integration
 
 ## Installation

prepmd/prep.py

@@ -204,11 +204,14 @@ def in_string(substr, text): return text == None or substr in text.lower()
         print("Fixing PDB")
         fix.fix(outmodel, outmodel, fix_missing_atoms=fix_missing_atoms)
 
-    print("Restoring metadata...")
-    if ".pdb" in inmodel:
-        fix.restore_metadata_pdb(inmodel, outmodel)
-    if ".cif" in inmodel or ".mmcif" in inmodel:
-        print("Metadata restoration not implemented for mmCif (yet)")
+    # TODO: why does this output broken pdbs?
+    # also - this was due for a refactor anyway
+    # maybe dump the data into another file instead
+    #print("Restoring metadata...")
+    #if ".pdb" in inmodel:
+    #    fix.restore_metadata_pdb(inmodel, outmodel)
+    #if ".cif" in inmodel or ".mmcif" in inmodel:
+    #    print("Metadata restoration not implemented for mmCif (yet)")
 
     print("Simulating "+code)
     run.test_sim(outmodel)

prepmd/run.py

@@ -297,10 +297,29 @@ def run(pdb,
     # run simulation
     # try and resolve steric clashes with variable langevin integrator
     if minimise:
-        print("Minimising...")
-        simulation.minimizeEnergy(maxIterations=max_minimise_iterations)
-        curr_state = simulation.context.getState(
-            getPositions=True).getPositions(asNumpy=True)
+        try:
+            print("Minimising...")
+            simulation.minimizeEnergy(maxIterations=max_minimise_iterations)
+            curr_state = simulation.context.getState(
+                getPositions=True).getPositions(asNumpy=True)
+        except OpenMMException as e:
+            if integrator != "VariableLangevinIntegrator":
+                print("Minimisation blew up. "
+                      "Trying variable langevin integrator...")
+                integrator = VariableLangevinIntegrator(temperature,
+                                                        friction_coeff,
+                                                        minimise_error)
+                simulation = Simulation(modeller.topology, system, integrator)
+                simulation.context.setPositions(modeller.positions)
+                integrator = "VariableLangevinIntegrator"
+                simulation.minimizeEnergy(
+                    maxIterations=max_minimise_iterations)
+                curr_state = simulation.context.getState(
+                    getPositions=True).getPositions(asNumpy=True)
+            else:
+                print("Could not minimise even with variable langevin "
+                      "integrator.")
+                raise e
     if test_run:
         try:
             print("Running test simulation...")