Merge branch 'master' of github.com:SimTk/openmm

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -890,7 +890,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
         else:
             raise Exception("Illegal value specified for implicit solvent model")
         for iAtom in range(prmtop.getNumAtoms()):
-            if gbmodel == 'OBC2':
+            if gbmodel == 'OBC2' and implicitSolventKappa == 0:
                 gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
             elif gbmodel == 'GBn2':
                 gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],

wrappers/python/simtk/openmm/app/internal/customgbforces.py

@@ -6,9 +6,9 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012 University of Virginia and the Authors.
+Portions copyright (c) 2012-2014 University of Virginia and the Authors.
 Authors: Christoph Klein, Michael R. Shirts
-Contributors: Jason M. Swails
+Contributors: Jason M. Swails, Peter Eastman
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -31,7 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 from __future__ import division
 
-from simtk.openmm import CustomGBForce
+from simtk.openmm import CustomGBForce, Discrete1DFunction
 
 d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
     2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
@@ -331,8 +331,8 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
     custom.addGlobalParameter("neckScale", 0.361825)
     custom.addGlobalParameter("neckCut", 0.68)
 
-    custom.addFunction("getd0", d0, 0, 440)
-    custom.addFunction("getm0", m0, 0, 440)
+    custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
+    custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
 
     custom.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
                                   "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
@@ -380,8 +380,8 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
     custom.addGlobalParameter("neckScale", 0.826836)
     custom.addGlobalParameter("neckCut", 0.68)
 
-    custom.addFunction("getd0", d0, 0, 440)
-    custom.addFunction("getm0", m0, 0, 440)
+    custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
+    custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
 
     custom.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
                                   "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -116,6 +116,8 @@ class PDBFile(object):
                             element = elem.lithium
                         elif upper.startswith('K'):
                             element = elem.potassium
+                        elif upper.startswith('ZN'):
+                            element = elem.zinc
                         elif( len( residue ) == 1 and upper.startswith('CA') ):
                             element = elem.calcium
                         else:

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -136,6 +136,10 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
 STEAL_OWNERSHIP = {("Platform", "registerPlatform") : [0],
                    ("System", "addForce") : [0],
                    ("System", "setVirtualSite") : [1],
+                   ("CustomNonbondedForce", "addTabulatedFunction") : [1],
+                   ("CustomGBForce", "addTabulatedFunction") : [1],
+                   ("CustomHbondForce", "addTabulatedFunction") : [1],
+                   ("CustomCompoundBondForce", "addTabulatedFunction") : [1],
 }
 
 # This is a list of units to attach to return values and method args.
@@ -179,6 +183,7 @@ UNITS = {
 ("*", "getSolventDielectric") : (None, ()),
 ("*", "getStepSize") : ("unit.picosecond", ()),
 ("*", "getSystem") : (None, ()),
+("*", "getTabulatedFunction") : (None, ()),
 ("*", "getUseDispersionCorrection") : (None, ()),
 ("*", "getTemperature") : ("unit.kelvin", ()),
 ("*", "getUseDispersionCorrection") : (None, ()),

wrappers/python/src/swig_doxygen/swig_lib/python/pythoncode.i

@@ -219,19 +219,21 @@ class State(_object):
 # Strings can cause trouble
 # as can any container that has infinite levels of containment
 def _is_string(x):
-     # step 1) String is always a container
-     # and its contents are themselves containers.
-     try:
-         first_item = iter(x).next()
-         inner_item = iter(first_item).next()
-         if first_item == inner_item:
-             return True
-         else:
-             return False
-     except TypeError:
-         return False
-     except StopIteration:
-         return False
+    # step 1) String is always a container
+    # and its contents are themselves containers.
+    try:
+        first_item = iter(x).next()
+        inner_item = iter(first_item).next()
+        if first_item == inner_item:
+            return True
+        else:
+            return False
+    except TypeError:
+        return False
+    except StopIteration:
+        return False
+    except ValueError:
+        return False
 
 def stripUnits(args):
     """