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

wrappers/python/simtk/openmm/app/data/amoeba2013.xml

 <ForceField>
  <Info>
-  <Source>amoebapro13.prm</Source>
+  <Source>amoebapro13_5-2014.prm</Source>
   <DateGenerated>2014-05-08</DateGenerated>
   <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
  </Info>
@@ -3853,6 +3853,7 @@
   <Torsion class1="1" class2="7" class3="8" class4="22"   amp1="-2.092" angle1="0.0"   amp2="0.2092" angle2="3.14159265359"   amp3="2.4058" angle3="0.0" />
   <Torsion class1="1" class2="7" class3="8" class4="26"   amp1="1.52716" angle1="0.0"   amp2="3.72376" angle2="3.14159265359"   amp3="0.0" angle3="0.0" />
   <Torsion class1="1" class2="7" class3="8" class4="30"   amp1="-8.6818" angle1="0.0"   amp2="4.30952" angle2="3.14159265359"   amp3="0.0" angle3="0.0" />
+  <Torsion class1="1" class2="7" class3="8" class4="32"   amp1="-8.6818" angle1="0.0"   amp2="4.30952" angle2="3.14159265359"   amp3="0.0" angle3="0.0" />
   <Torsion class1="1" class2="7" class3="8" class4="36"   amp1="-1.046" angle1="0.0"   amp2="1.6736" angle2="3.14159265359"   amp3="-2.32212" angle3="0.0" />
   <Torsion class1="3" class2="7" class3="8" class4="3"   amp1="-1.905812" angle1="0.0"   amp2="7.322" angle2="3.14159265359"   amp3="-0.414216" angle3="0.0" />
   <Torsion class1="3" class2="7" class3="8" class4="7"   amp1="1.54808" angle1="0.0"   amp2="0.56484" angle2="3.14159265359"   amp3="-2.753072" angle3="0.0" />
@@ -6403,12 +6404,12 @@
   <Multipole type="150" kz="149" kx="151" c0="-0.74313" d1="-0.00259508503093" d2="0.0" d3="-0.00933362760511" q11="-0.00035125843881" q21="0.0" q22="0.000351183764538" q31="-4.85849478888e-05" q32="0.0" q33="7.4674271491e-08"  />
   <Multipole type="151" kz="149" kx="150" c0="-0.28938" d1="0.00683591118057" d2="0.0" d3="-0.00445355538749" q11="0.000455550393231" q21="0.0" q22="-0.000651047635994" q31="-1.19198805867e-05" q32="0.0" q33="0.000195497242763"  />
   <Multipole type="152" kz="151" kx="149" c0="0.14092" d1="-0.000216433478313" d2="0.0" d3="-0.00903570083667" q11="3.05231084719e-06" q21="0.0" q22="-9.89434097255e-07" q31="0.000184016073522" q32="0.0" q33="-2.06287674994e-06"  />
-  <Multipole type="153" kz="8" kx="155" c0="-0.10324" d1="0.00449324367814" d2="0.0" d3="0.0182280381271" q11="0.000281568674941" q21="0.0" q22="-0.000680338618986" q31="0.00015695598439" q32="0.0" q33="0.000398769944046"  />
-  <Multipole type="154" kz="153" kx="155" c0="0.06492" d1="-0.000548756765308" d2="0.0" d3="-0.00732910433897" q11="-3.00937314109e-05" q21="0.0" q22="0.000103367860311" q31="-0.000256422114016" q32="0.0" q33="-7.32741289005e-05"  />
-  <Multipole type="155" kz="153" kx="157" c0="-0.35416" d1="-0.00396194976071" d2="0.0" d3="0.0158165775875" q11="-0.000920481741817" q21="0.0" q22="0.000343277626044" q31="-0.000176464637817" q32="0.0" q33="0.000577204115773"  />
-  <Multipole type="156" kz="155" kx="157" c0="0.06420" d1="-0.00887271425643" d2="0.0" d3="-0.0132183174934" q11="-2.96176829301e-05" q21="0.0" q22="0.000432662729019" q31="-0.000560701101774" q32="0.0" q33="-0.000403045046089"  />
-  <Multipole type="157" kz="158" kx="-158" c0="1.05691" d1="0.0033327580597" d2="0.0" d3="-0.00149757150031" q11="0.000269602122934" q21="0.0" q22="6.58813760229e-05" q31="0.000383872426883" q32="0.0" q33="-0.000335483498957"  />
-  <Multipole type="158" kz="157" kx="158" c0="-0.89737" d1="-0.00435989102157" d2="0.0" d3="-0.00160922789132" q11="-0.000454663636257" q21="0.0" q22="0.000505283458044" q31="5.79285661091e-05" q32="0.0" q33="-5.06198217869e-05"  />
+  <Multipole type="153" kz="8" kx="155" c0="-0.10324" d1="0.00520234113765" d2="0.0" d3="0.0178713726885" q11="0.000278030981329" q21="0.0" q22="-0.000689570225799" q31="-0.000116566537797" q32="0.0" q33="0.000411539244471"  />
+  <Multipole type="154" kz="153" kx="155" c0="0.06492" d1="0.00110968460641" d2="0.0" d3="-0.0078297059783" q11="8.49606523888e-05" q21="0.0" q22="0.000112739481383" q31="-0.000115203732343" q32="0.0" q33="-0.000197700133772"  />
+  <Multipole type="155" kz="153" kx="157" c0="-0.35416" d1="-0.00479963728191" d2="0.0" d3="0.0154805500601" q11="-0.000595088603795" q21="0.0" q22="3.75704928439e-05" q31="4.107084932e-05" q32="0.0" q33="0.000557518110952"  />
+  <Multipole type="156" kz="155" kx="157" c0="0.06420" d1="-0.0107639935999" d2="0.0" d3="-0.012900281991" q11="0.000155042456183" q21="0.0" q22="0.000257887596594" q31="-0.00090896323544" q32="0.0" q33="-0.000412930052777"  />
+  <Multipole type="157" kz="158" kx="-158" c0="1.05691" d1="-0.00460278336032" d2="0.0" d3="0.000458796639848" q11="0.000320025924758" q21="0.0" q22="-0.000212102933886" q31="0.000172646915687" q32="0.0" q33="-0.000107922990872"  />
+  <Multipole type="158" kz="157" kx="158" c0="-0.89737" d1="-0.00210453775856" d2="0.0" d3="-0.00500389968443" q11="-0.000606159064544" q21="0.0" q22="0.00075670239587" q31="0.000282455431915" q32="0.0" q33="-0.000150543331326"  />
   <Multipole type="159" kz="8" kx="161" c0="-0.10668" d1="0.015685870817" d2="0.0" d3="0.0150101115217" q11="0.000372017886284" q21="0.0" q22="-0.000384143121117" q31="3.98853952601e-05" q32="0.0" q33="1.21252348333e-05"  />
   <Multipole type="160" kz="159" kx="8" c0="0.09513" d1="-0.00311526622697" d2="0.0" d3="-0.00245538224786" q11="-3.37060992942e-05" q21="0.0" q22="-1.88179164157e-05" q31="-1.55882541737e-05" q32="0.0" q33="5.252401571e-05"  />
   <Multipole type="161" kz="159" kx="163" c0="-0.23637" d1="0.0183777952771" d2="0.0" d3="0.00489647671108" q11="-0.000378383867929" q21="0.0" q22="-3.22966224198e-06" q31="-0.000491440714966" q32="0.0" q33="0.000381613530171"  />
@@ -6638,7 +6639,7 @@
   <Polarize type="119" polarizability="0.00175" thole="0.3900" pgrp1="117" pgrp2="120" pgrp3="122" />
   <Polarize type="120" polarizability="0.0015" thole="0.3900" pgrp1="119" pgrp2="121" pgrp3="122" pgrp4="124" />
   <Polarize type="121" polarizability="0.000696" thole="0.3900" pgrp1="120" />
-  <Polarize type="122" polarizability="0.00175" thole="0.3900" pgrp1="119" pgrp2="123" pgrp3="126" />
+  <Polarize type="122" polarizability="0.00175" thole="0.3900" pgrp1="119" pgrp2="120" pgrp3="123" pgrp4="126" />
   <Polarize type="123" polarizability="0.000696" thole="0.3900" pgrp1="122" />
   <Polarize type="124" polarizability="0.00175" thole="0.3900" pgrp1="120" pgrp2="125" pgrp3="126" />
   <Polarize type="125" polarizability="0.000696" thole="0.3900" pgrp1="124" />
@@ -6673,7 +6674,7 @@
   <Polarize type="154" polarizability="0.000496" thole="0.3900" pgrp1="153" />
   <Polarize type="155" polarizability="0.001334" thole="0.3900" pgrp1="156" pgrp2="157" />
   <Polarize type="156" polarizability="0.000496" thole="0.3900" pgrp1="155" />
-  <Polarize type="157" polarizability="0.00175" thole="0.3900" pgrp1="158" />
+  <Polarize type="157" polarizability="0.00175" thole="0.3900" pgrp1="155" pgrp2="158" />
   <Polarize type="158" polarizability="0.0016" thole="0.3900" pgrp1="157" />
   <Polarize type="159" polarizability="0.001334" thole="0.3900" pgrp1="160" />
   <Polarize type="160" polarizability="0.000496" thole="0.3900" pgrp1="159" />

wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml

 <ForceField>
  <Info>
-  <Source>amoebapro13.prm</Source>
+  <Source>amoebapro13_5-2014.prm</Source>
   <DateGenerated>2014-05-08</DateGenerated>
   <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
  </Info>

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -1063,7 +1063,6 @@ class TrackedList(list):
     __delitem__ = _tracking(list.__delitem__)
     append = _tracking(list.append)
     extend = _tracking(list.extend)
-    __delslice__ = _tracking(list.__delslice__)
     __setitem__ = _tracking(list.__setitem__)
 
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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

@@ -263,7 +263,7 @@ class Modeller(object):
          - positiveIon (string='Na+') the type of positive ion to add.  Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
          - negativeIon (string='Cl-') the type of negative ion to add.  Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
            that not all force fields support all ion types.
-         - ionicString (concentration=0*molar) the total concentration of ions (both positive and negative) to add.  This
+         - ionicStrength (concentration=0*molar) the total concentration of ions (both positive and negative) to add.  This
            does not include ions that are added to neutralize the system.
         """
         # Pick a unit cell size.

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -272,7 +272,7 @@ UNITS = {
 ("AmoebaPiTorsionForce",                  "getPiTorsionParameters")                        :  ( None, (None, None, None, None, None,  None, 'unit.kilojoule_per_mole')),
 
 ("AmoebaStretchBendForce",                "getNumStretchBends")                            :  ( None, ()),
-("AmoebaStretchBendForce",                "getStretchBendParameters")                      :  ( None, (None, None, None, 'unit.nanometer', 'unit.nanometer', 'unit.radian', 'unit.kilojoule_per_mole/unit.nanometer')),
+("AmoebaStretchBendForce",                "getStretchBendParameters")                      :  ( None, (None, None, None, 'unit.nanometer', 'unit.nanometer', 'unit.radian', 'unit.kilojoule_per_mole/unit.nanometer/unit.degree')),
 
 ("AmoebaTorsionTorsionForce",             "getNumTorsionTorsions")                         :  ( None, ()),
 ("AmoebaTorsionTorsionForce",             "getNumTorsionTorsionGrids")                     :  ( None, ()),