--- a/tests/adhoc/TestMemoryUse.cpp
+++ /dev/null
@@ -1,170 +0,0 @@
-#include "Molmodel.h"
-#include <iostream>
-
-#if defined (__linux__)
-# include <sys/sysinfo.h>
-
-#elif defined(__APPLE__)
-# include <mach/task.h>
-# include <mach/mach_init.h>
-
-#elif defined(_WINDOWS)
-# include <windows.h>
-# include "psapi.h"
-
-#else
-# include <sys/resource.h>
-#endif
-
-/// The amount of memory currently being used by this process, in bytes.
-/// By default, returns the full virtual arena, but if resident=true,
-/// it will report just the resident set in RAM (if supported on that OS).
-size_t memory_used (bool resident=false)
-{
-#if defined(__linux__)
-    // Ugh, getrusage doesn't work well on Linux.  Try grabbing info
-    // directly from the /proc pseudo-filesystem.  Reading from
-    // /proc/self/statm gives info on your own process, as one line of
-    // numbers that are: virtual mem program size, resident set size,
-    // shared pages, text/code, data/stack, library, dirty pages.  The
-    // mem sizes should all be multiplied by the page size.
-    size_t size = 0;
-    FILE *file = fopen("/proc/self/statm", "r");
-    if (file) {
-        unsigned long vm = 0;
-        fscanf (file, "%ul", &vm);  // Just need the first num: vm size
-        fclose (file);
-       size = (size_t)vm * getpagesize();
-    }
-    return size;
-
-#elif defined(__APPLE__)
-    // Inspired by:
-    // http://miknight.blogspot.com/2005/11/resident-set-size-in-mac-os-x.html
-    struct task_basic_info t_info;
-    mach_msg_type_number_t t_info_count = TASK_BASIC_INFO_COUNT;
-    task_info(current_task(), TASK_BASIC_INFO, (task_info_t)&t_info, &t_info_count);
-    size_t size = (resident ? t_info.resident_size : t_info.virtual_size);
-    return size;
-
-#elif defined(_WINDOWS)
-    // According to MSDN...
-    PROCESS_MEMORY_COUNTERS count;
-    if (GetProcessMemoryInfo (GetCurrentProcess(), &count, sizeof (count)))
-        return count.PagefileUsage;
-    else return 0;
-
-#else
-    // No idea what platform this is
-    return 0;   // Punt
-#endif
-}
-
-#include <cstring>
-#include <ctime>
-
-using namespace SimTK;
-using namespace std;
-
-void testRnaResources(int sequenceLength)
-{
-    time_t initialTime; time(&initialTime);
-    size_t initialMemFootprint = memory_used();
-
-    char resBuf[100];
-    RNA rna("", false);
-    for (int b = 0; b < sequenceLength; ++b) {
-        // itoa(b+1, resBuf, 10);
-        sprintf(resBuf, "%d", b+1);
-        rna.appendResidue(resBuf, RibonucleotideResidue::Adenylate().withPhosphodiester());
-    }
-
-    time_t compoundTime; time(&compoundTime);
-    size_t compoundMemFootprint = memory_used();
-
-    CompoundSystem system;
-    SimbodyMatterSubsystem  matter(system);
-    GeneralForceSubsystem forces(system);
-    DuMMForceFieldSubsystem dumm(system);
-    dumm.loadAmber99Parameters();
-    dumm.setAllGlobalScaleFactors(0);
-    dumm.setBondTorsionGlobalScaleFactor(1);
-    rna.assignBiotypes();
-    system.adoptCompound(rna);
-
-    time_t preModelTime; time(&preModelTime);
-    system.modelCompounds();
-    time_t postModelTime; time(&postModelTime);
-
-    State state = system.realizeTopology();
-    system.realize(state, Stage::Position);
-    VerletIntegrator integrator(system, 1e-3);
-    TimeStepper timeStepper(system, integrator);
-    timeStepper.initialize(state);
-    timeStepper.stepTo(0.020);
-
-    time_t simTime; time(&simTime);
-    size_t systemMemFootprint = memory_used();
-
-    printf("Compound: %.2f Mb/%d bases", (compoundMemFootprint - initialMemFootprint)/1e6, sequenceLength);
-    printf("\tSystem: %.2f Mb/%d bases\n", (systemMemFootprint - compoundMemFootprint)/1e6, sequenceLength);
-
-    printf("Compound: %.2f s/%d bases", difftime(preModelTime, initialTime), sequenceLength);
-    printf("\tModel: %.2f s/%d bases", difftime(postModelTime, preModelTime), sequenceLength);
-    printf("\tSimulation: %.2f s/%d bases /0.020 ps\n", difftime(simTime, postModelTime), sequenceLength);
-}
-
-void testMemoryUse() 
-{
-    // testRnaResources(1);
-    testRnaResources(10);
-    // testRnaResources(100);
-    // testRnaResources(200);
-    testRnaResources(400);
-    // testRnaResources(800);
-    // testRnaResources(1600);
-    // testRnaResources(2000);
-    // testRnaResources(2200);
-    // testRnaResources(2300);
-    // testRnaResources(3000);
-    // testRnaResources(6000);
-    // testRnaResources(6200);
-    // testRnaResources(6250);
-    // testRnaResources(6260);
-    // testRnaResources(6270);
-    // testRnaResources(6280);
-    // testRnaResources(6282);
-    // testRnaResources(6284);
-    // testRnaResources(6285);
-    // testRnaResources(6286);
-    // testRnaResources(6288);
-    // testRnaResources(6290);
-    // testRnaResources(6300);
-    // testRnaResources(6350);
-    // testRnaResources(6400);
-    // testRnaResources(6450);
-    // testRnaResources(6500);
-    // testRnaResources(6700);
-    // testRnaResources(7000);
-    // testRnaResources(8000);
-    // testRnaResources(9000);
-    // testRnaResources(10000);
-    // testRnaResources(50000);
-}
-
-int main() {
-    try {
-        testMemoryUse();
-        cout << "PASSED" << endl;
-        return 0;
-    }
-    catch (const std::exception& e)
-    {
-        printf("EXCEPTION THROWN: %s\n", e.what());
-        return 1;
-    }
-    catch (...)
-    {
-        printf("UNKNOWN EXCEPTION THROWN\n");
-    }    return 1; 
-}
--- a/tests/TestDihedrals2.cpp
+++ /dev/null
@@ -1,111 +0,0 @@
-
-#include "SimTKmolmodel.h"
-#include "molmodel/internal/Pdb.h"
-
-#include <sstream>
-
-using namespace SimTK;
-using namespace std;
-
-int main() 
-{      
-    CompoundSystem system;
-    DuMMForceFieldSubsystem dumm(system);
-    dumm.loadAmber99Parameters();
-
-    const char* uudPdbString = ""
-"ATOM      1  P     G     1     -10.655  -7.494   9.276  1.00  0.00           P  \n"
-"ATOM      2  OP1   G     1     -11.450  -7.642   8.036  1.00  0.00           O  \n"
-"ATOM      3  OP2   G     1      -9.248  -7.952   9.308  1.00  0.00           O  \n"
-"ATOM      4  O5*   G     1     -10.689  -5.944   9.713  1.00  0.00           O  \n"
-"ATOM      5  C5*   G     1     -11.850  -5.146   9.440  1.00  0.00           C  \n"
-"ATOM      6 H5*1   G     1     -12.691  -5.536   9.997  1.00  0.00           H  \n"
-"ATOM      7 H5*2   G     1     -12.064  -5.200   8.363  1.00  0.00           H  \n"
-"ATOM      8  C4*   G     1     -11.678  -3.694   9.863  1.00  0.00           C  \n"
-"ATOM      9  H4*   G     1     -12.581  -3.135   9.623  1.00  0.00           H  \n"
-"ATOM     10  O4*   G     1     -11.419  -3.590  11.266  1.00  0.00           O  \n"
-"ATOM     11  C3*   G     1     -10.481  -3.050   9.181  1.00  0.00           C  \n"
-"ATOM     12  H3*   G     1      -9.675  -3.764   9.008  1.00  0.00           H  \n"
-"ATOM     13  O3*   G     1     -10.924  -2.423   7.974  1.00  0.00           O  \n"
-"ATOM     14  C2*   G     1     -10.085  -1.969  10.167  1.00  0.00           C  \n"
-"ATOM     15  H2*   G     1      -9.021  -1.742  10.071  1.00  0.00           H  \n"
-"ATOM     16  C1*   G     1     -10.357  -2.648  11.503  1.00  0.00           C  \n"
-"ATOM     17  H1*   G     1     -10.681  -1.907  12.234  1.00  0.00           H  \n"
-"ATOM     18  O2*   G     1     -10.882  -0.790  10.004  1.00  0.00           O  \n"
-"ATOM     19 HO2'   G     1     -10.518  -0.117  10.584  1.00  0.00           H  \n"
-"ATOM     20  N9    G     1      -9.145  -3.330  11.991  1.00  0.00           N  \n"
-"ATOM     21  C8    G     1      -8.821  -4.645  11.961  1.00  0.00           C  \n"
-"ATOM     22  H8    G     1      -9.493  -5.380  11.521  1.00  0.00           H  \n"
-"ATOM     23  N7    G     1      -7.681  -4.993  12.454  1.00  0.00           N  \n"
-"ATOM     24  C5    G     1      -7.164  -3.763  12.870  1.00  0.00           C  \n"
-"ATOM     25  C4    G     1      -8.055  -2.738  12.589  1.00  0.00           C  \n"
-"ATOM     26  C6    G     1      -5.926  -3.463  13.497  1.00  0.00           C  \n"
-"ATOM     27  N3    G     1      -7.907  -1.418  12.839  1.00  0.00           N  \n"
-"ATOM     28  C2    G     1      -6.740  -1.143  13.429  1.00  0.00           C  \n"
-"ATOM     29  N1    G     1      -5.797  -2.102  13.744  1.00  0.00           N  \n"
-"ATOM     30  H1    G     1      -4.939  -1.812  14.187  1.00  0.00           H  \n"
-"ATOM     31  N2    G     1      -6.432   0.114  13.748  1.00  0.00           N  \n"
-"ATOM     32  H21   G     1      -5.549   0.320  14.193  1.00  0.00           H  \n"
-"ATOM     33  H22   G     1      -7.081   0.860  13.544  1.00  0.00           H  \n"
-"ATOM     34  O6    G     1      -5.036  -4.227  13.814  1.00  0.00           O  \n"
-"END";
-
-    const char* uudPdbString2 = ""
-"ATOM      5  C5*   G     1       0.000   1.000   0.000  1.00  0.00           C  \n"
-"ATOM      8  C4*   G     1       0.000   0.000   0.000  1.00  0.00           C  \n"
-"ATOM     10  O4*   G     1       1.000   0.000   0.000  1.00  0.00           O  \n"
-"ATOM     11  C3*   G     1       0.000   0.000   1.000  1.00  0.00           C  \n"
-"END";
-
-    // std::ifstream inFileStream( "1UUD.pdb"); 
-    std::istringstream inFileStream(uudPdbString);
-
-    PdbStructure pdbStructure(inFileStream);
-    RNA myRNA("G");// GGC");
-
-    Compound::AtomTargetLocations atomTargets = myRNA.createAtomTargets(pdbStructure);
-
-    //for (Compound::BondIndex bondIx(0); bondIx < myRNA.getNumBonds(); ++bondIx) 
-    //{
-    //    myRNA.setBondMobility(BondMobility::Rigid, bondIx);
-    //}
-
-    // Four steps to a perfect match
-    myRNA.matchDefaultAtomChirality(atomTargets);
-    myRNA.matchDefaultBondLengths(atomTargets);
-    myRNA.matchDefaultBondAngles(atomTargets);
-    myRNA.matchDefaultDihedralAngles(atomTargets);
-    myRNA.matchDefaultTopLevelTransform(atomTargets);
-
-    Real residual = myRNA.getTransformAndResidual(atomTargets).residual;
-    Transform transform = myRNA.getTransformAndResidual(atomTargets).transform;
-
-    cout << "Transform = " << transform << endl;
-
-    cout << "Residual = " << residual << endl;
-
-    myRNA.writeDefaultPdb(std::cout);
-
-    // Make sure H3* atom is within 0.1 Angstrom of target location
-    Vec3 finalLocH3 = myRNA.getTopLevelTransform() * myRNA.calcDefaultAtomLocationInCompoundFrame("0/H3*");
-    Vec3 initialLocH3 = 0.10 * Vec3(-9.675,  -3.764,   9.008);
-    Vec3 errVec = finalLocH3 - initialLocH3;
-    Real error = std::sqrt( dot(errVec, errVec) );
-
-    if (error < 0.01) 
-    {
-        cout << "PASSED" << endl;
-
-        return 0;
-    }
-
-    else 
-    {
-        cout << "FAILED" << endl;    
-        cerr << "Initial H3* location was " << initialLocH3 << endl;
-        cerr << "Final H3* location was " << finalLocH3 << endl;
-
-        return 1;
-    }
-}
-
--- a/tests/TestLoadPdb.cpp
+++ /dev/null
@@ -1,220 +0,0 @@
-
-#include "molmodel/internal/Compound.h"
-
-#include "SimTKmolmodel.h"
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <ctime>
-
-using namespace SimTK;
-using namespace std;
-
-void testExactMatch(const std::string& pdbFileName) 
-{
-    time_t startTime = time(NULL);
-    
-    // In order for Biotypes to work correctly, 
-    // amber99 parameters must be loaded first?
-    CompoundSystem system;
-    SimbodyMatterSubsystem matter(system);
-    DuMMForceFieldSubsystem forces(system);
-    forces.loadAmber99Parameters();
-
-    cout << "Loading Structure from File..." << endl;
-    std::ifstream pdbInputStream(pdbFileName.c_str());
-    assert(pdbInputStream.is_open());
-    
-    // Check speed of various pdb file matching operations
-    PdbStructure inputPdbStructure(pdbInputStream);
-    pdbInputStream.close();
-    
-    time_t endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Creating internal coordinate model..." << endl;
-    RNA rna(inputPdbStructure);
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Noting target atom locations..." << endl;
-    Compound::AtomTargetLocations atomTargets = 
-            rna.createAtomTargets(inputPdbStructure);
-    cout << atomTargets.size() << " matches found" << endl;
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching chirality..." << endl;
-    rna.matchDefaultAtomChirality(atomTargets, 0.01);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching bond angles..." << endl;
-    rna.matchDefaultBondAngles(atomTargets);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching bond lengths..." << endl;
-    rna.matchDefaultBondLengths(atomTargets);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching dihedral angles..." << endl;
-    rna.matchDefaultDihedralAngles(atomTargets, Compound::DistortPlanarBonds);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching top level transform..." << endl;
-    rna.matchDefaultTopLevelTransform(atomTargets);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Creating simbody system..." << endl;
-    system.adoptCompound(rna);
-    rna.assignBiotypes();
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Creating multibody model..." << endl;
-    system.modelCompounds();
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Writing PDB file" << endl;
-    PdbStructure outputPdbStructure(rna);
-    std::ofstream pdbOutputStream("test1.pdb");
-    outputPdbStructure.write(pdbOutputStream);
-    pdbOutputStream.close();
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Done." << endl;
-}
-
-void testIdealizedMatch(const std::string& pdbFileName) 
-{
-    time_t startTime = time(NULL);
-    
-    // In order for Biotypes to work correctly, 
-    // amber99 parameters must be loaded first?
-    CompoundSystem system;
-    SimbodyMatterSubsystem matter(system);
-    DuMMForceFieldSubsystem forces(system);
-    forces.loadAmber99Parameters();
-
-    cout << "Loading Structure from File..." << endl;
-    std::ifstream pdbInputStream(pdbFileName.c_str());
-    assert(pdbInputStream.is_open());
-    
-    // Check speed of various pdb file matching operations
-    PdbStructure inputPdbStructure(pdbInputStream);
-    pdbInputStream.close();
-    
-    time_t endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Creating internal coordinate model..." << endl;
-    RNA rna(inputPdbStructure);
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Noting target atom locations..." << endl;
-    Compound::AtomTargetLocations atomTargets = 
-            rna.createAtomTargets(inputPdbStructure);
-    cout << atomTargets.size() << " matches found" << endl;
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching chirality..." << endl;
-    rna.matchDefaultAtomChirality(atomTargets, 90*Deg2Rad);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching dihedral angles..." << endl;
-    rna.matchDefaultDihedralAngles(atomTargets, Compound::KeepPlanarBonds);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Matching top level transform..." << endl;
-    rna.matchDefaultTopLevelTransform(atomTargets);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Final fitting..." << endl;
-    rna.fitDefaultConfiguration(atomTargets, 0.005);
-
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Creating simbody system..." << endl;
-    system.adoptCompound(rna);
-    rna.assignBiotypes();
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Creating multibody model..." << endl;
-    system.modelCompounds();
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Writing PDB file" << endl;
-    PdbStructure outputPdbStructure(rna);
-    std::ofstream pdbOutputStream("test2.pdb");
-    outputPdbStructure.write(pdbOutputStream);
-    pdbOutputStream.close();
-    
-    endTime = time(NULL);
-    cout << endTime - startTime << " s elapsed time" << endl;
-    startTime = endTime;
-    
-    cout << "Done." << endl;
-}
-
-int main(int argc, char *argv[]) 
-{
-    // PDB file name is required as argument
-    assert(argc > 1);
-    
-    const std::string pdbFileName(argv[1]);
-    
-    testExactMatch(pdbFileName);
-    testIdealizedMatch(pdbFileName);
-}
-
--- a/tests/TestPdb.cpp
+++ /dev/null
@@ -1,195 +0,0 @@
-/* -------------------------------------------------------------------------- *
- *                      SimTK Core: SimTK Simbody(tm)                         *
- * -------------------------------------------------------------------------- *
- * This is part of the SimTK Core biosimulation toolkit originating from      *
- * 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) 2006-7 Stanford University and the Authors.         *
- * Authors: Christopher Bruns                                                 *
- * Contributors:                                                              *
- *                                                                            *
- * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation  *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
- * and/or sell copies of the Software, and to permit persons to whom the      *
- * Software is furnished to do so, subject to the following conditions:       *
- *                                                                            *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software.                        *
- *                                                                            *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
- * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
- * -------------------------------------------------------------------------- */
-
-#include "SimTKmolmodel.h"
-#include "molmodel/internal/Pdb.h"
-
-#include <sstream>
-
-using namespace SimTK;
-using namespace std;
-
-#define ASSERT(cond) {SimTK_ASSERT_ALWAYS(cond, "Assertion failed");}
-
-void testInputMatchesOutput() {
-    // A very small protein
-    String inputPdb = ""\
-    "ATOM      1  N   HIS    19      28.165  29.227  23.618  1.00 91.78           N\n"
-    "ATOM      2  CA  HIS    19      27.004  29.173  22.731  1.00 91.74           C\n"
-    "ATOM      3  C   HIS    19      26.321  27.818  22.666  1.00 81.05           C\n"
-    "ATOM      4  O   HIS    19      25.105  27.739  22.805  1.00 89.56           O\n"
-    "ATOM      5  CB  HIS    19      27.248  29.629  21.270  1.00 98.21           C\n"
-    "ATOM      6  CG  HIS    19      27.954  30.936  21.082  1.00100.00           C\n"
-    "ATOM      7  ND1 HIS    19      28.852  31.112  20.015  1.00100.00           N\n"
-    "ATOM      8  CD2 HIS    19      27.882  32.111  21.798  1.00100.00           C\n"
-    "ATOM      9  CE1 HIS    19      29.310  32.368  20.116  1.00100.00           C\n"
-    "ATOM     10  NE2 HIS    19      28.753  32.997  21.176  1.00100.00           N\n"
-    "ATOM     11  N   SER    20      27.057  26.778  22.303  1.00 58.48           N\n"
-    "ATOM     12  CA  SER    20      26.412  25.501  22.190  1.00 45.35           C\n"
-    "ATOM     13  C   SER    20      26.089  24.909  23.558  1.00 30.40           C\n"
-    "ATOM     14  O   SER    20      26.808  25.067  24.542  1.00 29.60           O\n"
-    "ATOM     15  CB  SER    20      27.206  24.513  21.344  1.00 49.69           C\n"
-    "ATOM     16  OG  SER    20      26.466  23.310  21.049  1.00 22.13           O\n"
-    "TER\n"
-    "END\n";
-
-    istringstream inStream(inputPdb);
-    PdbStructure pdbStructure(inStream);
-
-    ostringstream outStream;
-    pdbStructure.write(outStream);
-
-    ASSERT(inputPdb == outStream.str());
-}
-
-
-// SimTK core bug 653
-// Avoid distorting input geometry
-void testMatchDefaultBreaksPlanarity() {
-    // A very small RNA
-    String pdbString = ""\
-    "ATOM      1  O5' A       1       0.000   0.000   0.000  1.00  0.00           O\n"
-    "ATOM      2  C5' A       1      -0.731   1.221   0.000  1.00  0.00           C\n"
-    "ATOM      3  H5' A       1      -0.380   1.863  -0.837  1.00  0.00           H\n"
-    "ATOM      4 H5'' A       1      -0.570   1.749   0.965  1.00  0.00           H\n"
-    "ATOM      5  C4' A       1      -2.202   0.927  -0.173  1.00  0.00           C\n"
-    "ATOM      6  H4' A       1      -2.775   1.880  -0.152  1.00  0.00           H\n"
-    "ATOM      7  O4' A       1      -2.416   0.262  -1.447  1.00  0.00           O\n"
-    "ATOM      8  C3' A       1      -2.649  -0.071   0.888  1.00  0.00           C\n"
-    "ATOM      9  H3' A       1      -1.861  -0.843   1.026  1.00  0.00           H\n"
-    "ATOM     10  O3' A       1      -2.867   0.610   2.118  1.00  0.00           O\n"
-    "ATOM     11  C2' A       1      -3.982  -0.569   0.339  1.00  0.00           C\n"
-    "ATOM     12  H2' A       1      -4.164  -1.607   0.693  1.00  0.00           H\n"
-    "ATOM     13  C1' A       1      -3.707  -0.583  -1.164  1.00  0.00           C\n"
-    "ATOM     14  H1' A       1      -4.620  -0.263  -1.711  1.00  0.00           H\n"
-    "ATOM     15  O2' A       1      -4.991   0.378   0.624  1.00  0.00           O\n"
-    "ATOM     16 HO2' A       1      -5.049   0.485   1.576  1.00  0.00           H\n"
-    "ATOM     17  N9  A       1      -3.416  -1.965  -1.639  1.00  0.00           N\n"
-    "ATOM     18  C8  A       1      -2.272  -2.678  -1.387  1.00  0.00           C\n"
-    "ATOM     19  H8  A       1      -1.653  -2.510  -0.518  1.00  0.00           H\n"
-    "ATOM     20  N7  A       1      -2.001  -3.578  -2.293  1.00  0.00           N\n"
-    "ATOM     21  C5  A       1      -3.039  -3.450  -3.209  1.00  0.00           C\n"
-    "ATOM     22  C4  A       1      -3.909  -2.469  -2.818  1.00  0.00           C\n"
-    "ATOM     23  C6  A       1      -3.333  -4.123  -4.406  1.00  0.00           C\n"
-    "ATOM     24  N3  A       1      -5.033  -2.063  -3.454  1.00  0.00           N\n"
-    "ATOM     25  C2  A       1      -5.370  -2.657  -4.589  1.00  0.00           C\n"
-    "ATOM     26  N1  A       1      -4.448  -3.699  -5.015  1.00  0.00           N\n"
-    "ATOM      1  H2  A       1      -6.262  -2.352  -5.114  1.00  0.00           H\n"
-    "ATOM     28  N6  A       1      -2.564  -5.104  -4.896  1.00  0.00           N\n"
-    "ATOM     29  H61 A       1      -1.732  -5.389  -4.399  1.00  0.00           H\n"
-    "ATOM     30  H62 A       1      -2.817  -5.558  -5.761  1.00  0.00           H\n"
-    "ATOM     31  P   A       1       1.610   0.000   0.000  1.00  0.00           P\n"
-    "ATOM     32  OP1 A       1       2.103   0.698   1.208  1.00  0.00           O\n"
-    "ATOM     33  OP2 A       1       2.103   0.698  -1.208  1.00  0.00           O\n"
-    "ATOM     34  OP3 A       1       2.103  -1.395   0.000  1.00  0.00           O\n";
-    istringstream pdbStream(pdbString);
-	PdbStructure pdbStructure(pdbStream);
-
-    // 1) First reproduce undesired behavior
-    RNA mol1("A");
-	Compound::AtomTargetLocations atomTargets = mol1.createAtomTargets(pdbStructure); 
-
-	mol1.matchDefaultAtomChirality(atomTargets);
-    mol1.matchDefaultBondLengths(atomTargets);
-    mol1.matchDefaultBondAngles(atomTargets);
-    mol1.matchDefaultDihedralAngles(atomTargets, Compound::DistortPlanarBonds);
-    mol1.matchDefaultTopLevelTransform(atomTargets);
-
-    // Most distorted part in problem report is distance between atoms N1 and C2
-    const ResidueInfo& res1 = mol1.getResidue( ResidueInfo::Index(0) );
-    Vec3 atomN1Pos = mol1.calcDefaultAtomFrameInCompoundFrame(res1.getAtomIndex("N1")).p();
-    Vec3 atomC2Pos = mol1.calcDefaultAtomFrameInCompoundFrame(res1.getAtomIndex("C2")).p();
-    Real bondLength = (atomN1Pos - atomC2Pos).norm();
-
-    ASSERT(bondLength > 0.20); // distorted
-
-
-    // 2) Repair with extra parameter on matchDefaultAtomChirality
-
-    RNA mol2("A");
-	atomTargets = mol2.createAtomTargets(pdbStructure); 
-
-	mol2.matchDefaultAtomChirality(atomTargets, 0.20);
-    mol2.matchDefaultBondLengths(atomTargets);
-    mol2.matchDefaultBondAngles(atomTargets);
-    mol2.matchDefaultDihedralAngles(atomTargets, Compound::DistortPlanarBonds);
-    mol2.matchDefaultTopLevelTransform(atomTargets);
-
-    // Most distorted part in problem report is distance between atoms N1 and C2
-    const ResidueInfo& res2 = mol2.getResidue( ResidueInfo::Index(0) );
-    atomN1Pos = mol2.calcDefaultAtomFrameInCompoundFrame(res2.getAtomIndex("N1")).p();
-    atomC2Pos = mol2.calcDefaultAtomFrameInCompoundFrame(res2.getAtomIndex("C2")).p();
-    bondLength = (atomN1Pos - atomC2Pos).norm();
-
-    cout << "bondLength = " << bondLength << endl;
-    mol2.writeDefaultPdb(cout);
-
-    ASSERT(bondLength < 0.20); // not distorted
-
-
-    // 3) Repair by not setting torsion of bonded planar atoms
-
-    RNA mol3("A");
-	atomTargets = mol3.createAtomTargets(pdbStructure); 
-
-	mol3.matchDefaultAtomChirality(atomTargets);
-    mol3.matchDefaultBondLengths(atomTargets);
-    mol3.matchDefaultBondAngles(atomTargets);
-    mol3.matchDefaultDihedralAngles(atomTargets, Compound::KeepPlanarBonds);
-    mol3.matchDefaultTopLevelTransform(atomTargets);
-
-    // Most distorted part in problem report is distance between atoms N1 and C2
-    const ResidueInfo& res3 = mol3.getResidue( ResidueInfo::Index(0) );
-    atomN1Pos = mol3.calcDefaultAtomFrameInCompoundFrame(res3.getAtomIndex("N1")).p();
-    atomC2Pos = mol3.calcDefaultAtomFrameInCompoundFrame(res3.getAtomIndex("C2")).p();
-    bondLength = (atomN1Pos - atomC2Pos).norm();
-
-    ASSERT(bondLength < 0.20); // not distorted
-}
-
-int main() {
-    try {
-        testInputMatchesOutput();
-        testMatchDefaultBreaksPlanarity();
-    }
-    catch (const std::exception& e) {
-        printf("EXCEPTION THROWN: %s\n", e.what());
-        return 1;
-    }
-    catch (...) {
-        printf("UNKNOWN EXCEPTION THROWN\n");
-        return 1;
-    }    
-    
-    cout << "Done" << endl;
-    return 0;
-}
-