[MMTK] MMTK -2.5.16 Examples test

[Mark Heslep]

I ran through all of the examples provided, had many problems and 
thought I would provide the results  here:

Linux Fedora Core 6 x86 32
MMTK-2.5.16 - compile from source, no MPI, no numpy, setup.py changed to 
find netcdf include & library on FC6
ScientificPython-2.6-6 FC6 binary package
netcdf-3.6.1-4 FC6 binary package
python-2.4.4-1
python-numeric-24.2-1 FC6 binary package
numpy-1.0.1-2  binary package
PDBVIEWER=/usr/bin/vmd      (VMD for linux 1.8.5)


Results from Examples:
-------------------------------------------------------------------------------------------------------
DNA
    construction                yes

Forcefield
    ElectricField
                C/test.py       yes
                pyrex           no - no module named Pyrex.Distutils on 
build
                python          no - NameError Scientific_vector.pyx, 
line 117 in Scientific_vector.vector.__mul__
    HarmonicOscillator
        C/test.py               yes
        pyrex/                  no - see above
        python/test.py          yes
        python/mdtest.py        no - segfault

LangevinDynamics
    setup.py build              no - ../MMTK/trajectory.h error netcdf.h 
No such file

Miscellaneous
    ccpn_data_model.py          no - ImportError: No module named 
ccp.api.molecule.MolSystem
    charge_fit.py               yes
    construct_from_pdb.py       no, pdb not found
    lattice.py                  yes. vdb viewer auto starts and looks good
    molecule_factory.py         yes
    vector_field.py             no - hangs in loop

MolecularDynamics
    argon.py                    ? never finishes but generates nc file
    md_in_python.py             yes
    protein.py                  yes
    restart.py                  yes
    solvation.py                yes
    solvent.py                  yes

MonteCarlo
    backbone.py                 no, hangs in loop

NormalModes
    brownian_modes.py           no, hangs
    calpha_modes.py             no, "Calculating 24 low freq modes" and 
hangs in loop
    constrained_modes.py        no, steps to 550 and hangs
    harmonic_force_field.py     no, BondFF.py, line23 IndexError tuple 
index out of range
    mode_analysis.py            no, ../MMTK/Utilility.py line255, 
IOError no file :'myhome/proteins/lysozyme/lysomeme.umodes' - i.e. its 
looking in the wrong place
    modes.py                    no, steps to 550 and hangs

Proteins/
    analysis_calpha.py          no, Database entry PDB/4q21.pdb.gz not found
    analysis.py                 no, same
    construction.py             ?   quits w/ no output
    rotamers.py                 no, Database entry 
'PDB//<myhome/hao/proteins/PDB/1931.pdb not found', ie looking in the 
wrong path.

Trajectories/
    calpha_trajectory.py        no, ../Scientific/IO/NetCDF.py, line 
177; IOError netcdf: no such file
    dcd_export.py               no, same
    dcd_import.py               no, Database entry PDB/rotation.pdb not 
found
    fluctuations.py             no, same as top
    snapshot.py                 ?
    traj average.py             no
    trag extraction.py          no
    view_trajectory.py          ? what format file does it want? Tried 
rotation.nc as an argument but have no animation viewer defined.
   
Visualization
    additional_objects.py       no VRML viewer installed (only vdb)
    graphics_data.py            no, hangs
---------------------------------------------------------------------------------------------------------------------

No doubt some of these had some interdependence ( run A, then B) but its 
not in the
docs and I lack the time to dig through.

Cheers,
Mark