- MDT-users - salilab.org

compiling problems
by Martin Plutinský 20 May '15

20 May '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I have problems compiling MDT. Running scons gives me this error message: scons: Reading SConscript files ... Determining sizeof(void *)... (cached) 8 Checking whether compiler supports -fvisibility...(cached) yes Checking for GLib2 using pkg-config...(cached) found, headers in /usr/include/glib-2.0 Checking for C header file hdf5.h... (cached) yes Checking for MODELLER using 'modeller' scons option...(cached) /afs/ics.muni.cz/home/pirat/modeller9.13 Checking for SWIG >= 1.3.39: 3.0.5 found Checking for numpy... not found scons: done reading SConscript files. scons: Building targets ... gcc -pthread -o pyext/mdt_wrap.os -c -Wall -g -O3 -fPIC - -fno-strict-aliasing -g -fwrapv -O3 -Wall -Wstrict-prototypes - -I/afs/ics.muni.cz/home/pirat/hdf-1.8.10/include - -I/afs/ics.muni.cz/home/pirat/lib/glib-2.44.1/include - -I/software/python-2.7.6/gcc/include/python2.7 - -I/afs/ics.muni.cz/home/pirat/modeller9.13/src/include - -I/afs/ics.muni.cz/home/pirat/modeller9.13/src/include/x86_64-intel8 - -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include pyext/mdt_wrap.c pyext/mdt_wrap.c:3433:3: error: invalid preprocessing directive #Wrap this is my config.py, written as advised, as I have dependencies in custom directories: # modeller path modeller = '/afs/ics.muni.cz/home/pirat/modeller9.13' # SWIG and pkg-config path path = '/afs/ics.muni.cz/home/pirat/swig-3.0.5/bin:/usr/bin' # hdf5 and glib-2.44.1 includepath = '/afs/ics.muni.cz/home/pirat/hdf-1.8.10/include:/afs/ics.muni.cz/home/pirat/lib/glib-2.44.1/include' best, martin -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJVWf4YAAoJEF2Es9UpCTZT1CAH/RDiREISSTKFbmm2Chmxzmjb ZArQM8enlN38k8YpsoVWtQpJ3UMoe6mGRiPNjNQ+0CpPPHgU9/rn9RQtcLne6UMw aFEaPWXtWvrQNXsqGH4WQzl5yvLzm4s1f4J4mvBXzy+7JFiXcArldL6XJecUlojv ArU/9y2NGiGp7s3a6Zp42x6E8fPHqby9COZb0FKw1DsNHUT3MoNuD/9tC8ByfcWz ZpJMjNCTFi5VRuKWbgBDqpCmlqxDX95MKvfLIrjDSbU98ELVDxWtBAaB4PTPLwEk USXPVXop6OxvCFXwM60q4wI5Rape7cKvQFtfTw+6Q3PyBweVteY5a4hGX8aGJ8c= =gNUw -----END PGP SIGNATURE-----

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MDT 5.3 release
by Ben Webb 19 May '15

19 May '15

I just released a new version (5.3) of MDT. Briefly, the changes relative to the last release are: # Fixes to work with newer SWIG versions and the latest MODELLER API. # A new function write_statpot() can generate a Modeller statistical potential file given a suitable input table. # A new feature Cluster allows clustering of two features into a single one. # A new feature AtomTable takes as input a table of precalculated per-atom values, and can be used to implement user-defined features or to use externally-calculated properties. # To save space, the data for the MDT table itself can be compressed when writing to an HDF5 file with Table.write_hdf5(). # Certain library information (such as the mapping from feature values to bin indices, and atom or tuple class information) and information about the last scan is now written into MDT files in HDF5 format by Table.write_hdf5(). # The maximum value of bond_span_range can now be -1, to allow atom pairs that have no path of bonds between them. This is helpful to include inter-chain interactions, for example. See http://salilab.org/mdt/ for download and documentation. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Fwd: help regarding installation of MDT
by Sharif Ahmed 08 Feb '13

08 Feb '13

Hi I tried to install Modeller & MDT. But I faced some issues: As we dont have root access to the server, we cant install using *rpm* packages on that Linux server. So instead I tried to install Modeller from source which works fine at our RedHat linux server now. But then I tries to install MDT in the same way, but it depends on many other dependent libraries. I installed few of them , but couldn't manage to install rest of them due to privilege issue, so MDT can't be installed. In salilab.org, its only discussed to install MDT for linux platform, not windows. I also tried to figure out how it can be done on Windows as we have admin privilege, but no help out there for that and it seems to me that on windows MDT is already installed with Modeller as I did it from .exe but while running MDT script I got import error for library MDT. Any comments, suggestion will be highly appreciated for linux without root access or windows with admin privilege. Thanks Sharif Ahmed PhD Student University of Missouri - Columbia

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