This is a minor feature and bugfix release. The structure.rmsd user
function can now calculate per-atom RMSDs, structure superimposition
is now orders of magnitude faster, the relax deployment scripts have
been improved and expanded to cover other GNU/Linux systems, OpenMPI
system testing scripts have been added, and the relax information
printout has been improved. Bugfixes include that the structure.rmsd
user function now correctly calculates the RMSD value, and the
inversion recovery relaxation curve-fitting equations are now correct.
For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_4.0.3 .
The new relax versions can be downloaded from
http://www.nmr-relax.com/download.html. If binary distributions are
not yet available for your platform and you manage to compile the
binary modules, please consider contributing these to the relax
project (described in section 3.6 of the relax manual,
http://www.nmr-relax.com/manual/relax_distribution_archives.html).
The full list of changes is:
Features:
* Per-atom RMSD calculation by the structure.rmsd user function.
* Much faster superimposition of structures.
* More relax deployment scripts for Google Cloud for different
GNU/Linux distributions.
* Addition of OpenMPI testing scripts.
* Improved relax information printout.
Changes:
* Addition of the atomic boolean argument to the
structure.rmsd user function front end. This will be used to enable
the calculation of per-atom RMSDs.
* Created the Structure.test_rmsd_spins system test for
checking the per-atom RMSD calculation. This is for the new option in
the structure.rmsd user function.
* Implemented the per-atom RMSD calculation for the
structure.rmsd user function.
* Fixes for the Relax_fit.test_inversion_recovery system test.
The wrong equation was used in the calc.py Python script used to
calculate the peak intensities in the
test_suite/shared_data/curve_fitting/inversion_recovery/*.list files.
The script and Sparky files have been updated. And the I0 value in
the script and system test has been changed from 30 to -30, so that
the curves start as negative.
* Huge speed up for the superimposition of a large number of
structures. The internal structural object validate_models() method
was being called once for each structure via the selection() method
prior performing the translations, and once prior to performing the
rotations, for creating the atomic selection object. This resulted in
the _translate() internal structural object method, which converts all
input data to formatted strings, being called hundreds of millions of
times. Therefore selection() method no longer calls
validate_models(). This may speed up quite a number of internal
structure object methods when large numbers of structures are present.
* Copying deployment script of Ubuntu to a Fedora version.
This is a response to bug #25084 (https://gna.org/bugs/?25084).
* Moving fedora to redhat. Google Cloud does not offer fedora images.
* Adding deploy script for RHEL 6.
* Added initial script for testing OpenMPI.
* Making a redhat 6 deploy script, which will upgrade Python
from 2.6 to 2.7 The normal installation through yum will have Python
2.6 and only numpy 2.4. This is not good.
* Moved deploy scripts. There would probably have to be a
deploy script for each system.
* Renamed the Ubuntu deploy script.
* Adding scripts to test OpenMPI installation and deploy in redhat.
* Change to pip install command, to source Python first.
* Adding installation of matplotlib to Redhat 6, Python 2.7.
* More changing to deploy scripts.
* Small change to deploy script to build wxPython.
* More changing to deployment scripts.
* Moving test script of OpenMPI to bash version.
* Made a copy of OpenMPI test script for tcsh shell.
* Again small changes to deployment scripts.
* Changed more to OpenMPI script.
* Altering test OpenMPI script to an alias function.
* Change to bash OpenMPI test script.
* Last changes to testing of OpenMPI.
* Small change to test OpenMPI script for bash
* Back to function in bash script for OpenMPI.
* Made a deployment script for CentOS 6.
* Scons on CentOS finds python2.6 instead of python2.7
* Try to make the script for tcsh and OpenMPI working on all
versions of tcsh.
* Added the MPI version information to the mpi4py information
printout.
* Windows scons C module compilation now defaults to 32-bit.
This is because the default Python downloads are 32-bit. And many
libraries (e.g. numpy and scipy) are only pre-compiled as 32-bit.
Hence a 64-bit relax build on Windows will require a lot of custom
compilation that most users will never do.
* Added support in the information printout for Windows
versions of the 'file' program. This enables the C modules to be
identified as 32 or 64-bit, if the 'file' program is installed.
Bugfixes:
* Fix for bug #24723 (https://gna.org/bugs/?24723). This is
the bug that the mean RMSD from the structure.rmsd user function is
incorrectly calculated - it should be a quadratic mean. The quadratic
mean and quadratic standard deviation are now correctly calculated,
and the structure.test_rmsd, structure.test_rmsd_molecules, and
structure.test_rmsd_ubi system tests have been updated for the fix.
* Bug fix for the inversion recovery equations (sr #3345,
https://gna.org/support/?3345). The inversion recovery experiment was
incorrectly implemented as I(t) = Iinf - I0 * exp(-R1 * t) whereas it
should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).
relax version 4.0.3.