there are now three startup files; ost_startup.py (former init_cl.py) initializes non-gui ost; dng_startup (former init.py) initializes dng; and gosty_startup initializes gosty (some issues remain what to put into dng_startup as opposed to gosty_startup). also, files are now properly placed into site-packages/ost (on osx and linux)

moved scene.Export to python layer to allow differentiated argument handling; more fixes to glx framebuffer memory handling

yet.

Conflicts:
	CMakeLists.txt

Conflicts:
	CMakeLists.txt

Marco Biasini authored 12 years ago and Bienchen committed 12 years ago

Mainly written by Valerio, with a few tweaks by me

parameters of RenumberChain function.

with the requested editor. Attention: Interface of RenumberChain has slightly
changed.

changed python unit tests to run with python instead of ost

Remarks
-------

Python unit tests using blast, clustalw or the compound lib where
skipped on my system. There might be still some missing imports in
these tests.

Changed in detail:
------------------

- removed DEPRECATED and unused code (slice and row pointers) in value holder
- switched from new allocatd array to std::vector
- removed explicit data initialization loop
- using size_t instead of unsigned int for memory allocation
- removed padding code
- removed try catch(...) statements
- added overflow check for big volumes
- optimized 3D index to linear index calculation
- removed physical extent for spatial domain (identical to logical extend not that padding is gone)
- switched FFT to out of place transforms

Benefits
--------

- memory for large images is correctly allocated
- if the memory can't be allocated an exception is thrown instead of crashing the program
- speed increase for FFT ca. 12% and for algorithms using direct value access (e.g. Stat) ca. 7%

Issues
-----

- FFTs are not out of place, leading to increased memory usage for c2c DFT backtransform and
  hc2r FFT/DFT backtransform (3x image size instead of 2x image size). If necessary it would
  be possible to add a fallback for these cases (i.e. catch bad_alloc for the tmp state) and
  do them in place in low memory conditions. Padding for the in-place transform could be added
  to the std::vector either at construction time or otherwise using reserve().

The feasibility check flag in the profile was ignored until now

The feasibility check flag in the profile was ignored until now

Conflicts:

	modules/io/doc/mmcif.rst

Mainly written by Valerio, with a few tweaks by me