[cctbxbb] changes to cctbx we have in ccp4

Pavel Afonine pafonine at lbl.gov
Mon Apr 4 08:31:47 PDT 2016

Hi Marcin,

> - probe and reduce are called in mmtbx through phenix wrappers
> (phenix.probe and phenix.reduce). We prefer to call them directly, but
> I guess it's not to be changed in cctbx. But after changing the name I
> also had to remove error checking in mmtbx/validation/clashscore.py
> that checks return code from phenix.reduce. Reduce itself quite often
> returns non-zero, it's just that the phenix.reduce wrapper ignores it
> and always returns 0 (probably not intentionally).

what you mean by "call them directly"?

Yes, there are multiple instances of calling these programs in mmtbx 
like this

trim = "phenix.reduce -quiet -trim -"
result = easy_run.fully_buffered(trim)

which is super-ugly! Ideally those C (or C++?) programs should be 
wrapped using boost.python and thus made available in Python.


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