proposal to remove iotbx.shelx.from_ins
Hello, since I am new here it seems an odd proposal, but could you not remove iotbx.shelx.from_ins.from_ins since its functionality is covered much better by xray.structure.from_shelx (at least it seems to me). The following is roughly identical with the first statement being inaccurate (anisotropic vs isotropic displacements parameters) and wrong (structures containing disorder) xs0 = iotbx.shelx.from_ins.from_ins(file_name='foo.ins') fc0 = xs0.structure_factors(d_min=0.7, algorithm='direct').f_calc() xs1 = cctbx.xray.structure.from_shelx(file=open('foo.ins')) fc1 = xs1.structure_factors(d_min=0.7, algorithm='direct').f_calc() As someone who (seldom) uses cctbx I stumbled first over iotbx.shelx.from_ins and only noticed after a while that it does not handle disorder properly (problem is in ins_record.if_10_added). from_ins is used only here ./iotbx/command_line/emma.py ./cctbx/adp_restraints/tst_ext.py Where it should be possible to substitute it though I have not tested it. Cordially Mirko Scholz
Hi Mirko,
since I am new here it seems an odd proposal, but could you not remove iotbx.shelx.from_ins.from_ins since its functionality is covered much better by xray.structure.from_shelx (at least it seems to me).
You are correct that the latter supersedes the former.
from_ins is used only here
./iotbx/command_line/emma.py ./cctbx/adp_restraints/tst_ext.py
Agreed. When I committed xray.structure.from_shelx I was probably afraid to break Phenix if I had removed from_ins.from_ins. But those 2 instances you quoted are the only ones I can find anywhere in the Phenix universe. So Nat, does it make sense to remove iotbx.shelx.from_ins.from_ins entirely? Luc
Hi, I'm replying as I wrote it back in 2003: yes, it's worth removing since it's obsolete. Pavel On 6/12/12 5:42 AM, Luc Bourhis wrote:
Hi Mirko,
since I am new here it seems an odd proposal, but could you not remove iotbx.shelx.from_ins.from_ins since its functionality is covered much better by xray.structure.from_shelx (at least it seems to me). You are correct that the latter supersedes the former.
from_ins is used only here
./iotbx/command_line/emma.py ./cctbx/adp_restraints/tst_ext.py Agreed. When I committed xray.structure.from_shelx I was probably afraid to break Phenix if I had removed from_ins.from_ins. But those 2 instances you quoted are the only ones I can find anywhere in the Phenix universe.
So Nat, does it make sense to remove iotbx.shelx.from_ins.from_ins entirely?
Luc
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On Tue, Jun 12, 2012 at 7:16 AM, Pavel Afonine
I'm replying as I wrote it back in 2003: yes, it's worth removing since it's obsolete.
Okay, do you have time to remove it and run the tests? (It would be better if someone who's familiar with the code handles this, I'm still not sure what we're talking about - but I'm 100% in favor of removing obsolete and redundant code.) -Nat
I'll do it today. Pavel On 6/12/12 7:54 AM, Nat Echols wrote:
On Tue, Jun 12, 2012 at 7:16 AM, Pavel Afonine
wrote: I'm replying as I wrote it back in 2003: yes, it's worth removing since it's obsolete. Okay, do you have time to remove it and run the tests? (It would be better if someone who's familiar with the code handles this, I'm still not sure what we're talking about - but I'm 100% in favor of removing obsolete and redundant code.)
-Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
participants (4)
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Luc Bourhis
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Mirko Scholz
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Nat Echols
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Pavel Afonine