<div dir="ltr">Hi Pavel,<br><div class="gmail_extra"><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div bgcolor="#FFFFFF" text="#000000">Currently model class has three selection methods:<br>
<br>
def selection(self, selstr, optional=True):<br></div></div></div></blockquote><div>Takes selection string, returns bool selection </div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div bgcolor="#FFFFFF" text="#000000">
def select(self, selection):<br></div></div></div></blockquote><div>Takes selection (bool or iselection), applies it to self and returns selected part of model object. </div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div bgcolor="#FFFFFF" text="#000000">
def iselection(self, selstr):<br></div></div></div></blockquote><div>Same as first, but returns iselection.</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div bgcolor="#FFFFFF" text="#000000">
which is hideously confusing with zero chance to remember, and also
inconsistent with the rest. <br></div></div></div></blockquote><div>Let me disagree on the point of inconsistency with the rest. </div><div>selection and iselection functions are available with exactly same meaning for atom_selection_cache.</div><div>select is available with exact same meaning (returning part of an object) in hierarchy, af_shared_atom, flex.vec3_double, xray_structure etc which you pointed out. </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div bgcolor="#FFFFFF" text="#000000">
Can we consolidate all three into one ".select()" that would allow
taking bool or int or str? </div></div></div></blockquote><div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">No, because they are doing different things. Selection and iselection wraps atom_selection_cache functionality and not duplicating those of select() function. ".select()" function already has the described functionality.</div></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div bgcolor="#FFFFFF" text="#000000">Or you think there are philosophical
arguments against it?<br></div></div></div></blockquote><div>Yes, and practical ones as well. I'm caching atom_selection_cache inside model object, so you don't have to construct it again if you use wrappers available in model class. hierarchy.atom_selection_cache() is not a free function to the point I had to pass the cache around to avoid constructing it again to achieve measurable speedup. Especially for larger models.</div><div><br></div><div>At the very least, please use model.get_atom_selection_cache() instead of constructing it.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div><div> <br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div bgcolor="#FFFFFF" text="#000000">
<br>
Pavel<br>
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<div class="m_5786486340573780857moz-cite-prefix">On 8/16/18 15:00, CCTBX commit wrote:<br>
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<blockquote type="cite">
<tt>Repository : <a class="m_5786486340573780857moz-txt-link-freetext">ssh://g18-sc-serv-04.diamond.<wbr>ac.uk/cctbx</a><br>
On branch : master<br>
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<hr><br>
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commit c98b44997e8eb7bf53ee828f510b93<wbr>3cd5167758<br>
Author: Oleg Sobolev <a class="m_5786486340573780857moz-txt-link-rfc2396E" href="mailto:osobolev@lbl.gov" target="_blank"><osobolev@lbl.gov></a><br>
Date: Thu Aug 16 15:00:20 2018 -0700<br>
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Proper use of model class<br>
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<br>
<hr><br>
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c98b44997e8eb7bf53ee828f510b93<wbr>3cd5167758<br>
mmtbx/model/model.py | 3 +--<br>
1 file changed, 1 insertion(+), 2 deletions(-)<br>
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diff --git a/mmtbx/model/model.py b/mmtbx/model/model.py<br>
index 6f2247452..87412f95c 100644<br>
<tt style="color:#800">--- a/mmtbx/model/model.py</tt><br>
<tt style="color:#008">+++ b/mmtbx/model/model.py</tt><br>
@@ -2312,8 +2312,7 @@ class manager(object):<br>
sizes = <a href="http://flex.int" target="_blank">flex.int</a>()<br>
h = self.get_hierarchy()<br>
if(macro_molecule_only):<br>
<tt style="color:#800">- asc = h.atom_selection_cache()</tt><br>
<tt style="color:#800">- s = asc.selection("protein or
nucleotide")</tt><br>
<tt style="color:#008">+ s = self.selection("protein or
nucleotide")</tt><br>
h = h.select(s)<br>
for r in h.residue_groups():<br>
sizes.append(r.atoms().<wbr>size())</tt><br>
</blockquote>
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</div>
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