[cctbxbb] [git/cctbx] master: Fix typo geobox (1ad3fe055)

[Nigel Moriarty]

Not sure if Gydo is seeing this but it may be outside his expertise. To me.
it highlights a wrinkle in the code. The only reason for not shifting is so
that the forcefields are consistent in the long range terms. I believe it
could be avoided by moving the entire model such that the submodel is in
the required position but the other atoms are in the correct relative
position.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Thu, Dec 20, 2018 at 5:02 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> Bad idea to hard-wire package name into lowest level code. Now imagine we
> need the same for afit, amber, quantumbio, rosetta, etc.. Are we going to
> have a page-long block of "if" statements. Please re-think and remove. For
> example, whether you want to shift it or not can be a parameter that you
> cast way level up in the context specific code.
>
> Pavel
>
> On 12/20/18 09:53, CCTBX commit wrote:
>
> Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx
> On branch  : master
>
> ------------------------------
>
>
> commit 1ad3fe05571162839e770c35ed032a7fc38a33b7
> Author: Gydo van Zundert <gydo.vanzundert at schrodinger.com>
> <gydo.vanzundert at schrodinger.com>
> Date:   Wed Dec 19 14:58:36 2018 -0500
>
>     Fix typo geobox
>
>
> ------------------------------
>
>
> 1ad3fe05571162839e770c35ed032a7fc38a33b7
> mmtbx/refinement/real_space/individual_sites.py | 4 ++--
> 1 file changed, 2 insertions(+), 2 deletions(-)
>
> diff --git a/mmtbx/refinement/real_space/individual_sites.py
> b/mmtbx/refinement/real_space/individual_sites.py
> index c61e88b01..20f38a6b0 100644
> --- a/mmtbx/refinement/real_space/individual_sites.py
> +++ b/mmtbx/refinement/real_space/individual_sites.py
> @@ -350,7 +350,7 @@ class box_refinement_manager(object):
>
>        # When using the Schrodinger force field, move the whole structure
> as the
>        # selected atoms are environment aware.
> -      if geobox.get_source() == 'SCHRODINGER':
> +      if geo_box.get_source() == 'SCHRODINGER':
>          geo_box.shift_cart(box.shift_cart)
>
>        rsr_simple_refiner = simple(
> @@ -377,7 +377,7 @@ class box_refinement_manager(object):
>          iselection, sites_cart_refined)
>        self.xray_structure.set_sites_cart(sites_cart_moving)
>        self.sites_cart = self.xray_structure.sites_cart()
> -      if geobox.get_source() == 'SCHRODINGER':
> +      if geo_box.get_source() == 'SCHRODINGER':
>          geo_box.shift_cart(shift_back)
>      else: # NCS constraints are present
>        # select on xrs, grm, ncs_groups
>
> ------------------------------
>
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