[Biopython-dev] [biopython] Added transform and copy method to Entity in biopython.PDB (#25)

[Eric Talevich]

On Tue, Feb 7, 2012 at 8:46 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Sorry, didn't realise this was direct to me and not the mailing list.
> Would everyone be OK with git pull requests coming straight here?
>
> Anyway - Eric, would this be something you could look at?
>
> Peter
>

At a glance, the code looks cool to me, though I faintly recall some
overlap with João's unmerged work (copy method). I'll try to find time to
test it, but would not be upset if someone else got to it first.
-E



> ---------- Forwarded message ----------
> From: benreynwar
> <
> reply+i-2958669-14408e039dee774169d6f09c683146c3f42dd0b9-63959 at reply.github.com
> >
> Date: Tue, Jan 24, 2012 at 11:12 PM
> Subject: [biopython] Added transform and copy method to Entity in
> biopython.PDB (#25)
> To: Peter Cock <p.j.a.cock at googlemail.com>
>
>
> Minor changes to biopython.PDB to allow transforms to be applied to
> entities and copies of entities to be made.  Also fixed a bug in the
> transform method of Atom.  Tests are included.
> The changes are from a few months ago but they still merge cleanly
> into the current master.
>
> You can merge this Pull Request by running:
>
>  git pull https://github.com/benreynwar/biopython master
>
> Or you can view, comment on it, or merge it online at:
>
>  https://github.com/biopython/biopython/pull/25
>
> -- Commit Summary --
>
> * Added tranform method to Entity.
> * Add test for transform method.
> * Adding copy method for Entities
> * Added an insert method to Entity.  This allows a child to be
> inserted into a specified position in the child_list which effects
> position in the PDB output.
> * Fixed bug in transform method of Atom (dot product order).
>
> -- File Changes --
>
> M Bio/PDB/Atom.py (14)
> M Bio/PDB/Entity.py (40)
> M Tests/test_PDB.py (70)
>
> -- Patch Links --
>
>  https://github.com/biopython/biopython/pull/25.patch
>  https://github.com/biopython/biopython/pull/25.diff
>
> ---
> Reply to this email directly or view it on GitHub:
> https://github.com/biopython/biopython/pull/25
>