I see this in 1.8.2.1:
#define _PyMOL_VERSION "1.8.2.1"
and in AtomInfo.h:
#if _PyMOL_VERSION_int < 1770
#define AtomInfoVERSION 176
#define BondInfoVERSION 176
#elif _PyMOL_VERSION_int < 1810
#define AtomInfoVERSION 177
#define BondInfoVERSION 177
#else
#define AtomInfoVERSION 181
#define BondInfoVERSION 181
#endif
So that must be where that 181 version indicator is coming from in a PSE
file saved by 1.8.2.3, right?
But when you look at AtomInfoType in that same file, we see:
typedef struct AtomInfoType {
union {
float * anisou; // only allocate with get_anisou
int64_t dummyanisou;
};
lexidx_t segi;
lexidx_t chain;
lexidx_t resn;
lexidx_t name;
lexidx_t textType;
lexidx_t custom;
lexidx_t label;
...
What am I missing?
Bob
On Mon, Aug 8, 2016 at 10:51 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> look here:
> https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/
> pymol/layer2/AtomInfoHistory.h
>
> The AtomInfoType_1_8_1 version (used in 1.8.2) stores ANISOU as shorts
> (PDB precision). The AtomInfoType_1_7_7 version (used in 1.8.0) doesn't
> support ANISOU (will indeed write an unused NULL pointer), at the time it
> was work in progress for a specific use case which didn't require ANISOU.
>
> Cheers,
> Thomas
>
> On 08 Aug 2016, at 11:32, Robert Hanson <hans...@stolaf.edu> wrote:
>
> > I do like the compactness of that and the quicker loading, but I do see
> how this could be a nightmare. I'm looking at a file that lists the dump
> version as 1.8.1, but I don't even see how that would ever work, since in
> that AtomInfo structure the ANISOU data is just a 64-bit pointer. That
> would end up just a useless reference, wouldn't it?
> >
> > On Mon, Aug 8, 2016 at 10:05 AM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
> > Hi Bob,
> >
> > I assume those are PSE files with setting "pse_binary_dump=on". This is
> not the default. You can load such files into PyMOL, set
> pse_binary_dump=off and save it as a regular serialized PSE. I definitely
> recommend the conversion step over reimplementing the "pse_binary_dump"
> decoding. Right now there are 3 binary atom layouts (for 1.7.6, 1.8.0 and
> 1.8.2). Grep the PyMOL code for "AtomInfoTypeConverter" if you're
> interested in the details.
> >
> > The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and
> with the "pse_export_version" setting you can also export for older PyMOL
> versions.
> >
> > Cheers,
> > Thomas
> >
> > On 08 Aug 2016, at 07:57, Robert Hanson <hans...@stolaf.edu> wrote:
> >
> > > Thomas,
> > >
> > > In reading PyMOL PSE files into Jmol I have recently run into the
> problem with some of these files (version 1.8.2.3). Jmol has no problem
> reading the standard Pickle format, but there seems to be an option in
> PyMOL to serialize binary data structures as BINSTRING or SHORT_BINSTRING
> format along with other standard strings. This sounds like a great idea; I
> have no doubt that this will lead to considerably smaller PSE files and
> also faster loading. However, I'm struggling with atom information
> deserialization.
> > >
> > > Q: Is this the default format now for saving PyMOL PSE files?
> > >
> > > Q: Is there a way to turn that off?
> > >
> > > Q: In order to do this properly, how many versions of the atom info
> data structure do I need to be able to process?
> > >
> > > Bob
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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