I've added symmetry-reading to my prototype, but I'm reticent to upload
it to the main branch until we get a few things settled:
1) Why isn't CifReader() advancing to a new model when it hits a _data
line?
2) In mmCIF files this advancement is happening when the model field is
being read. Does that mean that in those cases it is NOT supposed to
advance on _data? Or does it mean that mmCIF files don't separate the
models using _data?
3) Symmetry needs to be applied within the reader. This is because when
there are multiple data sets, we have to have all the atoms lined up
initially. That's what I've implemented. Anyone see a problem with this?
(Another alternative might be to save the fractional coordinates and
just leave place-holder atoms for filling out the symmetry later, but
that sounds like a real pain to me.)
4) How does one pass information from a script to the reader to indicate
whether or not to read the full data set, with symmetry, or just the raw
points? This should be possible with some sort of command such as
set applySymmetry TRUE
but I don't know the mechanism. I suggest that the default be the
current "set applySymmetry FALSE".
5) Anyone have any ideas how we would handle cloning multiple unit
cells? My inclination is to indicate this at file load time and require
a reload if more atoms are requested. In principle one could identify
atoms as being in different sets depending upon what application of
symmetry was applied to them, but it isn't always that easy.
6) An interesting issue with these CIF files is that the symmetry
operations don't always set the atoms within the current unit cell.
That's actually a good thing in a way, because that means the molecules
actually look like molecules. But is suggests another option we need to
pass along:
set normalizeCoordinates TRUE
which would pack all the coordinates into the unit cell. (This will
generally NOT be pretty, but it can be important so as to see the actual
packing.)
Bob
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