For the sake of completeness here is some working code.
`dump` exports the surface of map representations. They are all surfaces.
So I had to dump the map at each level (0.5 by 0.5 increment) in order to
get a filled volume. If you concatenate all xyz arrays you get the filled
volume of the level 20 surface.
Thank you for the support.
MIN_LEVEL = 0
MAX_LEVEL = 20
LEVEL_RANGE = np.arange(MIN_LEVEL, MAX_LEVEL+0.5, 0.5)
def _get_map(map_name):
dump_fhandle, dump_fname = tempfile.mkstemp()
open(dump_fhandle).close()
try:
levels = {}
skip = False
for level in LEVEL_RANGE:
if not skip:
# dump level
cmd.isodot('_i', map_name, level)
cmd.dump(dump_fname, '_i')
cmd.delete('_i')
# load level
with warnings.catch_warnings():
xyz = np.loadtxt(dump_fname)
warnings.simplefilter("ignore")
# handle empty maps
if skip or len(xyz) == 0:
xyz = np.ndarray((0, 3))
skip = True
xyz = xyz[:, :3]
levels[level] = xyz
return levels
finally:
os.unlink(dump_fname)
Em seg., 4 de nov. de 2019 às 01:38, Pedro Lacerda <[email protected]>
escreveu:
> Hi Jared,
>
> So COLLADA exports some kind of already rendered 3D image.
>
> Took me some time to figure out if dump exports the map points or
> something specific to the surface representation. In fact, it is yet to be
> figured out.
>
> Dump can export at least map and surface objects.
>
> When I export two different overlapping surfaces of the same map there is
> points of the outer surface that aren't in the inner. I expected all points
> of the inner to be present in both dumps.
>
> So I guess that when I dump surface objects it exports newly created
> points of the enclosed volume of that surface. Is it correct?
>
> To export the map directly would preserve the original points? (Which I
> hope to be the original grid count of the server's method)
>
> Is overlap is defined for map objects?
>
>
> Sorry maybe I'm not saying very clear.
>
> And about the get_volume_field(), if I remember correctly it returned on a
> call an ndarray of shape (28, 26, 15) and on other call an ndarray of shape
> (28, 28, 16). Something like that.
>
>
> Cheers,
>
>
> Em sex, 1 de nov de 2019 10:33, Jared Sampson <[email protected]>
> escreveu:
>
>> Hi Pedro -
>>
>> The COLLADA option exports unlabeled mesh objects so I couldn't figure
>> out which one is acceptor or donor.
>>
>> Yes, you're correct about that. This is due to the fact that COLLADA
>> export uses geometry after it is prepared for ray tracing, which doesn't
>> know about object names (see the primary function call
>> <https://github.com/schrodinger/pymol-open-source/blob/master/layer1/COLLADA.cpp#L667>).
>> It might be interesting/useful to export things in a more granular way
>> using pre-ray-tracing information as it is stored in the PyMOL session, but
>> that would involve substantial effort, and wasn't included when we planned
>> this export feature.
>>
>> If you wanted to know which mesh is which, you could export objects
>> one-at-a-time by disabling all the others, although to me, the dump command
>> output looks more helpful as it can be more easily parsed.
>>
>> Just one more question, what are these normal values?
>>
>>
>> The normal values Thomas refers to are the 3 components of the vector
>> indicating the direction toward the "outside" of the object, which is
>> normal to the surface the triangle mesh attempts to approximate. This is
>> used in shading.
>>
>> https://en.wikipedia.org/wiki/Vertex_normal
>>
>> The cmd.get_volume_field() returns a sparse ndarray with unknow layout
>> and all dimensions variables depending of the object. How to interpret such
>> array?
>> On PyMOL 1.x it returned -1 but in 2.x returned the array.
>>
>> The dump command worked (almost) like a charm.
>> I expect to extract the "dump" array from get_volume_field() so don't
>> need to write the file just to be read and deleted afterwards. Is it
>> possible?
>>
>>
>> I'm not familiar with `cmd.get_volume_field()`, so I'll defer to others
>> on those questions.
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>
--
Pedro Sousa Lacerda
*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*
*@pslacerda*
*+55 71 9 9981-1856*
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