[PyMOL] Trying to plug APBS into PyMOL for electrostatics (not working yet)

[Michael G. L. <ml...@um...>]

NOTE: this doesn't actually work yet, so most people can probably ignore
this message completely .. but i'd love some help! :)

Hi,

I've been doing all of my electrostatics calculations in MOE, but I'd like
to switch to PyMOL.  I looked/asked around a bit and found APBS
<http://agave.wustl.edu/apbs/>, a cool GPL'd Poisson Boltzmann solver.  I
figured that the first step in plugging APBS into PyMOL would just be
getting PyMOL to read dx files (that's APBS's default output format).  I
have this almost, but not quite, working.  I haven't messed around
much with PyMOL's internals, so I'm sure I've done a few things the
wrong way.  Here's what I did and where I'm stuck:

1) understand the dx file format - i was in a hurry here, so i just read
one of the APBS source files.  i don't know much about licenses, and i
don't know if that means that part of my code now needs to be GPL'd
instead of released under the PyMOL license.

3) wrote some Python code to read in a dx file and turn it into a nice
class.

4) gave that class the ability to spit out a list that i *think* matches
PyMOL's PyList version of an electrostatics map (ObjectMapState in
ObjectMap.h/c)

5) added a function
ObjectMap *ObjectMapLoadFromPyList(ObjectMap *I,PyObject *list,int state,int discrete);
to ObjectMap.h/c that should be able to load it.

Now, I wasn't sure exactly how I should get PyMOL to actually load the dx
files.  The most promising way looked like importing.load_object, so ..

6) added dx to importing.loadable (loadable.dx = 31) and #define'd
cLoadTypeDxPyListMap to be 31 in Cmd.c.  added a new case for
cLoadTypeDxPyListMap to the big switch in CmdLoadObject and made it call
through to ObjectMapLoadFromPyList.

7) made a little python script called dxMap.py that looks like this:

from pymol import importing
f = file('meoh.dx')
d = readDX(f)
f.close()
thing = d.getObjectMapState(asList=True)
importing.load_object(importing.loadable.dx, thing, 'map')

and a pml script that says

load methanol.pdb
show surface, methanol
run dxMap.py
ramp_new e_lvl, map, [-0.02,0.00,0.02]
set surface_color, e_lvl, methanol

At this point, things *almost* work.  If I click on "map" in the main
PyMOL window, it shows a box around my molecule (methanol in case you
haven't guessed yet :)) that looks like the right size.  But, the surface
is entirely white (and middle-clicking on the ramp and dragging doesn't
help).  Even more disturbing, when I try something like "isosurf surf1,
map, 0.008", PyMOL segfaults :(.

My guess is that I don't quite understand what PyMOL wants me to send to
ObjectMapLoadFromPyList or ObjectMapStateFromPyList.  I've tried lots of
prinf debugging throughout ObjectMap.c, Isosurf.c and Field.c and
everything looks right.

Anyone have any quick guesses as to what I might be doing wrong?  If I put
my little bit of Python and C code up on the web somewhere, would someone
be willing to take a look at it?  I'm pretty sure the problem is in one of
my Python classes (ObjectMapState, Isofield and Field) or in my C code,
rather than in the dx parsing, so looking at those things shouldn't force
the GPL taint upon you :).

In case it matters, I'm using the CVS version of PyMOL, compiled to use
Python2.3 (i don't have Python2.2 on my system, the cvs version of PyMOL
wants Python2.2 and the ext package includes Python2.1 ..).

thanks in advance,

-michael

--
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