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17:32:55
Bike
i guess it sets up a logical pathname host. feels more like an rc file thing, but it's in the mysterious bundle code
20:00:38
Nephromancer
@usha worst comes to worst, you can save as a mol2 with :use-sybyl-types t , and then run it through OpenBabel
20:24:18
Nephromancer
might be an atom types issue? CANDO writes mol2 files with GAFF atom types unless you set :use-sybyl-types to T
20:29:01
drmeister
The PDB format is a crappy format that really should be killed, buried, dug up, cremated and the ashes scattered in the desert.
20:30:29
drmeister
Usha: Generally - if you are looking for a function - use the 'apropos' function. (apropos "pdb") would bring up every symbol that has "pdb" in the name.
20:47:07
drmeister
We only really have pdb and mol2 and then clasp's internal formats. Mol2 is a better format - but amber doesn't load mol2 does it?
20:48:15
drmeister
Don't you load the pdb file into leap or cando and then generate a topology file from that?
21:04:08
kpoeck
in c++, what is the underlying datatype for a gc::fixnum? I suspect that MOST_NEGATIVE_FIXNUM -1 is a perfectly normal c++ number
21:05:13
Bike
the problem of course is that -most_negative_fixnum is not actually a fixnum, which is what your other bug is... but for printing it's probably okay since it stays in C
21:07:30
Bike
actually we should probably not expand into core:negate, since it's a function call for basic arithmetic
21:08:50
kpoeck
clasp_negate does return immediate_fixnum<Number_O>(-num.unsafe_fixnum()); and is just asuming that the result fits in a fixnum
21:09:58
Bike
it probably has to special case most-negative-fixnum only, which is weird but whatever.
21:26:11
kpoeck
Assuming that uc is a char, is this the right idiom to throw an error? SIMPLE_ERROR(BF("Illegal exponent character[%c]") % uc);
21:58:01
usha
@drmeister, I loaded the mol2 file in amber and could generate topology and parameters
21:58:36
usha
so just wanted to check if direct pdb from cando would also have that error that's all