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Monday, 17th of September 2018, 20:40:03 UTC
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?
20:47:26
drmeister
Amber loads topology files - what am I saying?
20:47:47
drmeister
Where do you use the pdb file in the comparison?
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
21:04:20
Bike
i believe it is an int64_t.
21:04:36
kpoeck
and fits perfectly into sprintf(txt, "%" PRFhex, fn);
21:05:09
kpoeck
so why would my fix to core__integer_to_string fail?
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
21:05:28
kpoeck
This is all in the c++ world, and no overflow will happen
21:06:09
kpoeck
The other thing i don't understand yet and will have to look
21:06:42
Bike
I think it's just the definition of core__negate
21:06:53
Bike
which for a fixnum just does make_fixnum(-input), basically
21:07:30
Bike
actually we should probably not expand into core:negate, since it's a function call for basic arithmetic
21:07:37
Bike
but i'd still like negate to not be busted
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
21:09:31
Bike
i mean, you're right, it's wrong
21:09:58
Bike
it probably has to special case most-negative-fixnum only, which is weird but whatever.
21:10:26
kpoeck
That looks easily fixable- with the special case you said -
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);
21:26:47
kpoeck
My problem is that Illegal exponent character[c] is printed
21:58:01
usha
@drmeister, I loaded the mol2 file in amber and could generate topology and parameters
21:58:20
usha
but when I converted that mol2 from cando to pdb, it generated an error
21:58:36
usha
so just wanted to check if direct pdb from cando would also have that error that's all
21:58:45
usha
I have sent an email regarding this too
5:25:20
beach
Good morning everyone!
Tuesday, 18th of September 2018, 8:40:03 UTC