On Nov 10, 2011, at 4:32 PM, Jan-Philip Gehrcke wrote:
> Hey,
>
> yes, obviously the `sName` attribute of the container corresponding to x
> is not set after loading x via loadpdb.
>
> I've done a small test to illustrate what is missing. In mol2File.c,
> around line 293, I've written:
>
> VP0(("sName before ContainerSetName: %s\n", uUnit->cHeader.sName));
> ContainerSetName(&uUnit->cHeader, "powername");
> VP0(("lol cHeader: %s\n", uUnit->cHeader.sName));
>
> The rest of the file is unchanged, especially this line is active again:
>
> strcpy(sTemp, sContainerName((CONTAINER) uUnit));
>
> The output is:
>
>> Writing mol2 file: test.mol2
>> sName before ContainerSetName:
>> sName after ContainerSetName: powername
>
> "powername" then appears in the MOL2 file, i.e.
> `sContainerName((CONTAINER) uUnit)` returned a non-empty string.
>
>
> Hence, we have to make sure that `ContainerSetName(&uUnit->cHeader,
> name);` is called at some point after loading a PDB file to an object
> with a proper name.
>
> Jan-Philip
>
That takes care of the pdb case, but there may be other ways of
creating/reading molecule (maybe in the future).
Don't know anything about leap code or the mol2 format, but I was
thinking along the line of an additional line after the allocation
of memory for the molecule structure. Just set the name to a default
there. If it is never overwritten, it will show up as the default
name. If other code (say loadFoo) overwrites it, then that is the
correct behavior as well. I think it should be an obvious name,
e.g, "XXX", which is pretty generally meant to indicate additional
editing is needed at a later time.
Bud
PS, you need to get someone commit whatever you decide if you don't
have privileges.
>
> On 10.11.2011 22:50, M. L. Dodson wrote:
>> Replying to myself again, it appears that when a molecule
>> is read in from a pdb, there is no molecule name assigned
>> (in the mol2-format sense). Maybe we should initialize the
>> molecule name in the code before we even get started. If we
>> need it for a molecule read from a pdb file, then the default
>> is there. I suggest something like REPLACEME. If the name
>> is assigned by some other way, then it overwrites the default.
>>
>> Bud
>>
>> On Nov 10, 2011, at 3:30 PM, M. L. Dodson wrote:
>>
>>> Replying to myself.
>>>
>>> If you write a pdb with x, then use it the way you describe,
>>> you get the behavior you indicated. Something is going
>>> wrong. What leap has after the combine is different from
>>> what it has from reading the pdb file:
>>>
>>> source leaprc.ff99SB
>>> x = combine {ACE THR NME}
>>> savepdb x test.pdb
>>> savemol2 x test.mol2 0
>>> y = loadmol2 test.mol2
>>> quit
>>>
>>> versus
>>>
>>> source leaprc.ff99SB
>>> x = loadpdb test.pdb
>>> savemol2 x test.mol2 0
>>> y = loadmol2 test.mol2
>>> quit
>>>
>>> One thing I noticed is that x from combine has TER cards in
>>> the written pdb file, whereas the pdb file I used in the
>>> second case had the TER cards removed. (But the behavior
>>> you described happened with or without the TER cards.)
>>>
>>> Puzzled,
>>> Bud
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Thu Nov 10 2011 - 16:00:03 PST
