Hi,
As far as I know none of extra fields are supported in OB, nor they are in
tools like Chimera. As you can see even GOLD's implementation of
"@<{PROPERTY_NAME}>" is absent in Sybyl's specs. I guess supporting those
extra fields with loads of undocumented quirks make it impossible to
maintain. The Chimera mailinglist you've cited also stated that they
support the "developers" way of commenting, although their ViewDock module
support GOLD i don't use it and must figure out what it does internally.
I second a "standard" property tag which should be present by default on
mol2 file format, and current comments style properties as an alternative.
It would be neat to squeeze it in 2.4.0 release.
PS. I use also GOLD regularly, but I use "SDF -> mol2 with comments (by OB)
-> UCSF Chimera" combo.
PS2. I have noticed that current comments lack support for multi-line
properties... Must fix that one...
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-12-08 2:41 GMT+01:00 Stefano Forli <fo...@scripps.edu>:
> I had miss that in the source code, but if I get this right, writing extra
> fields should be even easier that I thought (although I suspect that a lot
> of internal properties shouldn't be written in the mol2 file).
>
> In the meantime, I took a look at the Mol2 format standard [1] and I found
> that I could hijack many record types for my own purposes
> ("@<TRIPOS>NORMAL", " @<TRIPOS>ROTATABLE_BOND" and "@<TRIPOS>RING_CLOSURE",
> to name a few).
>
> Although, I'm not sure I've seen any of these mentioned in the OB source
> code.
> If that's the case, this means that some work is needed in any case, in
> both parsing and writing.
>
> For that, I'm wondering if it would be useful to support a generalized
> property tag, i.e.:
>
> @<{PROPERTY_NAME}>
> (value) (value) (value) ...
>
> another alternative could be:
>
> @<TRIPOS>{PROPERTY_NAME}
> (value) (value) (value) ...
>
> but I see no clear advantage in that over the first one.
> A real case example is the GOLD docking software, which adds properties to
> the docking output files in both SDF and Mol2 files.
> The SDF standard supports arbitrary properties, while for Mol2 files they
> user the first example I wrote above.
>
> Anyway, thanks for the help and the support in the discussion!
>
> S
>
>
>
>
>
> [1] http://www.tripos.com/data/support/mol2.pdf
>
>
>
> On 12/07/2015 01:25 AM, Maciek Wójcikowski wrote:
>
>> I noticed that "local" OBPairData are explicitly ignored, which may be
>> the reason they are
>> not written for you:
>>
>> https://github.com/openbabel/openbabel/pull/112/files#diff-d6e9941b72192e2ba1a2d244948450aeR535
>>
>> ----
>> Pozdrawiam, | Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl>
>>
>> 2015-12-07 10:21 GMT+01:00 Maciek Wójcikowski <mac...@wojcikowski.pl
>> <mailto:mac...@wojcikowski.pl>>:
>>
>> I forgot to mention - only the development version (git master
>> branch) has that
>> feature. You can check it by:
>>
>> obabel -Hmol2
>>
>>
>> ----
>> Pozdrawiam, | Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl>
>>
>> 2015-12-07 10:18 GMT+01:00 Maciek Wójcikowski <mac...@wojcikowski.pl
>> <mailto:mac...@wojcikowski.pl>>:
>>
>> Hi,
>> Writting comments works fine (-ac and -xc parameters in CLI). I
>> use them on daily
>> basis with UCSF Chimera, which was the reason for implementation.
>> The only problem
>> with them is skipping molecules - it also skips comments for the
>> first molecule
>> [https://github.com/openbabel/openbabel/issues/127].
>>
>> Eg. If you would like to convert SDF file to mol2 with
>> scores/properties:
>>
>> obabel -isdf test_in.sdf -omol2 -O test_out.mol2 *-xc*
>>
>>
>> To do the opposite:
>> obabel -imol2 *-ac* test_in.mol2 -osdf -O test_out.sdf
>>
>> It also work correctly in pybel:
>>
>> mol = pybel.readfile('mol2', 'test.mol2', opt={'c':None})
>>
>> And writing accordingly
>>
>> mol.write('mol2', 'test.mol2', opt={'c':None})
>>
>>
>> I hope that helps :)
>>
>> ----
>> Pozdrawiam, | Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl>
>>
>> 2015-12-04 21:59 GMT+01:00 Geoffrey Hutchison <
>> geoff.hutchi...@gmail.com
>> <mailto:geoff.hutchi...@gmail.com>>:
>>
>> > Are there any development plans to fill this gap in the
>> near future? (for variably large
>> > value of 'near'…).
>>
>> Sure, I don't think it would be terribly difficult.
>> Personally, I'd need to
>> see a few of these "commented" Mol2 files to make sure
>> they're being written
>> correctly - it's an extension that's not in the mol2 format
>> specification.
>>
>> -Geoff
>>
>>
>>
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>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor of Integrative
> Structural and Computational Biology,
> Molecular Graphics Laboratory
>
> Dept. of Integrative Structural
> and Computational Biology, MB-112F
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
>
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