Maciek,
I'm totally fine with the standard comment style, while I'm not sure I
understand what you
mean by "standard" property.
Are you referring to the finite list of Tripos standard properties or to the
"@<TRIPOS>wathever" format?
In any case, I had used GOLD in the past, and I remember that all parsers that
supported
its format relied on the "@<" tag to recognize that a property was encountered,
and all
following lines were appended to it until another "@<" tag was encountered (or
EOF, I
believe). Although, that was a while ago, so I don't know what modern programs
are doing now.
About the multi-line, yes, that's definitely useful (and required by some of
the standard
properties).
Needless to say, it would be great if the outcome of this thread would make it
into the
2.4.0 release. Count me in for any help I can provide (test cases, code
testing, etc..).
Cheers,
S
On 12/08/2015 01:43 AM, Maciek Wójcikowski wrote:
> 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 <mailto:mac...@wojcikowski.pl>
>
> 2015-12-08 2:41 GMT+01:00 Stefano Forli <fo...@scripps.edu
> <mailto: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>
> <mailto:mac...@wojcikowski.pl
> <mailto:mac...@wojcikowski.pl>>
>
> 2015-12-07 10:21 GMT+01:00 Maciek Wójcikowski <mac...@wojcikowski.pl
> <mailto:mac...@wojcikowski.pl>
> <mailto: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>
> <mailto:mac...@wojcikowski.pl
> <mailto:mac...@wojcikowski.pl>>
>
> 2015-12-07 10:18 GMT+01:00 Maciek Wójcikowski
> <mac...@wojcikowski.pl
> <mailto:mac...@wojcikowski.pl>
> <mailto: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>
> <mailto: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>
> <mailto: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
>
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with
> Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development
> environment.
> Design, debug & build mobile apps & 2D/3D high-impact
> games for
> multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
> <mailto:OpenBabel-Devel@lists.sourceforge.net>
> <mailto:OpenBabel-Devel@lists.sourceforge.net
> <mailto:OpenBabel-Devel@lists.sourceforge.net>>
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
>
>
>
>
> ------------------------------------------------------------------------------------------
> NOTE: This message was trained as non-spam. If this is wrong, please
> correct the
> training
> as soon as possible.
>
>
> --
>
> 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 <tel:%2B1%20%28858%29784-2055>
> fax: +1 (858)784-2860 <tel:%2B1%20%28858%29784-2860>
> email: fo...@scripps.edu <mailto:fo...@scripps.edu>
> http://www.scripps.edu/~forli/
>
>
--
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/
------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
