Re: [Chimera-users] [Open Babel] UCSF Dock mol2 files
Hi, This is a good suggestion. But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ? thanks, scott On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote:
Here you have two example files http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2
What OB should do (in my mind) is to take "Name:" value as target molecule name and pass all 3 grid scores (total, vdw and ele) somehow (i guess comment is a right place, since there is not much choice), so that it can output it in simmilar manner.
Maybe it would be easier to have an option "d" (aka. dock) which would copy ALL the ###### data, and some other one, such as "s" (aka. sufix) to take suffixed name into account. Disadvantage of above is that it wouldn't work for other formats. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl
W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < geoff@geoffhutchison.net> napisał:
I have a thought about mol2 files form Dock program, which contain additional information in commentary (###). Those information is being lost during openbabel operations, which is a pity. I'd like to propose a in/out option for mol2 for Dock'ed mol2's to read/write compatible information from those files. Especially conformer ID is important for further anylisis. Simmilar approach is used with pdbqt's contained in Autodock's .dlg files.
If you can give us a selection of example files and a list of what information you'd like retained, it's fairly easy to patch the parsers.
Cheers, -Geoff
For Chimera reference check out file UCSF-Chimera-XXX/share/ViewDock/Compound.py You can see many versions of Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the same comment method. This comments are only used by ViewDock module, as far as I know. For Dock reference you can see dock6/src/dock/library_file.cpp it seams fairy simple and always uses ##########. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell < sbrozell@rci.rutgers.edu> napisał:
Hi,
This is a good suggestion.
But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ?
thanks, scott
On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote:
Here you have two example files http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2
What OB should do (in my mind) is to take "Name:" value as target molecule name and pass all 3 grid scores (total, vdw and ele) somehow (i guess comment is a right place, since there is not much choice), so that it can output it in simmilar manner.
Maybe it would be easier to have an option "d" (aka. dock) which would copy ALL the ###### data, and some other one, such as "s" (aka. sufix) to take suffixed name into account. Disadvantage of above is that it wouldn't work for other formats. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl
W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < geoff@geoffhutchison.net> napisał:
I have a thought about mol2 files form Dock program, which contain additional information in commentary (###). Those information is being lost during openbabel operations, which is a pity. I'd like to propose a in/out option for mol2 for Dock'ed mol2's to read/write compatible information from those files. Especially conformer ID is important for further anylisis. Simmilar approach is used with pdbqt's contained in Autodock's .dlg files.
If you can give us a selection of example files and a list of what information you'd like retained, it's fairly easy to patch the parsers.
Cheers, -Geoff
Our approach to file formats in Chimera is to support the "native" form from the developers. The use of ########## for Dock mol2 format is obviously easiest for us since it is in use and already works in Chimera, but we're happy to accommodate a more broadly useful format. Conrad On 4/3/12 2:22 PM, Maciek Wójcikowski wrote:
For Chimera reference check out file UCSF-Chimera-XXX/share/ViewDock/Compound.py You can see many versions of Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the same comment method. This comments are only used by ViewDock module, as far as I know.
For Dock reference you can see dock6/src/dock/library_file.cpp it seams fairy simple and always uses ##########. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl <mailto:maciek@wojcikowski.pl>
W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell <sbrozell@rci.rutgers.edu <mailto:sbrozell@rci.rutgers.edu>> napisał:
Hi,
This is a good suggestion.
But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ?
thanks, scott
On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > Here you have two example files > http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 > http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2 > > What OB should do (in my mind) is to take "Name:" value as target molecule > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > comment is a right place, since there is not much choice), so that it can > output it in simmilar manner. > > Maybe it would be easier to have an option "d" (aka. dock) which would copy > ALL the ###### data, and some other one, such as "s" (aka. sufix) to take > suffixed name into account. Disadvantage of above is that it wouldn't work > for other formats. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > maciek@wojcikowski.pl <mailto:maciek@wojcikowski.pl> > > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff@geoffhutchison.net <mailto:geoff@geoffhutchison.net>> napisał: > > > > I have a thought about mol2 files form Dock program, which contain > > > additional information in commentary (###). Those information is being > > lost > > > during openbabel operations, which is a pity. I'd like to propose a > > in/out > > > option for mol2 for Dock'ed mol2's to read/write compatible information > > from > > > those files. Especially conformer ID is important for further anylisis. > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > files. > > > > > > If you can give us a selection of example files and a list of what > > information you'd like retained, it's fairly easy to patch the parsers. > > > > Cheers, > > -Geoff
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Maybe @<TRIPOS>COMMENT would be a better place for them? http://tripos.com/data/support/mol2.pdf ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang <conrad@cgl.ucsf.edu>napisał:
Our approach to file formats in Chimera is to support the "native" form from the developers. The use of ########## for Dock mol2 format is obviously easiest for us since it is in use and already works in Chimera, but we're happy to accommodate a more broadly useful format.
Conrad
On 4/3/12 2:22 PM, Maciek Wójcikowski wrote:
For Chimera reference check out file UCSF-Chimera-XXX/share/**ViewDock/Compound.py You can see many versions of Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the same comment method. This comments are only used by ViewDock module, as far as I know.
For Dock reference you can see dock6/src/dock/library_file.**cpp it seams fairy simple and always uses ##########. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl <mailto:maciek@wojcikowski.pl>
W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell <sbrozell@rci.rutgers.edu <mailto:sbrozell@rci.rutgers.**edu<sbrozell@rci.rutgers.edu>>> napisał:
Hi,
This is a good suggestion.
But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ?
thanks, scott
On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > Here you have two example files > http://dl.dropbox.com/u/**6846289/1afk_ligand_**conformers.mol2<http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2> > http://dl.dropbox.com/u/**6846289/3h78_ligand_**conformers.mol2<http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2> > > What OB should do (in my mind) is to take "Name:" value as target molecule > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > comment is a right place, since there is not much choice), so that it can > output it in simmilar manner. > > Maybe it would be easier to have an option "d" (aka. dock) which would copy > ALL the ###### data, and some other one, such as "s" (aka. sufix) to take > suffixed name into account. Disadvantage of above is that it wouldn't work > for other formats. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > maciek@wojcikowski.pl <mailto:maciek@wojcikowski.pl>
> > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff@geoffhutchison.net <mailto:geoff@geoffhutchison.**net<geoff@geoffhutchison.net>>> napisał:
> > > > I have a thought about mol2 files form Dock program, which contain > > > additional information in commentary (###). Those information is being > > lost > > > during openbabel operations, which is a pity. I'd like to propose a > > in/out > > > option for mol2 for Dock'ed mol2's to read/write compatible information > > from > > > those files. Especially conformer ID is important for further anylisis. > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > files. > > > > > > If you can give us a selection of example files and a list of what > > information you'd like retained, it's fairly easy to patch the parsers. > > > > Cheers, > > -Geoff
______________________________**_________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi, Sticking with ########## appears to be the best approach. Thanks everyone for the comments. scott ps. http://tripos.com/data/support/mol2.pdf @<TRIPOS>COMMENT Note: This RTI has not been implemented. Instead comments appear in the file immediately above the @<TRIPOS>ATOM line. On Wed, Apr 04, 2012 at 09:53:36PM +0200, Maciek Wójcikowski wrote:
Maybe @<TRIPOS>COMMENT would be a better place for them? http://tripos.com/data/support/mol2.pdf ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl
W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang <conrad@cgl.ucsf.edu>napisał:
Our approach to file formats in Chimera is to support the "native" form from the developers. The use of ########## for Dock mol2 format is obviously easiest for us since it is in use and already works in Chimera, but we're happy to accommodate a more broadly useful format.
Conrad
On 4/3/12 2:22 PM, Maciek Wójcikowski wrote:
For Chimera reference check out file UCSF-Chimera-XXX/share/**ViewDock/Compound.py You can see many versions of Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the same comment method. This comments are only used by ViewDock module, as far as I know.
For Dock reference you can see dock6/src/dock/library_file.**cpp it seams fairy simple and always uses ##########. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek@wojcikowski.pl <mailto:maciek@wojcikowski.pl>
W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell <sbrozell@rci.rutgers.edu <mailto:sbrozell@rci.rutgers.**edu<sbrozell@rci.rutgers.edu>>> napisał:
Hi,
This is a good suggestion.
But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ?
thanks, scott
On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > Here you have two example files > http://dl.dropbox.com/u/**6846289/1afk_ligand_**conformers.mol2<http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2> > http://dl.dropbox.com/u/**6846289/3h78_ligand_**conformers.mol2<http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2> > > What OB should do (in my mind) is to take "Name:" value as target molecule > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > comment is a right place, since there is not much choice), so that it can > output it in simmilar manner. > > Maybe it would be easier to have an option "d" (aka. dock) which would copy > ALL the ###### data, and some other one, such as "s" (aka. sufix) to take > suffixed name into account. Disadvantage of above is that it wouldn't work > for other formats. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > maciek@wojcikowski.pl <mailto:maciek@wojcikowski.pl>
> > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff@geoffhutchison.net <mailto:geoff@geoffhutchison.**net<geoff@geoffhutchison.net>>> napisał:
> > > > I have a thought about mol2 files form Dock program, which contain > > > additional information in commentary (###). Those information is being > > lost > > > during openbabel operations, which is a pity. I'd like to propose a > > in/out > > > option for mol2 for Dock'ed mol2's to read/write compatible information > > from > > > those files. Especially conformer ID is important for further anylisis. > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > files. > > > > > > If you can give us a selection of example files and a list of what > > information you'd like retained, it's fairly easy to patch the parsers. > > > > Cheers, > > -Geoff
participants (3)
-
Conrad Huang -
Maciek Wójcikowski -
Scott Brozell