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From: Joerg K. W. <we...@in...> - 2004-02-10 12:24:36
|
Hi all, The tutorial was updated. PDF version increases from 77 to 90 pages :-) The missing HTML descriptorions for the new descriptors where added to CVS and are availabale direct from CVS or from the next release (in 2-3 weeks). Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
|
From: Joerg W. <we...@in...> - 2004-02-01 17:37:50
|
Hi, i will check the settings in the ant build file for creating a binary distribution. I will have a look at the descriptor informations. In fact, these warnings are not critical, but if these informations (if available) can be used to show informations about the calculation rule used. So i will have a look at the documentation, which is not up-to-date ... one step after another. The descriptor informations need to be generateed from DocBook XML and i will fix this as soon as possible. The missing documentation was caused by the new descriptor calculation methods, which requests documentation to force developers (here: ME!) to add informations for these classes. So other users can understand these methods without forced to go into the source code. The directory structures has not changed, but i moved these classes from our internal JCompChem library to JOELib, so it could be possible, that i missed to change the description path for the new descriptor calculation facilities. Regards, Joerg On Fri, 30 Jan 2004, will welch wrote: > hi, > i just pulled down the 2004-01-16 distributions from sourceforge, and > have been trying to run the very first thing in the readme.txt file: > > sh convert.sh joelib/test/test.mol > > looks like the test directory wasn't included in the binary dist, so i > pulled down the source distro and grabbed it from there. now when i run > i get a bunch of warnings of the form: > > 20:35:58 [WARN ] joelib.desc.DescriptorHelper - HTML > description is missing for joelib.desc.types.BurdenModifiedEigenvalues > in docs/desc/BurdenModifiedEigenvalues > 20:35:58 [WARN ] joelib.desc.DescriptorHelper - HTML > description is missing for > joelib.desc.types.GlobalTopologicalChargeIndex in > docs/desc/GlobalTopologicalChargeIndex > 20:35:58 [WARN ] joelib.desc.DescriptorHelper - HTML > description is missing for > joelib.desc.types.WeightedBurdenModifiedEigenvalues in > docs/desc/WeightedBurdenModifiedEigenvalues > > looks to me like the desired files actually live in > docs/api/joelib/desc rather than docs/desc. is this the expected > behavior, or am i losing to some kind of bad environment variable > setting, or did the directory structure just get rearranged with the > current release and something's out of date with respect to that? > > -- will > > Will Welch > 650 Second Street #203 > San Francisco, CA 94107 > ph: 415-546-9172 > > > > ------------------------------------------------------- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > _______________________________________________ > Joelib-help mailing list > Joe...@li... > https://lists.sourceforge.net/lists/listinfo/joelib-help > Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
|
From: will w. <li...@qu...> - 2004-01-31 15:20:31
|
hi, i just pulled down the 2004-01-16 distributions from sourceforge, and have been trying to run the very first thing in the readme.txt file: sh convert.sh joelib/test/test.mol looks like the test directory wasn't included in the binary dist, so i pulled down the source distro and grabbed it from there. now when i run i get a bunch of warnings of the form: 20:35:58 [WARN ] joelib.desc.DescriptorHelper - HTML description is missing for joelib.desc.types.BurdenModifiedEigenvalues in docs/desc/BurdenModifiedEigenvalues 20:35:58 [WARN ] joelib.desc.DescriptorHelper - HTML description is missing for joelib.desc.types.GlobalTopologicalChargeIndex in docs/desc/GlobalTopologicalChargeIndex 20:35:58 [WARN ] joelib.desc.DescriptorHelper - HTML description is missing for joelib.desc.types.WeightedBurdenModifiedEigenvalues in docs/desc/WeightedBurdenModifiedEigenvalues looks to me like the desired files actually live in docs/api/joelib/desc rather than docs/desc. is this the expected behavior, or am i losing to some kind of bad environment variable setting, or did the directory structure just get rearranged with the current release and something's out of date with respect to that? -- will Will Welch 650 Second Street #203 San Francisco, CA 94107 ph: 415-546-9172 |
|
From: Joerg W. <we...@in...> - 2004-01-19 23:07:20
|
Hi Gerd, thanks for your efforts. I've only tried with WebStart. I've a project meeting this week and will have a look as soon as possible. But not before the end of next week. Thanks again for your debugging abilities. Regards, Joerg > Hi, > > Is there any reason why the ResourceLoader unpacks zip/jars > 'by hand', i.e. why did you use the getBytesFromArchive() and > getBytesFromFile() methods instead of useing > ClassLoader.getResourceAsStream() directly ? I've tried this and > it seems to work. > > The problem with the current implemenation is, that it doesn't > work with applets, since jars are loaded via http. If you use > ClassLoader.getResourceAsStream() this is no problem anymore > since the JDK does all the ugly stuff. > > I've attached my version of ResourceLoader.java so that you > may take a look on it. > > Best Regards, > gerd > > ________________________________________________________________ > Gerd Mueller ge...@sm... > SMB GmbH http://www.smb-tec.com > Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
|
From: Gerd M. <Ger...@sm...> - 2004-01-19 17:02:58
|
Hi, Is there any reason why the ResourceLoader unpacks zip/jars 'by hand', i.e. why did you use the getBytesFromArchive() and getBytesFromFile() methods instead of useing ClassLoader.getResourceAsStream() directly ? I've tried this and it seems to work. The problem with the current implemenation is, that it doesn't work with applets, since jars are loaded via http. If you use ClassLoader.getResourceAsStream() this is no problem anymore since the JDK does all the ugly stuff. I've attached my version of ResourceLoader.java so that you may take a look on it. Best Regards, gerd ________________________________________________________________ Gerd Mueller ge...@sm... SMB GmbH http://www.smb-tec.com |
|
From: Joerg K. W. <we...@in...> - 2004-01-16 13:44:37
|
Hi all, i've published a huge amount of descriptor calculation methods (at all 78 classes). This enables you to calculate, e.g. up to 3500 descriptors. The definitions for the CESTATE can be found in the publications using JOELib: http://www-ra.informatik.uni-tuebingen.de/software/joelib/users.html If you are interested there is now also the AtomPair descriptor available ! Please let me know, if you will use it, because a detailed analysis can eventually be used to publish a paper. So, be a nice scientist and let me know !!! Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
|
From: Gerd M. <Ger...@sm...> - 2004-01-05 13:33:37
|
Hi, The SMARTS encoder writes Stereo-Up as '\' and Stereo-Down as '/' but the specs says it vise versa. Best Regards, gerd ________________________________________________________________ Gerd Mueller ge...@sm... SMB GmbH http://www.smb-tec.com |
|
From: Joerg K. W. <we...@in...> - 2003-12-18 16:09:51
|
Hi Wayne, you're right, added as support request as additional flag in joelib.properties: https://sourceforge.net/tracker/index.php?func=detail&aid=862349&group_id=39708&atid=425970 Should not be too difficult :-) If you've already implemented such a method in MDLSD i would be happy to check this in. It's not necessary to implement things twice ! Regards, Joerg > bondPairs is a HashMap. The intent is to make sure that an aromatic > atom is involved in at most one double-bond. If an atom has not > participated in a double-bond and an aromatic atom it is attached to > also has not participated in a double-bond, then bondType is set to 2. > Both atoms are then added to the bondPairs HashMap, with the target of > one atom's HashMap pointing to the other atom. > > If what I wrote it correct at all, though, it could just be a > java.util.HashSet I guess. Doesn't need to be a HashMap. > > >>-----Original Message----- >>From: Joerg K. Wegner [mailto:we...@in...] >>Sent: Monday, December 15, 2003 8:12 AM >>To: Wayne Volkmuth >>Cc: Joe...@li... >>Subject: Re: [Joelib-help] aromaticity in SD files >> >>Hi Wayne, >> >>what contains the 'bondPairs'-variable ? Seems to be a HashMap or >>something related, but what's their content. >> >>Regards, Joerg >> >> >>>Hi Joerg, >>> >>>A couple weeks ago I asked about the bond type "4" in the sd files >>>produced by JOELib. You said >>> >>> >>> >>>>ah, o.k., but that's not a bug that's a feature! These bonds are >>>>aromatic and you will find this also in the SD-FILE definition of > > MDL. > >>>>That why you should use JOELib or OpenBabel, because they have a >>>>really >>>>great chemical expert system behind 'simple' file conversion. Only > > if > >>>>you know aromatic atoms/bonds you can create e.g. a MOL2 file !!! >>> >>> >>>I went and looked at the sd file definition on the mdl web site. A > > bond > >>>type of "4" is only permitted (required?) for structures intended > > for > >>>use as queries (against, presumably, a database). I'm sure you'll > > find > >>>that particular distinction as odd as I do but at any rate, that's > > their > >>>standard. >>> >>>>From what I've seen JOELib seems to be focused on representing > > specific, > >>>rather than generic (i.e. query), molecules so it seems as though > > the sd > >>>writer should put out alternating 1's and 2's. Or perhaps it's > > sensible > >>>to have behavior depend on a flag, so you can ask the sd writer to > > use > >>>type "4" bonds if desired. >>> >>>Here's a fragment of code that I think will do the trick. Let me > > know > >>>what you think. >>> >>>Wayne >>> >>> //check, if aromatic bond >>> if (atom.isAromatic() && nbr.isAromatic() || >>>(bond.getBO() == JOEBond.JOE_AROMATIC_BOND_ORDER)) >>> { >>> // Non-query structures must use Kekule >>>representation >>> if (bondPairs.containsKey(new >>>Integer(atom.getIdx())) || bondPairs.containsKey(new >>>Integer(nbr.getIdx()))) >>> { >>> bondType = 1; // single bond >>> } >>> else >>> { >>> bondType = 2; // double bond >>> bondPairs.put(new > > Integer(atom.getIdx()), > >>>new Integer(nbr.getIdx())); >>> bondPairs.put(new Integer(nbr.getIdx()), > > new > >>>Integer(atom.getIdx())); >>> } >>> } >>> else >>> { >>> // 1 single >>> // 2 double >>> bondType = bond.getBO(); >>> } >>> >>> > > ------------------------------------------------------------------------ > >>--------------------------------------------- >> >>>This email may contain material that is confidential and privileged > > and > >>is for the sole use of the intended recipient. Any review, reliance or >>distribution by others or forwarding without express permission is >>strictly prohibited. If you are not the intended recipient, please > > contact > >>the sender and delete all copies. >> >>> >>> >>>------------------------------------------------------- >>>This SF.net email is sponsored by: IBM Linux Tutorials. >>>Become an expert in LINUX or just sharpen your skills. Sign up for >> >>IBM's >> >>>Free Linux Tutorials. Learn everything from the bash shell to sys >> >>admin. >> >>>Click now! http://ads.osdn.com/?ad_id78&alloc_id371&op=click >>>_______________________________________________ >>>Joelib-help mailing list >>>Joe...@li... >>>https://lists.sourceforge.net/lists/listinfo/joelib-help >>> >> >> >>-- >>Dipl. Chem. Joerg K. Wegner >>Center of Bioinformatics Tuebingen (ZBIT) >>Department of Computer Architecture >>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany >>Phone: (+49/0) 7071 29 78970 >>Fax: (+49/0) 7071 29 5091 >>E-Mail: mailto:we...@in... >>WWW: http://www-ra.informatik.uni-tuebingen.de >>-- >>Never mistake motion for action. >> E. Hemingway >> > > > > --------------------------------------------------------------------------------------------------------------------- > This email may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. > > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
|
From: Wayne V. <vol...@re...> - 2003-12-15 20:39:33
|
bondPairs is a HashMap. The intent is to make sure that an aromatic
atom is involved in at most one double-bond. If an atom has not
participated in a double-bond and an aromatic atom it is attached to
also has not participated in a double-bond, then bondType is set to 2.
Both atoms are then added to the bondPairs HashMap, with the target of
one atom's HashMap pointing to the other atom.
If what I wrote it correct at all, though, it could just be a
java.util.HashSet I guess. Doesn't need to be a HashMap.
> -----Original Message-----
> From: Joerg K. Wegner [mailto:we...@in...]
> Sent: Monday, December 15, 2003 8:12 AM
> To: Wayne Volkmuth
> Cc: Joe...@li...
> Subject: Re: [Joelib-help] aromaticity in SD files
>=20
> Hi Wayne,
>=20
> what contains the 'bondPairs'-variable ? Seems to be a HashMap or
> something related, but what's their content.
>=20
> Regards, Joerg
>=20
> > Hi Joerg,
> >
> > A couple weeks ago I asked about the bond type "4" in the sd files
> > produced by JOELib. You said
> >
> >
> >>ah, o.k., but that's not a bug that's a feature! These bonds are
> >>aromatic and you will find this also in the SD-FILE definition of
MDL.
> >>That why you should use JOELib or OpenBabel, because they have a
> >> really
> >>great chemical expert system behind 'simple' file conversion. Only
if
> >>you know aromatic atoms/bonds you can create e.g. a MOL2 file !!!
> >
> >
> > I went and looked at the sd file definition on the mdl web site. A
bond
> > type of "4" is only permitted (required?) for structures intended
for
> > use as queries (against, presumably, a database). I'm sure you'll
find
> > that particular distinction as odd as I do but at any rate, that's
their
> > standard.
> >
> >>From what I've seen JOELib seems to be focused on representing
specific,
> > rather than generic (i.e. query), molecules so it seems as though
the sd
> > writer should put out alternating 1's and 2's. Or perhaps it's
sensible
> > to have behavior depend on a flag, so you can ask the sd writer to
use
> > type "4" bonds if desired.
> >
> > Here's a fragment of code that I think will do the trick. Let me
know
> > what you think.
> >
> > Wayne
> >
> > //check, if aromatic bond
> > if (atom.isAromatic() && nbr.isAromatic() ||
> > (bond.getBO() =3D=3D JOEBond.JOE_AROMATIC_BOND_ORDER))
> > {
> > // Non-query structures must use Kekule
> > representation
> > if (bondPairs.containsKey(new
> > Integer(atom.getIdx())) || bondPairs.containsKey(new
> > Integer(nbr.getIdx())))
> > {
> > bondType =3D 1; // single bond
> > }
> > else
> > {
> > bondType =3D 2; // double bond
> > bondPairs.put(new
Integer(atom.getIdx()),
> > new Integer(nbr.getIdx()));
> > bondPairs.put(new Integer(nbr.getIdx()),
new
> > Integer(atom.getIdx()));
> > }
> > }
> > else
> > {
> > // 1 single
> > // 2 double
> > bondType =3D bond.getBO();
> > }
> >
> >
------------------------------------------------------------------------
> ---------------------------------------------
> > This email may contain material that is confidential and privileged
and
> is for the sole use of the intended recipient. Any review, reliance or
> distribution by others or forwarding without express permission is
> strictly prohibited. If you are not the intended recipient, please
contact
> the sender and delete all copies.
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: IBM Linux Tutorials.
> > Become an expert in LINUX or just sharpen your skills. Sign up for
> IBM's
> > Free Linux Tutorials. Learn everything from the bash shell to sys
> admin.
> > Click now! http://ads.osdn.com/?ad_id=1278&alloc_id371&op=3Dclick
> > _______________________________________________
> > Joelib-help mailing list
> > Joe...@li...
> > https://lists.sourceforge.net/lists/listinfo/joelib-help
> >
>=20
>=20
> --
> Dipl. Chem. Joerg K. Wegner
> Center of Bioinformatics Tuebingen (ZBIT)
> Department of Computer Architecture
> Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
> Phone: (+49/0) 7071 29 78970
> Fax: (+49/0) 7071 29 5091
> E-Mail: mailto:we...@in...
> WWW: http://www-ra.informatik.uni-tuebingen.de
> --
> Never mistake motion for action.
> E. Hemingway
>=20
-------------------------------------------------------------------------=
--------------------------------------------
This email may contain material that is confidential and privileged and =
is for the sole use of the intended recipient. Any review, reliance or =
distribution by others or forwarding without express permission is =
strictly prohibited. If you are not the intended recipient, please =
contact the sender and delete all copies.
|
|
From: Joerg K. W. <we...@in...> - 2003-12-15 16:06:41
|
Hi Wayne,
what contains the 'bondPairs'-variable ? Seems to be a HashMap or
something related, but what's their content.
Regards, Joerg
> Hi Joerg,
>
> A couple weeks ago I asked about the bond type "4" in the sd files
> produced by JOELib. You said
>
>
>>ah, o.k., but that's not a bug that's a feature! These bonds are
>>aromatic and you will find this also in the SD-FILE definition of MDL.
>>That why you should use JOELib or OpenBabel, because they have a
>> really
>>great chemical expert system behind 'simple' file conversion. Only if
>>you know aromatic atoms/bonds you can create e.g. a MOL2 file !!!
>
>
> I went and looked at the sd file definition on the mdl web site. A bond
> type of "4" is only permitted (required?) for structures intended for
> use as queries (against, presumably, a database). I'm sure you'll find
> that particular distinction as odd as I do but at any rate, that's their
> standard.
>
>>From what I've seen JOELib seems to be focused on representing specific,
> rather than generic (i.e. query), molecules so it seems as though the sd
> writer should put out alternating 1's and 2's. Or perhaps it's sensible
> to have behavior depend on a flag, so you can ask the sd writer to use
> type "4" bonds if desired.
>
> Here's a fragment of code that I think will do the trick. Let me know
> what you think.
>
> Wayne
>
> //check, if aromatic bond
> if (atom.isAromatic() && nbr.isAromatic() ||
> (bond.getBO() == JOEBond.JOE_AROMATIC_BOND_ORDER))
> {
> // Non-query structures must use Kekule
> representation
> if (bondPairs.containsKey(new
> Integer(atom.getIdx())) || bondPairs.containsKey(new
> Integer(nbr.getIdx())))
> {
> bondType = 1; // single bond
> }
> else
> {
> bondType = 2; // double bond
> bondPairs.put(new Integer(atom.getIdx()),
> new Integer(nbr.getIdx()));
> bondPairs.put(new Integer(nbr.getIdx()), new
> Integer(atom.getIdx()));
> }
> }
> else
> {
> // 1 single
> // 2 double
> bondType = bond.getBO();
> }
>
> ---------------------------------------------------------------------------------------------------------------------
> This email may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies.
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: IBM Linux Tutorials.
> Become an expert in LINUX or just sharpen your skills. Sign up for IBM's
> Free Linux Tutorials. Learn everything from the bash shell to sys admin.
> Click now! http://ads.osdn.com/?ad_id78&alloc_id371&op=click
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help
>
--
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
E. Hemingway
|
|
From: Wayne V. <vol...@re...> - 2003-12-12 05:33:53
|
Hi Joerg,
A couple weeks ago I asked about the bond type "4" in the sd files
produced by JOELib. You said
> ah, o.k., but that's not a bug that's a feature! These bonds are=20
> aromatic and you will find this also in the SD-FILE definition of MDL.
> That why you should use JOELib or OpenBabel, because they have a
really=20
> great chemical expert system behind 'simple' file conversion. Only if=20
> you know aromatic atoms/bonds you can create e.g. a MOL2 file !!!
I went and looked at the sd file definition on the mdl web site. A bond
type of "4" is only permitted (required?) for structures intended for
use as queries (against, presumably, a database). I'm sure you'll find
that particular distinction as odd as I do but at any rate, that's their
standard.
From what I've seen JOELib seems to be focused on representing specific,
rather than generic (i.e. query), molecules so it seems as though the sd
writer should put out alternating 1's and 2's. Or perhaps it's sensible
to have behavior depend on a flag, so you can ask the sd writer to use
type "4" bonds if desired.
Here's a fragment of code that I think will do the trick. Let me know
what you think.
Wayne
//check, if aromatic bond
if (atom.isAromatic() && nbr.isAromatic() ||
(bond.getBO() =3D=3D JOEBond.JOE_AROMATIC_BOND_ORDER))
{
// Non-query structures must use Kekule
representation
if (bondPairs.containsKey(new
Integer(atom.getIdx())) || bondPairs.containsKey(new
Integer(nbr.getIdx())))=20
{
bondType =3D 1; // single bond
}
else
{
bondType =3D 2; // double bond
bondPairs.put(new Integer(atom.getIdx()),
new Integer(nbr.getIdx()));
bondPairs.put(new Integer(nbr.getIdx()), new
Integer(atom.getIdx()));
}
}
else
{
// 1 single
// 2 double
bondType =3D bond.getBO();
}
-------------------------------------------------------------------------=
--------------------------------------------
This email may contain material that is confidential and privileged and =
is for the sole use of the intended recipient. Any review, reliance or =
distribution by others or forwarding without express permission is =
strictly prohibited. If you are not the intended recipient, please =
contact the sender and delete all copies.
|
|
From: Joerg K. W. <we...@in...> - 2003-12-09 11:57:08
|
Hi Gerd, could you please change these things and send me the complete ResourceLoader, so i must not check these things on my own. Thanks and best regards, Joerg > On Mon, 08 Dec 2003 15:51:34 +0100 > "Joerg K. Wegner" <we...@in...> wrote: > > >>Hi Gerd, >> >> >>>and try to load a molecule from a file I get an error that >>>joelib can't load the file atomtypes.txt although the jar contains >>>it. If I unpack joelib.jar it works. >>>I found out that the error occurs if the jar resists in a directory >>>with whitespaces in the pathname. Also I saw that >>>wsi.ra.tools.ResourceLoader replaces '%20' in the pathname with ' ' which >>>seems to be the problem here. Why is this done ? Any hints for fixing this >>>problem ? >> >>111. As you can see also the replacement takes only an effect for >>'files' which are not contained in a .zip or .jar file ! > > > Yes, and this seems to be the problem. I've used java.net.URLDecoder > to decode the urlToZipArchive in getBytesFromArchive() and everything > works fine. So the solution seems to be move the '%20' replacement > code a few lines up, so that also archive paths are handled. Also > I would recomment to use java.net.URLDecoder instead of using > regexp. This way you don't need to care about other %-sign that > may occur. > > best regards, > gerd > > ________________________________________________________________ > Gerd Mueller ge...@sm... > SMB GmbH http://www.smb-tec.com > > > ------------------------------------------------------- > This SF.net email is sponsored by: IBM Linux Tutorials. > Become an expert in LINUX or just sharpen your skills. Sign up for IBM's > Free Linux Tutorials. Learn everything from the bash shell to sys admin. > Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click > _______________________________________________ > Joelib-help mailing list > Joe...@li... > https://lists.sourceforge.net/lists/listinfo/joelib-help > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
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From: Gerd M. <Ger...@sm...> - 2003-12-09 11:19:05
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On Mon, 08 Dec 2003 15:51:34 +0100 "Joerg K. Wegner" <we...@in...> wrote: > Hi Gerd, > > > and try to load a molecule from a file I get an error that > > joelib can't load the file atomtypes.txt although the jar contains > > it. If I unpack joelib.jar it works. > > I found out that the error occurs if the jar resists in a directory > > with whitespaces in the pathname. Also I saw that > > wsi.ra.tools.ResourceLoader replaces '%20' in the pathname with ' ' which > > seems to be the problem here. Why is this done ? Any hints for fixing this > > problem ? > > 111. As you can see also the replacement takes only an effect for > 'files' which are not contained in a .zip or .jar file ! Yes, and this seems to be the problem. I've used java.net.URLDecoder to decode the urlToZipArchive in getBytesFromArchive() and everything works fine. So the solution seems to be move the '%20' replacement code a few lines up, so that also archive paths are handled. Also I would recomment to use java.net.URLDecoder instead of using regexp. This way you don't need to care about other %-sign that may occur. best regards, gerd ________________________________________________________________ Gerd Mueller ge...@sm... SMB GmbH http://www.smb-tec.com |
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From: Joerg K. W. <we...@in...> - 2003-12-08 14:46:08
|
Hi Gerd,
> and try to load a molecule from a file I get an error that
> joelib can't load the file atomtypes.txt although the jar contains
> it. If I unpack joelib.jar it works.
> I found out that the error occurs if the jar resists in a directory
> with whitespaces in the pathname. Also I saw that wsi.ra.tools.ResourceLoader
> replaces '%20' in the pathname with ' ' which seems to be the
> problem here. Why is this done ? Any hints for fixing this problem ?
111. As you can see also the replacement takes only an effect for
'files' which are not contained in a .zip or .jar file !
So the question is, why is this not recognized (line 161) ?
Switch
log4j.category.wsi.ra.tool.ResourceLoader=INFO
to
log4j.category.wsi.ra.tool.ResourceLoader=DEBUG
in build/log4.properties and src/log4j.properties
and try again. Then you could see a little bit more informations !
Otherwise you should add some System.out.println("abc"); to the
ResourceLoader class to see why this check fails !
So three way plan:
1. increase verbosity in logging
2. add console informations and recompile sources
3. check again your example.
I added the replacement of white space characters (FOR FILES), because
other users had the same path problem. So, we must find a way to combine
the solutions for both problems at once.
222. Which way are you using for loading your file. ?
Stream, SimpleReader, ResourceLoader, ... ?
333. Have you anything changed in joelib.properties ?
There you can define another 'atomtype.txt'-path. Typically JOELib uses
the resource-load mechanism to be independant from user-paths.
Regards, Joerg
--
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
E. Hemingway
|
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From: Gerd M. <Ger...@sm...> - 2003-12-08 14:19:06
|
Hi, If I call java -jar joelib.jar:myclasses.jar my.Main.Class and try to load a molecule from a file I get an error that joelib can't load the file atomtypes.txt although the jar contains it. If I unpack joelib.jar it works. I found out that the error occurs if the jar resists in a directory with whitespaces in the pathname. Also I saw that wsi.ra.tools.ResourceLoader replaces '%20' in the pathname with ' ' which seems to be the problem here. Why is this done ? Any hints for fixing this problem ? Best Regards, gerd ________________________________________________________________ Gerd Mueller ge...@sm... SMB GmbH http://www.smb-tec.com |
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From: Joerg K. W. <we...@in...> - 2003-11-27 09:08:34
|
Hi Wayne, > I grabbed JOELib-bin-20031117 and some data from the nci database, as I= =20 > wanted to compare property calculations from JOELib to other=20 > calculators. I queried for all structures that had an experimental log= =20 > P associated with them, 3576 structures came back. >=20 > I saw a number of discrepancies between what=92s calculated by JOELib a= nd=20 > what was recorded in the NCI dataset. For example : >=20 > - In 16% of the cases # of rotational bonds disagreed >=20 > - In ~29% of the cases, Number_of_HBA2 disagreed with the number of=20 > acceptors in the nci database >=20 > - In ~1% of the cases, Number_of_HBD1 disagreed with the number of=20 > donors in the nci database >=20 > - JOELib logP had a correlation of 0.64 with the experimental log P=20 > values; KOW & acd labs predictions in nci had correlations of 0.98 and = 0.92 >=20 > Below is a snippet of the code I=92m using=97before I look any further = at=20 > the reasons for the differences noted above, could you let me know if=20 > I=92m using the library correctly? Sounds reasonably !!! I've actually submitted two 'model-building-papers' which includes the=20 following sentences: 'For comparing models it should be guaranteed that the descriptors are=20 using all the same atom typer, aromaticity- and hybridization-model.=20 Because many programs use text definitions for the atom types=20 [JOELib,OpnBabel] we recommend to use the same definitions or the same=20 data processing workflow to avoid bad prediction results for new molecule= s.' As already mentioned several times, the descriptor calculation process=20 is the LAST step after processing four expert systems: http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomty= per.html In my opinion most of the programs have their own atom typer, which is=20 really critical !!! I thrust, taking my descriptor calculation=20 experience into account, mostly JOELib and OpenBabel, because both uses=20 the same atom typing definitions, which are open-source, open-content=20 and based on text files !!! Let's say these expert systems fails for some compounds, we can at least=20 be sure that they will also fail for analogue compounds, so we will have=20 a systematic error. Because these models have a long tradition they are=20 still really good, in my opinion. My cooperation partner told me that=20 the models are sometimes better than Sybyl. So far the results for the first definition of rotatable bonds, H-donors=20 and H-acceptors. The second definition is based on YOUR definition of=20 these descriptors. JOELib supports e.g. two different kind of donors and=20 acceptors, and will be never a gurantee for completeness !!! Most of the=20 authors in the literature gives their SMARTS pattern for this definition=20 or say, which is VERY BAD, we used program XYZ. A program is from the=20 computer scientist standpoint of view not transparent !!! Use always SMARTS or detailed descriptions of these descriptors !!! To LogP. I've already published a paper for LogP prediction. As you=20 surely know there are two main ways to predict values: 1. GroupContribution approach: The open-source model in JOELib is such=20 one. The model is really not that good (i checked this). See literature=20 reference in source code. 2. Descriptor/DataMining approach: Part of my published paper: J. K. Wegner, A. Zell, Prediction of Aqueous Solubility and Partition=20 Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection=20 Method, Journal of Chemical Information and Computer Science (JCICS),=20 2003, 43(3), 1077-1084, DOI: 10.1021/ci034006u Concluding my mail i will say that my main work i'm paid for is Chemical=20 DataMining, so i know a lot of the problems in this area, please don't=20 hesitate to ask me, although these topics can be a little bit off-topic=20 for this mailing list. Do you know the JOELib interface to Weka ??? Regards, Joerg >=20 > Thanks, > Wayne >=20 > =20 >=20 > public class test { >=20 > =20 >=20 > public test() { >=20 > } >=20 > =20 >=20 > /** >=20 > * @param args the command line arguments >=20 > */ >=20 > public static void main(String[] args) throws Exception { >=20 > SimpleReader sdfile =3D new SimpleReader(args[0]); >=20 > JOEMol mol =3D new JOEMol(); >=20 > =20 >=20 > PrintStream out =3D new PrintStream(new FileOutputStream("out.d= at")); >=20 > =20 >=20 > DescResult LogP =3D null; >=20 > =20 >=20 > out.println("E_NSC\tjoe_logP\tkow_LogP\texp_logP\tacd_logP"); >=20 > while (sdfile.readNext(mol)) { >=20 > //System.out.println(mw.getDoubleValue(mol)); >=20 > LogP =3D DescriptorHelper.instance().descFromMol(mol, "LogP= "); >=20 > =20 >=20 > String kow_LogP =3D convert(mol.getData("E_LOGP")); >=20 > String exp_LogP =3D convert(mol.getData("E_LOGP/2")); >=20 > String acd_LogP =3D convert(mol.getData("E_LOGP/3")); >=20 > =20 >=20 > String nsc =3D mol.getData("E_NSC").toString(); >=20 > =20 >=20 > out.print(nsc + "\t" + LogP + "\t" + kow_LogP + "\t"); >=20 > out.println(exp_LogP + "\t" + acd_LogP); >=20 > } >=20 > } >=20 > =20 >=20 > static String convert(joelib.data.JOEGenericData in) { >=20 > String result =3D ""; >=20 > if (in !=3D null) { >=20 > result =3D in.toString().trim().substring(0,=20 > in.toString().indexOf(' ' >=20 > , 1)); >=20 > } >=20 > if (result =3D=3D null) { >=20 > return ""; >=20 > } else { >=20 > return result; >=20 > } >=20 > } >=20 > } >=20 > =20 >=20 > The =93convert=94 function is used to clean off spaces & a zero appende= d to=20 > the field containing the predicted log p values. I don=92t know why th= e=20 > sd file dump from the nci has that. >=20 > =20 >=20 > -----------------------------------------------------------------------= --------------------------=20 >=20 > This email may contain material that is confidential and privileged and= =20 > is for the sole use of the intended recipient. Any review, reliance or=20 > distribution by others or forwarding without express permission is=20 > strictly prohibited. If you are not the intended recipient, please=20 > contact the sender and delete all copies. >=20 --=20 Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
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From: Joerg K. W. <we...@in...> - 2003-11-27 08:42:43
|
Hi Hongmei, > How could I remove all H atoms in a JOEMol? JOEMol mol; mol=YourGetMolecule(); mol.deletetHydrogens(); BTW, I've found a dead-loop-bug in mol.deletetHydrogen(); which works independantly from mol.deletetHydrogens(); so all will be fine for you. I will check in the bug fixes with some code cleanup (hopefully) this week. Regards, Joerg > > Happy Thanksgiving. > > > Thanks. > > Hongmei > > > -----Original Message----- > From: Joerg K. Wegner [mailto:we...@in...] > Sent: Thursday, November 13, 2003 2:20 AM > To: Sun, Hongmei* > Cc: 'joe...@li...' > Subject: Re: [Joelib-help] aromatize a molecule > > Hi all, > > if you have loaded a molecule and then call, e.g. > JOEAtom atom=mol.getAtom(); > boolean isAromatic=atom.isAromatic(); > > JOELib will determine the aromaticity on it's own; only once if you will > not change atoms or bonds for beeing faster. That's one reason for the > beginModify and endModify flags when working on molecules. > > When you want to check the state on your own you can call: > boolean assignedAlready=molecule.hasAromaticPerceived(); > > or you can assign the flags on your own: > JOEAromaticTyper.instance().assignAromaticFlags(molecule); > > For a short description see: > http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomtyper > .html > and all TEXT DEFINITION files in joelib/src/joelib/data/plain or online at: > http://cvs.sourceforge.net/viewcvs.py/joelib/joelib/src/joelib/data/plain/ > which are based on SMARTS, so if you want to change things in the expert > system models feel free to do so. > > Regards, Joerg > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
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From: Wayne V. <vol...@re...> - 2003-11-27 02:58:34
|
I grabbed JOELib-bin-20031117 and some data from the nci database, as I
wanted to compare property calculations from JOELib to other
calculators. I queried for all structures that had an experimental log
P associated with them, 3576 structures came back.
=20
I saw a number of discrepancies between what's calculated by JOELib and
what was recorded in the NCI dataset. For example :
- In 16% of the cases # of rotational bonds disagreed
- In ~29% of the cases, Number_of_HBA2 disagreed with the number of
acceptors in the nci database
- In ~1% of the cases, Number_of_HBD1 disagreed with the number of
donors in the nci database
- JOELib logP had a correlation of 0.64 with the experimental log P
values; KOW & acd labs predictions in nci had correlations of 0.98 and
0.92
=20
Below is a snippet of the code I'm using-before I look any further at
the reasons for the differences noted above, could you let me know if
I'm using the library correctly?
=20
Thanks,
Wayne
=20
public class test {
=20
public test() {
}
=20
/**
* @param args the command line arguments
*/
public static void main(String[] args) throws Exception {
SimpleReader sdfile =3D new SimpleReader(args[0]);
JOEMol mol =3D new JOEMol();
=20
PrintStream out =3D new PrintStream(new
FileOutputStream("out.dat"));
=20
DescResult LogP =3D null;
=20
out.println("E_NSC\tjoe_logP\tkow_LogP\texp_logP\tacd_logP");
while (sdfile.readNext(mol)) {
//System.out.println(mw.getDoubleValue(mol));
LogP =3D DescriptorHelper.instance().descFromMol(mol, =
"LogP");
=20
String kow_LogP =3D convert(mol.getData("E_LOGP"));
String exp_LogP =3D convert(mol.getData("E_LOGP/2"));
String acd_LogP =3D convert(mol.getData("E_LOGP/3"));
=20
String nsc =3D mol.getData("E_NSC").toString();
=20
out.print(nsc + "\t" + LogP + "\t" + kow_LogP + "\t");
out.println(exp_LogP + "\t" + acd_LogP);
}
}
=20
static String convert(joelib.data.JOEGenericData in) {
String result =3D "";
if (in !=3D null) {
result =3D in.toString().trim().substring(0,
in.toString().indexOf(' '
, 1));
}
if (result =3D=3D null) {
return "";
} else {
return result;
}
}
}
=20
The "convert" function is used to clean off spaces & a zero appended to
the field containing the predicted log p values. I don't know why the
sd file dump from the nci has that.
=20
-------------------------------------------------------------------------=
--------------------------------------------
This email may contain material that is confidential and privileged and =
is for the sole use of the intended recipient. Any review, reliance or =
distribution by others or forwarding without express permission is =
strictly prohibited. If you are not the intended recipient, please =
contact the sender and delete all copies.
|
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From: Sun, Hongmei* <HS...@nc...> - 2003-11-26 19:34:49
|
Hello, there, How could I remove all H atoms in a JOEMol? Happy Thanksgiving. Thanks. Hongmei -----Original Message----- From: Joerg K. Wegner [mailto:we...@in...] Sent: Thursday, November 13, 2003 2:20 AM To: Sun, Hongmei* Cc: 'joe...@li...' Subject: Re: [Joelib-help] aromatize a molecule Hi all, if you have loaded a molecule and then call, e.g. JOEAtom atom=mol.getAtom(); boolean isAromatic=atom.isAromatic(); JOELib will determine the aromaticity on it's own; only once if you will not change atoms or bonds for beeing faster. That's one reason for the beginModify and endModify flags when working on molecules. When you want to check the state on your own you can call: boolean assignedAlready=molecule.hasAromaticPerceived(); or you can assign the flags on your own: JOEAromaticTyper.instance().assignAromaticFlags(molecule); For a short description see: http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomtyper .html and all TEXT DEFINITION files in joelib/src/joelib/data/plain or online at: http://cvs.sourceforge.net/viewcvs.py/joelib/joelib/src/joelib/data/plain/ which are based on SMARTS, so if you want to change things in the expert system models feel free to do so. Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
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From: Joerg K. W. <we...@in...> - 2003-11-25 11:02:06
|
Hi Gerd, > I'm trying to use subtructure search with SMARTS, but somehow > it doesn't work. I do the following: > 1. Load a Molecule from the SMILES string 'C1CCCCC1 .' > 2. Create a SMARTS pattern with 'c1ccccc1' > > But the match method returns false. I have to admit that I'm > not chemist but a computer scientist, so maybe I've overseen > something. But shouldn't the pattern match the given structure > since they are the same ? No, the patterns are really different. The SMILES string creates a 6ring with single bonds. The SMARTS string looks for an aromatic ring with conjugated single-bond-double-bond system (aromatic). In SMILES/SMARTS all kind of aromatic atoms, are described by lowerCase letters. So C, c and #6 describes aliphatic C, aromatic C and aliphatic/aromatic C Please have a look at the SMILES/SMARTS references in the tutorial. http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/bibliography.html The SMARTS Patterns can get really complex, so you can always refer to the examples in joelib/src/joelib/data/plain/*, especially when handling atom environments [$(#6);$(*=O);$(*~c)] which means any carbon connected with a double bond to an oxygen and with an any bond to an aromatic C. Best regards, Joerg > > Best Regards, > gerd > > ________________________________________________________________ > Gerd Mueller ge...@sm... > SMB GmbH http://www.smb-tec.com > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > _______________________________________________ > Joelib-help mailing list > Joe...@li... > https://lists.sourceforge.net/lists/listinfo/joelib-help > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
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From: Gerd M. <Ger...@sm...> - 2003-11-25 10:50:07
|
Hi, I'm trying to use subtructure search with SMARTS, but somehow it doesn't work. I do the following: 1. Load a Molecule from the SMILES string 'C1CCCCC1 .' 2. Create a SMARTS pattern with 'c1ccccc1' But the match method returns false. I have to admit that I'm not chemist but a computer scientist, so maybe I've overseen something. But shouldn't the pattern match the given structure since they are the same ? Best Regards, gerd ________________________________________________________________ Gerd Mueller ge...@sm... SMB GmbH http://www.smb-tec.com |
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From: Joerg K. W. <we...@in...> - 2003-11-18 16:31:47
|
Hi Wayne, ah, o.k., but that's not a bug that's a feature! These bonds are aromatic and you will find this also in the SD-FILE definition of MDL. That why you should use JOELib or OpenBabel, because they have a really great chemical expert system behind 'simple' file conversion. Only if you know aromatic atoms/bonds you can create e.g. a MOL2 file !!! 1. If you don't want that, you should use your own SDF writer resolving the aromaticity flags into a conjugated system using single and double bonds. Just modify joelib.io.types.MDLSD to joelib.io.types.MyMDLSD and tell joelib the new defintion at joelib.properties joelib.filetypes.1.name = SDF joelib.filetypes.1.representation = joelib.io.types.MyMDLSD 2. The unelegant way would be to supress the aromaticity typer, by saying: 'aromaticity was already assigned' ! Which will cause a lot of problems, e.g. if you will try to find aromatic rings or much more serious assigning correct atom types for general file conversions ... Regards, Joerg > Thanks Joerg. I'll follow your suggestions, in particular I'll grab the > latest release. You can see the exact problem I had in the atom > connection section of the sd file, I've grabbed just a few lines to > illustrate : > > Input file : > 4 5 2 0 0 0 0 > 4 9 1 0 0 0 0 > 5 6 1 0 0 0 0 > 5 19 1 0 0 0 0 > 6 7 2 0 0 0 0 > > Output file : > 4 5 4 0 0 0 0 > 4 9 4 0 0 0 0 > 5 6 4 0 0 0 0 > 5 19 1 0 0 0 0 > 6 7 4 0 0 0 0 > > See all the 4's? > > I'll try grabbing the latest release and see if that works--I had bad > timing, you must have put up the new release a day or two after I > downloaded JOELib. I'll use one of the mailing lists if I still have a > problem. > > Thanks > Wayne > > >>-----Original Message----- >>From: Joerg K. Wegner [mailto:we...@in...] >>Sent: Tuesday, November 18, 2003 2:47 AM >>To: Wayne Volkmuth >>Subject: Re: JOELib question >> >>Hi Wayne, >> >>1. New release was submitted yesterday with improved PDF writer. >> >>2. I don't get it. What is the exact problem ? >>I've simply replaced "out.sdf" by "out.pdf" and here is the result. > > I've > >>shortly compared this to the original 55.sdf and can't see any > > problems. > >>Your code works as it should or did you expect another result ? >> >>3.1. Please explain problems in more detail and contact me again. >>You can also use the helping mailing or developer mailing list for >>further responses to avoid e-mail redundancies. >>3.2. You are still using a simple writer, if you want handle special >>cases like corrupted input SDF entries (e.g. missing bond definitions) >>or somethings else you should use the complex reader/writer mechanism >>explained in joelib.test.ConvertSkip >> >>BTW, image output properties can be set in joelib.properties, look for >>Renderer2DModel and Mol2Image and PDF options ! >> >>Regards, Joerg >> >> >>>I downloaded JOELib a few days ago and got stuck with simply reading > > in > >>>an sd file then writing it back out. I've attached the short > > program I > >>>wrote, along with test input and output. I'm getting ring > > structures > >>>that have four bonds shared between the atoms, I'm not sure what I'm >>>doing wrong. I'd appreciate it if you are able to tell me what I > > should > >>>be doing. >>> >>> >>> >>>Thanks >>> >>>Wayne >>> >>> > > ------------------------------------------------------------------------ > >>------------------------- >> >>>This email may contain material that is confidential and privileged > > and > >>>is for the sole use of the intended recipient. Any review, reliance > > or > >>>distribution by others or forwarding without express permission is >>>strictly prohibited. If you are not the intended recipient, please >>>contact the sender and delete all copies. >>> >> >> >>-- >>Dipl. Chem. Joerg K. Wegner >>Center of Bioinformatics Tuebingen (ZBIT) >>Department of Computer Architecture >>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany >>Phone: (+49/0) 7071 29 78970 >>Fax: (+49/0) 7071 29 5091 >>E-Mail: mailto:we...@in... >>WWW: http://www-ra.informatik.uni-tuebingen.de >>-- >>Never mistake motion for action. >> E. Hemingway > > > > --------------------------------------------------------------------------------------------------------------------- > This email may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. > > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
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From: Joerg K. W. <we...@in...> - 2003-11-13 08:14:54
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Hi all, if you have loaded a molecule and then call, e.g. JOEAtom atom=mol.getAtom(); boolean isAromatic=atom.isAromatic(); JOELib will determine the aromaticity on it's own; only once if you will not change atoms or bonds for beeing faster. That's one reason for the beginModify and endModify flags when working on molecules. When you want to check the state on your own you can call: boolean assignedAlready=molecule.hasAromaticPerceived(); or you can assign the flags on your own: JOEAromaticTyper.instance().assignAromaticFlags(molecule); For a short description see: http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomtyper.html and all TEXT DEFINITION files in joelib/src/joelib/data/plain or online at: http://cvs.sourceforge.net/viewcvs.py/joelib/joelib/src/joelib/data/plain/ which are based on SMARTS, so if you want to change things in the expert system models feel free to do so. Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
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From: Sun, Hongmei* <HS...@nc...> - 2003-11-10 19:52:46
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Hello, all, How to aromatize a molecule in JOELIB? Thanks. Hongmei |
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From: Joerg K. W. <we...@in...> - 2003-11-05 21:47:07
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Hi Boryeu, i can speak only for JOELib: 1.1. Download latest source code release 1.2. Replace joelib/data/JOEAromaticTyper by the file given at http://sourceforge.net/tracker/index.php?func=detail&aid=823931&group_id=39708&atid=425969 1.3. compile complete project with: joelib> sh build.sh compile (works without ant installation) OR joelib/ant> ant compile (ant must be installed) 2.1. get complete new CVS version (recommended, to avoid side effects): Follow instruction at: http://sourceforge.net/cvs/?group_id=39708 Use: cvs -d:pserver:ano...@cv...:/cvsroot/joelib co joelib 2.2. compile complete project with: joelib> sh build.sh compile (works without ant installation) OR joelib/ant> ant compile (ant must be installed) For OpenBabel you should add the extended root atom picking to the aromatic typer, which is not too difficult. Regards, Joerg |
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