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From: <we...@in...> - 2002-12-04 07:37:55
|
Hello henrik, > * uniqueness of the SMILES patterns > do you think here about a 'normalization' like the one in daylight? I mean that generated SMILES patterns should be always independent from the numeration of the given molecule (e.g. from SDF file). This will then allow to use the UNIQUE SMILES String as specific ID in a database or something. Or you can calculate the hash code for a molecule using atom types and unique numeration for getting (hopefully) a unique ID, ... > > Can give me a hint where to look at in the SMARTS-parser where the chiral-information is read in? joelib/src/joelib/smart/ParseSmart:375 > Regards, > henrik Regards, Joerg > dr. henrik kuhn > new technologies > morphochem AG > gmunder str. 37-37a > 81379 muenchen > > tel. ++49-89-78005-0 > fax ++49-89-78005-555 > > hen...@mo... > http://www.morphochem.de > > -----Original Message----- > From: Jörg K. Wegner [SMTP:we...@in...] > Sent: Monday, December 02, 2002 10:24 AM > To: hen...@mo...; joe...@li... > Subject: Re: [Joelib-devel] going chiral? > > Hello Henrik, > >>are you thinking about implementing chiral-capabilities into joelib as soon as possible? You need help for that purpose? > > Any help would be great ! I've an long additional wish list :-) > > Some parts are already available --> Take a look at: > > 1. joelib/src/joelib/smiles/SmilesParser:1056 > for @ and @@ > > 2. joelib/src/joelib/molecule/JOEMol:2767 in method findChiralCenters() > uses GraphPotentials (see API docu under joelib/src/joelib/desc/types) > > 3. joelib/src/joelib/molecule/JOEAtom:1980 in method isChiral() > > Mail to the developer mailing list, if you have further questions. > Because i can not handle all open fronts, i would be glad if you would > adapt JOELib for your needs and if you would help me with the development. > > Now some additional comments: > 1. JOELib has no direct 2D layout facility. It uses the CDK layout tool, > but this could be eventually a problem with chiral centers (i've never > evaluated that). > > 2. I'm not sure about the uniqueness of the SMILES patterns generated by > JOELib (must be evaluated). If you need a unique (re)numbering i could > offer you the Morgan-Agorithm code WITH solving renumbering ties (some > students work) !!! > > >>Regards, >>henrik > > Regards, Joerg > > -- Dipl. Chem. Joerg K. Wegner Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de |
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From: henrik k. <hen...@mo...> - 2002-12-02 15:24:52
|
Two more notes/questions: * uniqueness of the SMILES patterns do you think here about a 'normalization' like the one in daylight? Can give me a hint where to look at in the SMARTS-parser where the = chiral-information is read in? Regards, henrik dr. henrik kuhn new technologies morphochem AG gmunder str. 37-37a 81379 muenchen tel. ++49-89-78005-0 fax ++49-89-78005-555 hen...@mo... http://www.morphochem.de -----Original Message----- From: J=F6rg K. Wegner [SMTP:we...@in...] Sent: Monday, December 02, 2002 10:24 AM To: hen...@mo...; joe...@li... Subject: Re: [Joelib-devel] going chiral? Hello Henrik, > are you thinking about implementing chiral-capabilities into joelib as = soon as possible? You need help for that purpose? Any help would be great ! I've an long additional wish list :-) Some parts are already available --> Take a look at: 1. joelib/src/joelib/smiles/SmilesParser:1056 for @ and @@ 2. joelib/src/joelib/molecule/JOEMol:2767 in method findChiralCenters() uses GraphPotentials (see API docu under joelib/src/joelib/desc/types) 3. joelib/src/joelib/molecule/JOEAtom:1980 in method isChiral() Mail to the developer mailing list, if you have further questions.=20 Because i can not handle all open fronts, i would be glad if you would adapt JOELib for your needs and if you would help me with the = development. Now some additional comments: 1. JOELib has no direct 2D layout facility. It uses the CDK layout tool, = but this could be eventually a problem with chiral centers (i've never=20 evaluated that). 2. I'm not sure about the uniqueness of the SMILES patterns generated by = JOELib (must be evaluated). If you need a unique (re)numbering i could=20 offer you the Morgan-Agorithm code WITH solving renumbering ties (some=20 students work) !!! > Regards, > henrik Regards, Joerg --=20 Dipl. Chem. Joerg K. Wegner Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, = Germany Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Joelib-devel mailing list Joe...@li... https://lists.sourceforge.net/lists/listinfo/joelib-devel |
|
From: <we...@in...> - 2002-12-02 09:23:08
|
Hello Henrik, > are you thinking about implementing chiral-capabilities into joelib as soon as possible? You need help for that purpose? Any help would be great ! I've an long additional wish list :-) Some parts are already available --> Take a look at: 1. joelib/src/joelib/smiles/SmilesParser:1056 for @ and @@ 2. joelib/src/joelib/molecule/JOEMol:2767 in method findChiralCenters() uses GraphPotentials (see API docu under joelib/src/joelib/desc/types) 3. joelib/src/joelib/molecule/JOEAtom:1980 in method isChiral() Mail to the developer mailing list, if you have further questions. Because i can not handle all open fronts, i would be glad if you would adapt JOELib for your needs and if you would help me with the development. Now some additional comments: 1. JOELib has no direct 2D layout facility. It uses the CDK layout tool, but this could be eventually a problem with chiral centers (i've never evaluated that). 2. I'm not sure about the uniqueness of the SMILES patterns generated by JOELib (must be evaluated). If you need a unique (re)numbering i could offer you the Morgan-Agorithm code WITH solving renumbering ties (some students work) !!! > Regards, > henrik Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de |
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From: henrik k. <hen...@mo...> - 2002-12-02 08:33:18
|
Hi JOELIB-devs, are you thinking about implementing chiral-capabilities into joelib as soon as possible? You need help for that purpose? Regards, henrik henrikDOTkuhnATmorphochemDOTde |
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From: Joerg K. W. <we...@in...> - 2002-10-16 08:42:13
|
Hi all, I've released my templates for the Eclipse IDE which faciliates the algorithm development and the JOELib standard tasks, like: - iterate over all atoms - iterate over all bonds - SMARTS substructure search See: www.eclipse.org Download:http://sourceforge.net/project/showfiles.php?group_id=39708&release_id=116627 Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de |
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From: Joerg K. W. <we...@in...> - 2002-09-20 10:17:02
|
Hello,
two initial comments:
1. this is an easy example and i will be glad to help you
2. This topic would be better placed in the help mailing list (for
future request).
Look at the appended descriptor class. Copy this file to
joelib/src/joelib/desc/types
and add
joelib.descriptor.9.representation
=joelib.desc.types.MolecularWeight
to line 102 in joelib/src/joelib.properties
The descriptor is accessible by "Molecular_weight".
A little bit of programming experience would not be a bad choice.
1. abstract - means that this class needs a child ! That's not the case
for this class.
2. The rest seems to be o.k., but the parent class (this is an abstract
one)
forces you to implement the double value calculation in
public double getDoubleValue(JOEMol mol)
{
double aValue=Double.NaN;
return aValue;
}
if you want it to use with your scheme you can use
public double getDoubleValue(JOEMol mol)
{
return getMolWt(mol);
}
Regards, Joerg
Pekka Suomalainen wrote:
>
> Trying to use getMolWt to calculate molecular weight.
> The code below fails. I have no programming experience so any help would be
> appreciated.
>
> public abstract class MW extends SimpleDoubleDesc
> {
> /*
> *
> -------------------------------------------------------------------------*
> * public static member variables
> *
> -------------------------------------------------------------------------
> */
> * Obtain a suitable logger.
> */
> private static Category logger =
> Category.getInstance("joelib.desc.types.MW");
>
> /*
> *
> -------------------------------------------------------------------------*
> * constructor
> *
> -------------------------------------------------------------------------
> */
> /*
> * Constructor for the MW object
> */
> public MW()
> {
> descInfo = DescriptorHelper.generateDescInfo("MW",
> this.getClass(),
> "topological",
> 2,
> null,
> "joelib.desc.result.AtomDoubleResult");
> }
>
> /*
> *
> -------------------------------------------------------------------------*
> * public methods
> *
> -------------------------------------------------------------------------
> */
> * Gets the molWt attribute of the <tt>JOEMol</tt> object
> *
> * @return The molWt value
> */
> public double getMolWt(JOEMol mol)
> {
> double molwt = 0.0f;
> JOEAtom atom;
> AtomIterator ait = mol.atomIterator();
> while (ait.hasNext())
> {
> atom = ait.nextAtom();
> molwt += JOEElementTable.instance().getMass(atom.getAtomicNum());
> }
>
> return molwt;
> }}
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Joelib-devel mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-devel
--
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen,
Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de |
|
From: Pekka S. <pe...@ki...> - 2002-09-20 09:53:44
|
Trying to use getMolWt to calculate molecular weight.
The code below fails. I have no programming experience so any help would be
appreciated.
public abstract class MW extends SimpleDoubleDesc
{
/*
*
-------------------------------------------------------------------------*
* public static member variables
*
-------------------------------------------------------------------------
*/
* Obtain a suitable logger.
*/
private static Category logger =
Category.getInstance("joelib.desc.types.MW");
/*
*
-------------------------------------------------------------------------*
* constructor
*
-------------------------------------------------------------------------
*/
/*
* Constructor for the MW object
*/
public MW()
{
descInfo = DescriptorHelper.generateDescInfo("MW",
this.getClass(),
"topological",
2,
null,
"joelib.desc.result.AtomDoubleResult");
}
/*
*
-------------------------------------------------------------------------*
* public methods
*
-------------------------------------------------------------------------
*/
* Gets the molWt attribute of the <tt>JOEMol</tt> object
*
* @return The molWt value
*/
public double getMolWt(JOEMol mol)
{
double molwt = 0.0f;
JOEAtom atom;
AtomIterator ait = mol.atomIterator();
while (ait.hasNext())
{
atom = ait.nextAtom();
molwt += JOEElementTable.instance().getMass(atom.getAtomicNum());
}
return molwt;
}}
|
|
From: Joerg W. <we...@in...> - 2002-09-07 11:59:18
|
Hi all,
here are some theoretical aspects at loading molecule files with JOELib:
0. TEST: loading speed 07/09/2002, AMD1400+, ASUS board, 1GB DDR RAM,
Win2K, SUN JDK1.4.0-beta2-b77
At the moment the loading process is very transparent, because of using
text based files and maximal flexible,
because descriptors can be simple integer/double value but also user
defined values, like integer/double array/matrices,
mixed input formats used for CTX files or anything you can imagine. For
descriptor development and processng that's really
great, but let's now talk about speeding up the loading process...
1. Molecular data
only molecules
10000 molecules successful loaded in 11406 ms.
20000 molecules successful loaded in 22562 ms.
30000 molecules successful loaded in 33228 ms.
-->1.1seconds/1000molecules
2. Molecular with descriptor data
with 204 double value descriptors
10000 molecules successful loaded in 92663 ms.
20000 molecules successful loaded in 185727 ms.
30000 molecules successful loaded in 273794 ms.
-->9.13seconds/1000molecules
OPTIMIZATION POSSIBILITIES:
The question is, what do we want exactly ...
0. Techniques
a. Can we define a faster SDF loader or an user defined loader ? YES,
import/export types can be dynamically be defined.
b. The text loading process can be optimized by defining a loader which
works directly on the input stream, which makes it
necessary to define a stream SDF parser. One possibility can be to
write an own parser or to use the JavaCompilerCompiler
to generate a parser.
Both possibilities are a lot of work, i assume the loading process
can speeded up to a factor of 1.3 to 1.9
c. Use a binary import format for which you can define a loader. That's
less flexible and less transparent, but the speed up
should be very high (i assume a factor greater 2).
1. Molecular data
a. Speeding up loading molecular data especially is only possibly by
using techniques from 0.
2. Descriptor data
a. Speeding up loading descriptor data especially is possible by using
a text or binary based flat file format or the techniques 0. Descriptor
data sets have a greter potential for optimization.
Regards, Joerg K. Wegner
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
|
|
From: Joerg K. W. <we...@in...> - 2002-07-16 08:19:01
|
Hello Egon, > i've noticed two small bugs in the *.sh files: > > if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" || [ "$OSTYPE" = > "posix" ] ; then > CLASSPATH=`cygpath --path --windows "$CLASSPATH"` > fi > > there seems to be missing one ']'... You're right ... fixed > Egon Joerg > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Joelib-devel mailing list > Joe...@li... > https://lists.sourceforge.net/lists/listinfo/joelib-devel -- Dipl. Chem. Joerg K. Wegner Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de |
|
From: Egon W. <eg...@sc...> - 2002-07-15 20:11:41
|
Hi, i've noticed two small bugs in the *.sh files: if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" || [ "$OSTYPE" = "posix" ] ; then CLASSPATH=`cygpath --path --windows "$CLASSPATH"` fi there seems to be missing one ']'... Egon |
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