joelib-help — JOELib-Help

[Joelib-help] pre-alpha-JOELib2 release

[Joerg K. W. <we...@in...>]

Hi all,

JOELib was heavily redesigned. The new version contains the following 
changes:
- homogenized class names and package names
- better interface/implementation separation for molecule/bond/atom
- common assignment tasks (aromaticity, kekule, closure bonds, ...) are 
now treated as atom/bond labels, the caching is done by the feature 
caching, which was already available, e.g. for distance matrix, BCUT, 
RDF, ...
This means that JOELib supports now 136 features, where 65 are ONLY the 
atom and bond labels, so by using features using them, e.g. RDF, we can 
easily calculate: 40atomlabels x 100RDF = 4000RDF, if we also use ... :-)

Please note that this version is absolutely incompatible with previous 
releases, and it is still pre-alpha, so the interface and the 
implementation can still change, but not as heavily as already done.

What are the problem:
- Time!!!
- So any helping hands updating the API documentation are highly welcome !!!
- Furthermore some comments on the actual interface would be fine.
   !Rich!

These version is available via CVS:
cvs checkout joelib2

The pre-alpha distributions will be published at the web site.

Kind 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Canonified version?

[Andreas M. <an...@ma...>]

If I use

------------------CODE BEGIN---------------------
// create mol object out of this smiles string
JOESmilesParser.smiToMol(mol, smiles, smiles);
			=09
// clone the molecule
// and recalculate
// numbers
JOEMol tMol =3D (JOEMol) mol.clone(false);
morgan.calculate(tMol);
JOEMol rMol =3D morgan.renumber(tMol); // (*)
JOEMol rMol =3D tMol;

// create mol to smiles converter=20
m2s.init();

// do some correction
m2s.correctAromaticAmineCharge(rMol);

// String buffer to hold the canonified string
m2s.createSmiString(rMol, smilesb);
return smilesb.toString();
------------------CODE BEGIN---------------------

I get a NULL pointer exception at (*) with the following:
Exception in thread "main" java.lang.NullPointerException
	at joelib.algo.morgan.Morgan.getBFS(Morgan.java:329)
	at joelib.algo.morgan.Morgan.renumber(Morgan.java:261)
	at SmilesCanonifier.canonify(SmilesCanonifier.java:35)
	at SmilesCanonifier.main(SmilesCanonifier.java:52)
=09
Without (*), however, it works quite well, too.
Only in some molecules it switches from (for example)
'C12CC3CC(CC(C3)C2)C1' to
'C12CC3CC(CC(C3)C1)C2',
but that's not so problematic.
Also, the missing salt support is no acute problem.
What does (*) do, exactly?

Greetings,
Andreas
=09
On Tue, Nov 30, 2004 at 08:17:37AM +0100, Joerg K. Wegner wrote:
> Hi Andreas,
>=20
> here is the code fragment used by joelib.io.types.Smiles. Please note=20
> that the actual morgan algorithm  can not deal with salts. A solution=20
> would be to get all contiguous fragments in decreasing order (method=20
> mol.contiguousFragments(List)) and apply the morgan algorithm to each=20
> fragment. Then you must simply connect those fragments in the SMILES=20
> String with frag1smiles.frag2smiles.frag3smiles
>=20
> Mmhh, its not a big deal but i'm at the moment heavily busy with the=20
> JOELib2 refactoring. Anyway, here is the code:
>=20
> if (doCanonical)
> {
>   JOEMol tMol =3D (JOEMol) mol.clone(false);
>   morgan.calculate(tMol);
>   JOEMol rMol =3D morgan.renumber(tMol);
>   m2s.correctAromaticAmineCharge(rMol);
>   m2s.createSmiString(rMol, smilesb);
> }
> else
> {
>   m2s.correctAromaticAmineCharge(mol);
>   m2s.createSmiString(mol, smilesb);
> }
>=20
> MfG, Joerg
>=20
> >with the following code I read in a SMILES, build a molecule out of=20
> >it and reencode it as a string:
> >
> >----------------- BEGIN CODE --------------------------------
> >
> >import joelib.molecule.*;
> >import joelib.smiles.*;
> >
> >public class SmilesCanonifier {
> >       =20
> >	public String canonify(String smiles) {
> >                JOEMol mol=3Dnew JOEMol();
> >                JOEMol2Smi m2s =3D new JOEMol2Smi(); m2s.init();
> >	        StringBuffer smilesb =3D new StringBuffer(1000);
> >
> >                // create mol object out of this smiles string
> >                JOESmilesParser.smiToMol(mol, smiles, smiles);
> >
> >	        // create mol to smiles converter
> >	        m2s.init();
> >	        // do some correction
> >        	m2s.correctAromaticAmineCharge(mol);
> >
> >	        // String buffer to hold the canonified string
> >	        m2s.createSmiString(mol, smilesb);
> >	        return smilesb.toString();
> >        }
> >
> >        public static void main(String args[]) {
> >                String smiles =3D args[0];
> >                System.out.println(smiles);
> >                SmilesCanonifier sc =3D new SmilesCanonifier();
> >                System.out.println(sc.canonify(smiles));
> >        }
> >}
> >
> >----------------- END CODE ----------------------------------
> >
> >When I try this on a SMILES s0 I get an equivalent output smiles s1.
> >When I try it on s1, I get an equivalent output smiles s2, which is=20
> >different from s1.
> >When I try it on s2, I get an equivalent output smiles s3, which is=20
> >the same as s1, s3=3Ds1.
> >When I try it on s3=3Ds1, I get an equivalent output smiles s4, which=20
> >is the same as s2, s4=3Ds2.
> >
> >The process repeats from now on, switching between two SMILES=20
> >versions.
> >Is there no canonical version? Otherwise, how can I get one?
> >
> >Greetings,
> >Andi
> >
> >
> >
> >-------------------------------------------------------
> >SF email is sponsored by - The IT Product Guide
> >Read honest & candid reviews on hundreds of IT Products from real=20
> >users.
> >Discover which products truly live up to the hype. Start reading=20
> >now. http://productguide.itmanagersjournal.com/
> >_______________________________________________
> >Joelib-help mailing list
> >Joe...@li...
> >https://lists.sourceforge.net/lists/listinfo/joelib-help
> >
>=20
>=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
> Never mistake action for meaningful action.
>                                (Hugo Kubinyi,2004)
>=20
>=20
>=20
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real=20
> users.
> Discover which products truly live up to the hype. Start reading now.=20
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help

Viele Gr=FC=DFe,
Andi
--=20
http://www.maunz.de

      Yoda of Borg are we: Futile is resistance. Assimilate you, we will.

Re: [Joelib-help] Canonified version?

[Joerg K. W. <we...@in...>]

Hi Andreas,

here is the code fragment used by joelib.io.types.Smiles. Please note 
that the actual morgan algorithm  can not deal with salts. A solution 
would be to get all contiguous fragments in decreasing order (method 
mol.contiguousFragments(List)) and apply the morgan algorithm to each 
fragment. Then you must simply connect those fragments in the SMILES 
String with frag1smiles.frag2smiles.frag3smiles

Mmhh, its not a big deal but i'm at the moment heavily busy with the 
JOELib2 refactoring. Anyway, here is the code:

if (doCanonical)
{
   JOEMol tMol = (JOEMol) mol.clone(false);
   morgan.calculate(tMol);
   JOEMol rMol = morgan.renumber(tMol);
   m2s.correctAromaticAmineCharge(rMol);
   m2s.createSmiString(rMol, smilesb);
}
else
{
   m2s.correctAromaticAmineCharge(mol);
   m2s.createSmiString(mol, smilesb);
}

MfG, Joerg

> with the following code I read in a SMILES, build a molecule out of it and reencode it as a string:
> 
> ----------------- BEGIN CODE --------------------------------
> 
> import joelib.molecule.*;
> import joelib.smiles.*;
> 
> public class SmilesCanonifier {
>         
> 	public String canonify(String smiles) {
>                 JOEMol mol=new JOEMol();
>                 JOEMol2Smi m2s = new JOEMol2Smi(); m2s.init();
> 	        StringBuffer smilesb = new StringBuffer(1000);
> 
>                 // create mol object out of this smiles string
>                 JOESmilesParser.smiToMol(mol, smiles, smiles);
> 
> 	        // create mol to smiles converter
> 	        m2s.init();
> 	        // do some correction
>         	m2s.correctAromaticAmineCharge(mol);
> 
> 	        // String buffer to hold the canonified string
> 	        m2s.createSmiString(mol, smilesb);
> 	        return smilesb.toString();
>         }
> 
>         public static void main(String args[]) {
>                 String smiles = args[0];
>                 System.out.println(smiles);
>                 SmilesCanonifier sc = new SmilesCanonifier();
>                 System.out.println(sc.canonify(smiles));
>         }
> }
> 
> ----------------- END CODE ----------------------------------
> 
> When I try this on a SMILES s0 I get an equivalent output smiles s1.
> When I try it on s1, I get an equivalent output smiles s2, which is different from s1.
> When I try it on s2, I get an equivalent output smiles s3, which is the same as s1, s3=s1.
> When I try it on s3=s1, I get an equivalent output smiles s4, which is the same as s2, s4=s2.
> 
> The process repeats from now on, switching between two SMILES versions.
> Is there no canonical version? Otherwise, how can I get one?
> 
> Greetings,
> Andi
> 
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now. 
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Canonified version?

[Andreas M. <an...@ma...>]

Hi,

with the following code I read in a SMILES, build a molecule out of it and reencode it as a string:

----------------- BEGIN CODE --------------------------------

import joelib.molecule.*;
import joelib.smiles.*;

public class SmilesCanonifier {
        
	public String canonify(String smiles) {
                JOEMol mol=new JOEMol();
                JOEMol2Smi m2s = new JOEMol2Smi(); m2s.init();
	        StringBuffer smilesb = new StringBuffer(1000);

                // create mol object out of this smiles string
                JOESmilesParser.smiToMol(mol, smiles, smiles);

	        // create mol to smiles converter
	        m2s.init();
	        // do some correction
        	m2s.correctAromaticAmineCharge(mol);

	        // String buffer to hold the canonified string
	        m2s.createSmiString(mol, smilesb);
	        return smilesb.toString();
        }

        public static void main(String args[]) {
                String smiles = args[0];
                System.out.println(smiles);
                SmilesCanonifier sc = new SmilesCanonifier();
                System.out.println(sc.canonify(smiles));
        }
}

----------------- END CODE ----------------------------------

When I try this on a SMILES s0 I get an equivalent output smiles s1.
When I try it on s1, I get an equivalent output smiles s2, which is different from s1.
When I try it on s2, I get an equivalent output smiles s3, which is the same as s1, s3=s1.
When I try it on s3=s1, I get an equivalent output smiles s4, which is the same as s2, s4=s2.

The process repeats from now on, switching between two SMILES versions.
Is there no canonical version? Otherwise, how can I get one?

Greetings,
Andi

[Joelib-help] Compiler errors

[Joerg K. W. <we...@in...>]

Hi Ambrish,

1. please use the mailing list, such things are interesting for all 
users. I forward it automatically, hope you don't mind.

 > 4. i have put all the necessary jar files in JOELib\lib.
 > but when i run Test.java i get errors like
 > package joelib.molecule does not exist import joelib.molecule.JOEAtom;
 > package joelib.data does not exist import joelib.data.JOEPairData;
 > and similar errors.
The compiler does not find the sources and/or the build directory or the 
joelib.jar. Do you have set also JOELIBDIR?
2. Installation is the most critical step. I strongly recommend to use 
'cygwin' instead of the DOS prompt. Unfortunately this is tricky to 
install. Then you can work with the shell scripts build.sh.

Sorry, i might have no quick fix for this problem, so i tell you 
possible solutions and you can decide which one might be the fastest:

2.1. Use the joelib.jar-file (only if you don't need the interface 
classes, like CDK, Java3D, Ghemical, ...)

2.2. Use Windows with BAT-files. Problem: The classpath must be checked 
by hand, that it includes all required .jar files and directories. 
Please check if you have set:
JAVA_HOME
ANT_HOME
JOELIBDIR

2.3. Use Windows/Cygwin or Linux, then you can use the shell scripts SH. 
They will find all required jar files in the lib directory 
automatically. So, this is much easier than fixing them by hand. If you 
are a Windows user, installing Cygwin might be a problem, because the 
installation menu is not optimal.
Please check if you have set:
JAVA_HOME
ANT_HOME
JOELIBDIR

2.4. Install ANT and add it to your PATH environment. If this was done 
you can use: 'joelib/ant/ant compile'. That's what is done, by the 
build.sh anyway. Then you must not set JOELIBDIR, because only the shell 
scripts require this environment option.

> I am soory to bother you so much but i need ur help immediately as i have to complete my project before 10th December.
> Can you please tell me in detail how to start using and copiling all the packages....
> Looking forrward for an early reply.
> Ambrish
> Bioinformatics Centre
Sorry, for this late reply.

Kind regards, Joerg
>  
>  
> "Joerg K. Wegner" <we...@in...> wrote:
> Hi Ambrish,
> 
> 1. LOG4J requires its property file in the classpath. If you use the 
> source code distribution (strongly recommended) this will be copied 
> automatically to
> joelib/build/log4j.properties
> 
> 2. Seems that there are the required libraries missing which are located 
> under joelib/lib/log4j.jar
> 
> Please check carefully if the properties and the libraries are part of 
> your classpath.
> You can resolve such things dynamically via ANT or the included shell 
> scripts. For Windows and your own potential application you must check 
> such things 'by hand'.
> 
> Kind regards, Joerg
> 
> 
> 
>>hi
>>thanx for the prompt reply.....
>>i am having problem s like
>>1.package org.apache.log4j does not exist import org.apache.log4j.Category;
>>2. private static Category logger = Category.getInstance(
>>
>>I tried to configure log4j but still the problem persists. i also searched for the solution but got some hits like This class has been deprecated and replaced by the Logger subclass
>>should i replace that in my program.
>>
>>
>>
>>
>>
>>"Joerg K. Wegner" wrote:
>>Hi Ambrish,
>>
>>
>>
>>>i am a new user to JOELib but am not able to make out how to get started with the package....
>>>Can somebody write to me in detail how to start and if i want to write a program using this package where will i have to store the program i.e whether in same directory?
>>
>>I recommend to start with all examples in joelib/src/joelib/test
>>Have a look at them and try to understand them, then you will know the 
>>basic functionalities.
>>
>>
>>
>>>Also i am getting problem with setting with JOELib enviornment.
>>
>>That's to sloppy fomulated.
>>What are your problems: Java, ANT, eclipse, properties files, 
>>protonation model, atom typer, ...
>>
>>Kind 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Mol2 file read error

[Joerg K. W. <we...@in...>]

Dear Koyama_Takahiko,

yes, i know, here is the bug fix. Please replace the ScanfReader.java

http://sourceforge.net/tracker/index.php?func=detail&aid=1075208&group_id=39708&atid=425969

Kind regards, Joerg

> Hello,
> 
> I am having a trouble with reading a mol2 file using JOElib. 
> The error seems occur when the coordinate entry is negative. For instance,
> 
> @<TRIPOS>ATOM
> 1	C1	1.207	2.091	0.000	C.ar	1	BENZENE	0.000
> 2	C2	2.414	1.394	0.000	C.ar	1	BENZENE	0.000
> 3	C3	2.414	0.000	0.000	C.ar	1	BENZENE	0.000
> 4	C4	1.207 -0.697	0.000	C.ar	1	BENZENE	0.000
> 
> upto 3rd atom is successfully read yet, 4th atom which has minus in y-coordinate causes throwing an exception (cformat.ScanfMatchException: Malformed floating point number: no digits). 
> 
> This is the (simplified) code I am using.
> 
> String inputFile="benzene.mol2";
> SimpleReader reader = null;
>  IOType inType = IOTypeHolder.instance().filenameToType(inputFile);
>  reader = new SimpleReader(input, inType);
>  JOEMol mol = new JOEMol(inType, inType);    
>  reader.readNext(mol));
> 
> I will appreciate for your help on this matter.
> 
> Takahiko Koyama
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now. 
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> 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)

Never mistake action for meaningful action.
                               (Hugo Kubinyi,2004)

[Joelib-help] Mol2 file read error

[<Koy...@ta...>]

Hello,

I am having a trouble with reading a mol2 file using JOElib. 
The error seems occur when the coordinate entry is negative. For instance,

@<TRIPOS>ATOM
1	C1	1.207	2.091	0.000	C.ar	1	BENZENE	0.000
2	C2	2.414	1.394	0.000	C.ar	1	BENZENE	0.000
3	C3	2.414	0.000	0.000	C.ar	1	BENZENE	0.000
4	C4	1.207 -0.697	0.000	C.ar	1	BENZENE	0.000

upto 3rd atom is successfully read yet, 4th atom which has minus in y-coordinate causes throwing an exception (cformat.ScanfMatchException: Malformed floating point number: no digits). 

This is the (simplified) code I am using.

String inputFile="benzene.mol2";
SimpleReader reader = null;
 IOType inType = IOTypeHolder.instance().filenameToType(inputFile);
 reader = new SimpleReader(input, inType);
 JOEMol mol = new JOEMol(inType, inType);    
 reader.readNext(mol));

I will appreciate for your help on this matter.

Takahiko Koyama

Re: [Joelib-help] what is descNameFile format for descSelection.sh?

[Joerg K. W. <we...@in...>]

Hi Egon,

> I've likely oversaw it in the help, but what does the format of descNameFile 
> for descSelection.sh look like?

its a simple text file separated with EOL:
descriptor1
descriptor2
...

Kind 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] what is descNameFile format for descSelection.sh?

[Egon W. <e.w...@sc...>]

Hi Joerg,

I've likely oversaw it in the help, but what does the format of descNameFil=
e=20
for descSelection.sh look like?

Egon

=2D-=20
e.w...@sc...
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
http://www.cac.science.ru.nl/people/egonw/
GPG: 1024D/D6336BA6

[Joelib-help] JOELib at eChemInfo

[Joerg K. W. <we...@in...>]

Hi all,

i don't know if i've already announced that JOELib is presented at the 
eChemInfo 2004, so here we go:

eChemInfo 2004
http://echeminfo.colayer.net/

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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] 'joelib2-redesign' branch opened in CVS

[Joerg K. W. <we...@in...>]

Hi all,

i've started a 'joelib2-redesign'-branch in CVS. This has the following 
consequences:

1. The standard JOELib-version will only be bugfixed, there will be no 
new releases on this version.

2. All new features, changes and releases will be in the future named 
JOELib2. This will switch this project back to an alpha-version, because 
the class structure will be changed fullfilling several design criterias.
ALL interface wishes and conventions are welcome and will be discussed 
on the developer mailing list. All suggestions must take the actual 
structure into account, because this will be an refactoring driven 
redesign and not a 'we-invent-the-wheel-twice' approach.

If there are no further suggestions, i will follow the points:
- Better interface and implementation separation
- All developers must follow the PMD-rules
- Redesign for easier and faster descriptor access

The first changes were checked in to CVS.

Kind 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Re: JOELib web page 'Applications'

[Joerg K. W. <we...@in...>]

Dear Dong Sun Park,

> I'm using your JOELib at my work, It's very useful for me.
Fine.
Please use the mailing lists to avoid me answering questions twice.
http://sourceforge.net/mail/?group_id=39708
Analoge mail (deprecated):
http://sourceforge.net/mailarchive/message.php?msg_id=4505039

> When I convert SMILES to MOL file using Convert script. I got a Mol file without coordinate of atoms.
> all of coordinate are 0. I really need convert program. 
> you have this kind of function in the JOELib, 
> If you don't have it. Would you recommed any program I can use convert function...
To formalize things, i would distinguish between those two functionalities:

1. Conversion: For me this means that atom types are mapped correctly
between formats and that the internal atom typer and the internal expert
systems work correctly. You can also define in this step your own
protonation model, if you want.

2. 2D/3D structure generation: This means that there exists a graph
layout algorithm optimized for the layout of molecular structures.
JOELib provides three possibilities:
2.1. CDK-2D-Layout using joelib.util.cdk.CDKTools
2.2. slow 3D-Layout using MM: joelib.util.ghemical.GhemicalInterface
     This is restricted to Linux systems with IBM-Java-SDK and
     Windows-Cygwin, because it uses a platform dependant JNI-interface
2.3. fast 3D-Layout using Corina (not public, but available): Interface
     works only with a piping mechanism, which is only available for
     Linux systems (Corina problem)

Other possibilities would be:
- CDK: primitive atom typer and expert systems, e.g. good aromaticity
       detection
- Marvin: Good beans interface and commercial

Kind 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)

Never mistake action for meaningful action.
                               (Hugo Kubinyi,2004)

Re: [Joelib-help] canonifier?

[Joerg K. W. <we...@in...>]

Hi Andreas,

i assume that this is a salt and morgan is not implemented for salts, 
which require to renumber each fragment separately.
So mol.stripSalt() will help, but this will skip the smaller salt 
fragment, or you must extend the actual morgan implementation.

You should at first renumber the molecule and then apply the smiles 
conversion.

Kind regards, Joerg

> Hi Joerg,
>  
> this code is derived from your advice:
>  
> public static void main(String args[]) {
>                 String smiles = args[0];
>                 JOEMol mol=new JOEMol();
>                 Morgan morgan = new Morgan(new BasicTieResolver());
>  
>                 JOESmilesParser.smiToMol(mol, smiles, smiles);
>                 JOEMol tMol = (JOEMol) mol.clone(false);
>                 morgan.calculate(tMol);
>                 JOEMol rMol = morgan.renumber(tMol);
>  
>         }
>  
> and it returns the following error:
>  
> Exception in thread "main" java.lang.NullPointerException
>         at joelib.algo.morgan.Morgan.getBFS(Morgan.java:329)
>         at joelib.algo.morgan.Morgan.renumber(Morgan.java:261)
>         at SmilesCanonifier.main(SmilesCanonifier.java:64)
>  
> What's wrong here?
>  
> Greetings
> Andreas
> 
> On Mon, Oct 18, 2004 at 05:44:03PM +0200, Joerg K. Wegner wrote:
> 
>>Hi Andreas,
>>
>>sorry for the late reply i was in holiday for three weeks.
>>
>>
>>>does Joelib provide a functionality to obtain a canonified version of a 
>>>SMILES string?
>>
>>Definitely, as far as the Morgan algorithm can be used for canonization.
>>
>>Just set
>>joelib.io.types.Smiles.canonical=false
>>in joelib.properties to 'true'
>>
>>or copy code fragment from:
>>joelib.io.types.Smiles
>>
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> Use IT products in your business? Tell us what you think of them. Give us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
> http://productguide.itmanagersjournal.com/guidepromo.tmpl
> _______________________________________________
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> 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] canonifier?

[Andreas M. <an...@ma...>]

Hi Joerg,
 
this code is derived from your advice:
 
public static void main(String args[]) {
                String smiles = args[0];
                JOEMol mol=new JOEMol();
                Morgan morgan = new Morgan(new BasicTieResolver());
 
                JOESmilesParser.smiToMol(mol, smiles, smiles);
                JOEMol tMol = (JOEMol) mol.clone(false);
                morgan.calculate(tMol);
                JOEMol rMol = morgan.renumber(tMol);
 
        }
 
and it returns the following error:
 
Exception in thread "main" java.lang.NullPointerException
        at joelib.algo.morgan.Morgan.getBFS(Morgan.java:329)
        at joelib.algo.morgan.Morgan.renumber(Morgan.java:261)
        at SmilesCanonifier.main(SmilesCanonifier.java:64)
 
What's wrong here?
 
Greetings
Andreas

On Mon, Oct 18, 2004 at 05:44:03PM +0200, Joerg K. Wegner wrote:
> Hi Andreas,
> 
> sorry for the late reply i was in holiday for three weeks.
> 
> >does Joelib provide a functionality to obtain a canonified version of a 
> >SMILES string?
> Definitely, as far as the Morgan algorithm can be used for canonization.
> 
> Just set
> joelib.io.types.Smiles.canonical=false
> in joelib.properties to 'true'
> 
> or copy code fragment from:
> joelib.io.types.Smiles
> 

Re: [Joelib-help] JOEAtom

[Joerg K. W. <we...@in...>]

Hi again,

>> I understand that these fields have no real chemical meaning, and are 
>> therefore not included in your class, but for my purpose they are 
>> essential. If you suggest Joelib is not suitable for this then I'll 
>> try something else.
They are included. The index can be accessed by
atom.getIdx()

and the element by
JOEElementTable.instance().getSymbol(atom.getAtomicNum())

Further things like rings, atomTypes and chemical properties can be also 
accessed and internally calculated, so what you request is the basic 
graph of the molecular interpretation and this is not that difficult.

Please have a look at the examples and the tutorial and contact me, if 
you get stuck into the JOELib downs.

Kind regards, Joerg
>>
>> Thijs
>>
>> On Oct 18, 2004, at 11:28 AM, Joerg K. Wegner wrote:
>>
>>> Hi Thijs Beuming,
>>>
>>> as far as i can see i can't recommend this way to proceed.
>>> You shouldn't mess around with the Atom class in this way.
>>>
>>> You should use joelib.io.types.SybylMol2 to read MOL2 entries, e.g. 
>>> on your String block for one entry.
>>>
>>> As you can see an interl conversion is required, which will be 
>>> applied automatically, when using this class.
>>>
>>> JOETypeTable ttab = JOETypeTable.instance();
>>> ttab.setFromType("SYB");
>>> ttab.setToType("ATN");
>>> str1 = ttab.translate(str);
>>> atom.setAtomicNum(Integer.parseInt(str1));
>>> ttab.setToType("INT");
>>> str1 = ttab.translate(str);
>>> atom.setType(str1);
>>>
>>> Kind regards, Joerg
>>>
>>>> I am trying to modify the JOEAtom class to contain a field for the 
>>>> atom name,
>>>> e.g by reading the second token of a sybylmol2 atom line with
>>>>             atom.setAtomName(atom_name) in the SybylMol2 class
>>>> and the methods in JOEAtom.
>>>>     public void setAtomName(String atomname)
>>>>     {
>>>>         _atomname = new String(atomname);
>>>>     }
>>>>     public String getAtomName()
>>>>     {
>>>>         return (_atomname);
>>>>     }
>>>> I can't retrieve the stored names however when i iterate over the 
>>>> atoms from a JOEMol:
>>>>       for(int i=1;i<=mol.numAtoms();i++){
>>>>             JOEAtom atom = mol.getAtom(i);
>>>>             System.out.println(atom.getAtomName());
>>>>     }
>>>> all the names are null.
>>>> Any suggestions?
>>>> Thanks.
>>>> ---
>>>> Thijs Beuming
>>>> Harel Weinstein Lab
>>>> Department of Physiology & Biophysics
>>>> Weill Medical College of Cornell University
>>>> 1300 York Avenue, Box 75
>>>> New York, NY 10021
>>>> Tel: (212) 7466539
>>>> Fax: (212) 746-6361
>>>> th...@me...
>>>> -------------------------------------------------------
>>>> This SF.net email is sponsored by: IT Product Guide on 
>>>> ITManagersJournal
>>>> Use IT products in your business? Tell us what you think of them. 
>>>> Give us
>>>> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find 
>>>> out more
>>>> http://productguide.itmanagersjournal.com/guidepromo.tmpl
>>>> _______________________________________________
>>>> 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)
>>>
>>> Never mistake action for meaningful action.
>>>                                (Hugo Kubinyi,2004)
>>>
>>>
>> ---
>> Thijs Beuming
>> Harel Weinstein Lab
>> Department of Physiology & Biophysics
>> Weill Medical College of Cornell University
>> 1300 York Avenue, Box 75
>> New York, NY 10021
>> Tel: (212) 7466539
>> Fax: (212) 746-6361
>> th...@me...
>>
>>
> 
> 


-- 
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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] JOEAtom

[Joerg K. W. <we...@in...>]

Hi Thijs Beuming,

i've never said it is not suitable, but you should not violate the 
internal conventions, which stores only 'C' and then assigns internal 
atom types, which can be transformed to Sybyl MOL2 atom types and vice 
versa.

Of course it is more complicated to use JOElib and not a simple line 
parser, but there is also a much greater benefit. Or what is your goal 
when using JOElib?

Here a more detailed explanation of what i mean (hava also a look at the 
tutorial):

// please see examples under joelib.test
1. So take an single MOL2 file.

2. Open an input stream (file based or buffer based)

3. Load the molecule with
    joelib.io.types.SybylMol2
    read(myMolObject);

4. access element and atom type:
    JOEElementTable.instance().getSymbol(atom.getAtomicNum())

    // please see example joelib.test.TestMolecule

Kind regards, Joerg

> Hi Joerg,
> 
> Consider the "atom lines" in a mol2 file.
> 
>       1 C3          1.9861    2.4354    1.0036 C.3       1 FIP270     
> 15.2100
>       2 C9          2.5381    1.1184    0.8986 C.3       0 <0>        
> 15.9400
>       3 C8          3.9341    1.2354    1.0666 C.3       0 <0>        
> 12.2200
> 
> I am just looking for a way to store the first two fields (i.e. 1 and 
> C3, or 2 and C9), i don't particularly care how its done, as long as I 
> can access them after later.
> I understand that these fields have no real chemical meaning, and are 
> therefore not included in your class, but for my purpose they are 
> essential. If you suggest Joelib is not suitable for this then I'll try 
> something else.
> 
> Thanks for your attention,
> 
> Thijs
> 
> On Oct 18, 2004, at 11:28 AM, Joerg K. Wegner wrote:
> 
>> Hi Thijs Beuming,
>>
>> as far as i can see i can't recommend this way to proceed.
>> You shouldn't mess around with the Atom class in this way.
>>
>> You should use joelib.io.types.SybylMol2 to read MOL2 entries, e.g. on 
>> your String block for one entry.
>>
>> As you can see an interl conversion is required, which will be applied 
>> automatically, when using this class.
>>
>> JOETypeTable ttab = JOETypeTable.instance();
>> ttab.setFromType("SYB");
>> ttab.setToType("ATN");
>> str1 = ttab.translate(str);
>> atom.setAtomicNum(Integer.parseInt(str1));
>> ttab.setToType("INT");
>> str1 = ttab.translate(str);
>> atom.setType(str1);
>>
>> Kind regards, Joerg
>>
>>> I am trying to modify the JOEAtom class to contain a field for the 
>>> atom name,
>>> e.g by reading the second token of a sybylmol2 atom line with
>>>             atom.setAtomName(atom_name) in the SybylMol2 class
>>> and the methods in JOEAtom.
>>>     public void setAtomName(String atomname)
>>>     {
>>>         _atomname = new String(atomname);
>>>     }
>>>     public String getAtomName()
>>>     {
>>>         return (_atomname);
>>>     }
>>> I can't retrieve the stored names however when i iterate over the 
>>> atoms from a JOEMol:
>>>       for(int i=1;i<=mol.numAtoms();i++){
>>>             JOEAtom atom = mol.getAtom(i);
>>>             System.out.println(atom.getAtomName());
>>>     }
>>> all the names are null.
>>> Any suggestions?
>>> Thanks.
>>> ---
>>> Thijs Beuming
>>> Harel Weinstein Lab
>>> Department of Physiology & Biophysics
>>> Weill Medical College of Cornell University
>>> 1300 York Avenue, Box 75
>>> New York, NY 10021
>>> Tel: (212) 7466539
>>> Fax: (212) 746-6361
>>> th...@me...
>>> -------------------------------------------------------
>>> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
>>> Use IT products in your business? Tell us what you think of them. 
>>> Give us
>>> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find 
>>> out more
>>> http://productguide.itmanagersjournal.com/guidepromo.tmpl
>>> _______________________________________________
>>> 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)
>>
>> Never mistake action for meaningful action.
>>                                (Hugo Kubinyi,2004)
>>
>>
> ---
> Thijs Beuming
> Harel Weinstein Lab
> Department of Physiology & Biophysics
> Weill Medical College of Cornell University
> 1300 York Avenue, Box 75
> New York, NY 10021
> Tel: (212) 7466539
> Fax: (212) 746-6361
> th...@me...
> 
> 


-- 
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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] canonifier?

[Joerg K. W. <we...@in...>]

Hi Andreas,

sorry for the late reply i was in holiday for three weeks.

> does Joelib provide a functionality to obtain a canonified version of a SMILES string?
Definitely, as far as the Morgan algorithm can be used for canonization.

Just set
joelib.io.types.Smiles.canonical=false
in joelib.properties to 'true'

or copy code fragment from:
joelib.io.types.Smiles

Kind 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] JOEAtom

[Joerg K. W. <we...@in...>]

Hi Thijs Beuming,

as far as i can see i can't recommend this way to proceed.
You shouldn't mess around with the Atom class in this way.

You should use joelib.io.types.SybylMol2 to read MOL2 entries, e.g. on 
your String block for one entry.

As you can see an interl conversion is required, which will be applied 
automatically, when using this class.

JOETypeTable ttab = JOETypeTable.instance();
ttab.setFromType("SYB");
ttab.setToType("ATN");
str1 = ttab.translate(str);
atom.setAtomicNum(Integer.parseInt(str1));
ttab.setToType("INT");
str1 = ttab.translate(str);
atom.setType(str1);

Kind regards, Joerg

> 
> I am trying to modify the JOEAtom class to contain a field for the atom 
> name,
> 
> e.g by reading the second token of a sybylmol2 atom line with
> 
>             atom.setAtomName(atom_name) in the SybylMol2 class
> 
> and the methods in JOEAtom.
> 
>     public void setAtomName(String atomname)
>     {
>         _atomname = new String(atomname);
>     }
> 
>     public String getAtomName()
>     {
>         return (_atomname);
>     }
> 
> I can't retrieve the stored names however when i iterate over the atoms 
> from a JOEMol:
> 
>       for(int i=1;i<=mol.numAtoms();i++){
>             JOEAtom atom = mol.getAtom(i);
>             System.out.println(atom.getAtomName());
>     }
> 
> all the names are null.
> 
> Any suggestions?
> 
> Thanks.
> 
> 
> ---
> Thijs Beuming
> Harel Weinstein Lab
> Department of Physiology & Biophysics
> Weill Medical College of Cornell University
> 1300 York Avenue, Box 75
> New York, NY 10021
> Tel: (212) 7466539
> Fax: (212) 746-6361
> th...@me...
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> Use IT products in your business? Tell us what you think of them. Give us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
> http://productguide.itmanagersjournal.com/guidepromo.tmpl
> _______________________________________________
> 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] JOEAtom

[Thijs B. <th...@me...>]

Hi,

I am trying to modify the JOEAtom class to contain a field for the atom 
name,

e.g by reading the second token of a sybylmol2 atom line with

             atom.setAtomName(atom_name) in the SybylMol2 class

and the methods in JOEAtom.

     public void setAtomName(String atomname)
     {
         _atomname = new String(atomname);
     }

     public String getAtomName()
     {
         return (_atomname);
     }

I can't retrieve the stored names however when i iterate over the atoms 
from a JOEMol:

       for(int i=1;i<=mol.numAtoms();i++){
             JOEAtom atom = mol.getAtom(i);
             System.out.println(atom.getAtomName());
	}

all the names are null.

Any suggestions?

Thanks.


---
Thijs Beuming
Harel Weinstein Lab
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021
Tel: (212) 7466539
Fax: (212) 746-6361
th...@me...

[Joelib-help] canonifier?

[Andreas M. <ma...@in...>]

Hi all,

does Joelib provide a functionality to obtain a canonified version of a SMILES string?
Greetings,

Andi

[Joelib-help] JOELib and the Eclipse IDE

[Joerg K. W. <we...@in...>]

Hi,

i've added a short 'How-To' to the SF documentation system:
http://sourceforge.net/docman/display_doc.php?docid=24799&group_id=39708

Kind 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Parameterize the image output

[Joerg K. W. <we...@in...>]

Dear Christophe JOASSARD,

the default properties are defined in joelib/src/joelib.properties.

If the following list does not fulfill your requirements (e.g. SMARTS 
highlighting) you should implement your own wrapper to the 
joelib.gui.render.Mol2Image class. See also io/types/BMP, io/types/GIF 
and io/types/PDF for more details.

##############################################################################
# 2D rendering options
##############################################################################
joelib.gui.render.Renderer2DModel.bond.length=30.0
joelib.gui.render.Renderer2DModel.bond.distance=6.0
joelib.gui.render.Renderer2DModel.bond.width=2.0
joelib.gui.render.Renderer2DModel.drawNumbers=false
joelib.gui.render.Renderer2DModel.useKekuleStructure=true
joelib.gui.render.Renderer2DModel.showEndCarbons=true
joelib.gui.render.Renderer2DModel.atomColoring=false
joelib.gui.render.Renderer2DModel.drawCarbonAtoms=false
joelib.gui.render.Renderer2DModel.orthoLineOffset=20
joelib.gui.render.Renderer2DModel.arrowOffset=10
joelib.gui.render.Renderer2DModel.arrowSize=5

joelib.gui.render.Renderer2DModel.background.color.r=255
joelib.gui.render.Renderer2DModel.background.color.g=255
joelib.gui.render.Renderer2DModel.background.color.b=255

joelib.gui.render.Renderer2DModel.foreground.color.r=0
joelib.gui.render.Renderer2DModel.foreground.color.g=0
joelib.gui.render.Renderer2DModel.foreground.color.b=0

joelib.gui.render.Renderer2DModel.highlight.color.r=255
joelib.gui.render.Renderer2DModel.highlight.color.g=0
joelib.gui.render.Renderer2DModel.highlight.color.b=0

joelib.gui.render.Renderer2DModel.number.color.r=0
joelib.gui.render.Renderer2DModel.number.color.g=0
joelib.gui.render.Renderer2DModel.number.color.b=255

joelib.gui.render.Renderer2DModel.conjugatedRing.color.r=0
joelib.gui.render.Renderer2DModel.conjugatedRing.color.g=0
joelib.gui.render.Renderer2DModel.conjugatedRing.color.b=0

joelib.gui.render.Renderer2DModel.arrow.color.r=0
joelib.gui.render.Renderer2DModel.arrow.color.g=255
joelib.gui.render.Renderer2DModel.arrow.color.b=0

joelib.gui.render.Renderer2DModel.orthogonalLine.color.r=0
joelib.gui.render.Renderer2DModel.orthogonalLine.color.g=0
joelib.gui.render.Renderer2DModel.orthogonalLine.color.b=255


> We have tested your java component to convert molfile to an image and we wish to know if we can parameterize easily :
>   a.. the background color,
> 
>   b.. the chemical representation (display or not hetero,...)...
> How can we do that ?
> 
> regards
> 
> 
> This message contains information that may be privileged or confidential and is the property of the Capgemini Group. It is intended only for the person to whom it is addressed. If you are not the intended recipient,  you are not authorized to read, print, retain, copy, disseminate,  distribute, or use this message or any part thereof. If you receive this  message in error, please notify the sender immediately and delete all  copies of this message.
> 


-- 
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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Parameterize the image output

[Christophe J. <chr...@ca...>]

We have tested your java component to convert molfile to an image and we=
 wish to know if we can parameterize easily :
  a.. the background color,=0D
  b.. the chemical representation (display or not hetero,...)...
How can we do that ?

regards


This message contains information that may be privileged or confidential=
 and is the property of the Capgemini Group. It is intended only for the=
 person to whom it is addressed. If you are not the intended recipient, =
 you are not authorized to read, print, retain, copy, disseminate, =
 distribute, or use this message or any part thereof. If you receive this =
 message in error, please notify the sender immediately and delete all =
 copies of this message.

[Joelib-help] Re: java.lang.NoClassDefFoundError when running TestSMILES in Eclipse

[Joerg K. W. <we...@in...>]

Dear Nikolaus,

> I just started playing around with JOELib and Eclipse and after a few hours of 
> work had the joelib.jar in eclipse running. For a first test I copied the 
> TestSMILES.java file into Eclipse and started the project. 
great ! I'm working under eclipse, too.
BUT i'm not using their build mechanism, i'm using only and directly ant 
in eclipse.

If i understand you correctly you have managed to use JOELib with the 
build mechansim in eclipse. If you have time you can send a detailed 
installation report how doiing this to this list.
The problem are the text definition and properties file, because they 
must always be copied to the build directory also.


> It runs fine until it arrives in the 
> instance.loadfiletypes() 
> function where I get in 
> mfType = JOEFileFormat.getMoleculeFileType(ioType);
> the following error:
> java.lang.NoClassDefFoundError: com/lowagie/text/DocumentException
> mfType = (MoleculeFileType) Class.forName(type.getRepresentation())
>                                              .newInstance();
> for PDF. All the other file extension before are working !
This means that the required itext-0.94.jar library is missing. Please 
check your classpath.
If you are using ANT you do not need such things, not for testing examples.
You need these libraries only to avoid error messages in the source code 
editor. This will allow you also the autocompletion when typing:
mol.
to
mol.beginModify()
mol.deleteHydrogens()
...

> Since I am new to JAVA and JOELib (I worked mainly with OpenBabel and C++ 
> before) I really do have a problem here and any kind of help is appreciated.
No problem, i've started with OELib (now: OpenBabel), too.
The difference is not too big


> Many thanks in advance,

Was me a pleasure, 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] PMD 'coupling' code cleanup

[Joerg K. W. <we...@in...>]

Dear users,

default users of the main functionality should not be affected by these 
changes.
------------

Dear developers,
I've started with refactoring the sources following the PMD rules.

First, this is important to hide the internal JOELib development 
process, e.g. using a more efficient implementation.
Second, these changes are at the moment only available in the CVS and if 
you are a developer this may affect your implementation. So, the next 
JOELib release will switch back into beta-release mode with focus on a 
more stable release for the future.
Beta-release mode for the next release means that i've decided to change 
method calls and signatures if necessary. So developers ... be warned.

Example: Load descriptors of unkown size. Load them into a data 
structure, e.g. Vector, which causes a lot of memory swapping processes. 
So, a LinkedList would be more efficient here.
So, the PMD coupling rule recommend to use always a List interface for 
the user, so the user have not to know which implementation is used 
internally.
This was not the case, because i've often used a Vector in method headers.

Until now i've corrected the 'basic','coupling' and 'import' rules. Two 
of them causes no problems.
But the 'coupling' rule has forced me to change 'Vector-->List',
'HashMap-->Map'. So, this affects method calls and forces you to
change these things also, if you are using the JOELib library for
your own implementations.
This causes three main changes for you:
      0. joelibMethod(myVector);
         Nothing to do here, because List is an interface for the Vector
         class
      1. Vector myVector=joelibMethod();
         Must be changed to:
         List myList=joelibMethod();
         or you should use casting from Vector to List and vice versa.
         Depends on your implementation.
      2. Vector myVector=joelibMethod();
         Enumeration enum=myVector.enumeration();
         enum.hasNextElement();
         enum.nextElement();
         Must be changed to:
         Iteration iter=myVector.iterator();
	iter.hasNext();
         iter.next();
      3. All users which have used the 'addElement', 'getElementAt'
         should use the access method, which are recommended from the
         interface:
         'add' and 'get'
         And 'setElementAt(object, index)' should be replaced by
         'setElementAt(index, object)' interchanging the order of the
         arguments.

Kind 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)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)