Thread: [Joelib-devel] Re: JOELib

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Hello,

> Let me explain my environment:
> 
> Windows 2000
> Java : jdk1.3.1 and jdk1.4
> JRE: j2re1.4.1_02 and j2re1.4.0
> Ant: 1.5.3
> 
> Fortunately jchem from chemaxon is working perfect for database
> management and viewing the molecules
> in JOELib viewer I could not load the molecule (SDF) 
> is it because of missing parameters other than molecule
> connection table and co-ordinate information.
Marvin is really great, you're right.

> pl write step by step instruction for the above environment
> I can reinstall the program or configure / setup the environment
> as per the direction.
O.k., let's go:

set the required environment variables:
set JOELIBDIR=D:\workingAt\joelib (in MS-DOS-Shell)
or
setenv JOELIBDIR /cygdrive/d/workingAt/joelib (Cygwin, with tcsh)
or
export JOELIBDIR=/cygdrive/d/workingAt/joelib (Cygwin, with bash)

check this path with
echo %JOELIBDIR% (in MS-DOS-Shell)
or
echo $JOELIBDIR (in Cygwin)

Mainly there are three ways:
1. For things like compiling,  building distributions and so i recommend 
ANT, that's the only usefull way ! A long time ago i used scripts, too, 
but that's really cryptic for complex tasks.
build.bat   (MS-DOS Shell)
sh build.sh (Cygwin)
should work.

2. Using Cygwin for windows and work with the .sh shell scripts, that's 
the recommended way, because you can use well known shell scripts 
functions like 'find'.
sh viewer.sh
sh convert.sh
...
all required libraries will be added automatically.

3. Using plain .bat batch scripts. A problem is, that all library and 
classpath's must be coded explicitely, because there is no 'find' 
analogue tool.
If you will not code all required path's JOELib will not be able to 
resolve the required property files, like
3.1. joelib.properties:
   if this can not be found, it will return
   0 input/output types found (12 would be expected)
   This file must be available in the base CLASSPATH or in a .jar file.
   I recommend the plain file in a directory structure, for enabling
   simple property extensions or changes, e.g. choosing another pH
   value correction model or something else.
3.2. chemical definition files for the atomType-, aromaticity-, and 
phValueCorrection-models.

Please ensure that you've added all required path's to the classpath:
set CLASSPATH=%CLASSPATH%;lib\ant.jar;
set CLASSPATH=%CLASSPATH%;lib\crimson.jar;
set CLASSPATH=%CLASSPATH%;lib\jaxp.jar;
set CLASSPATH=%CLASSPATH%;lib\junit-3.2.jar;
set CLASSPATH=%CLASSPATH%;lib\log4j.jar;
set CLASSPATH=%CLASSPATH%;lib\xerces.jar;
set CLASSPATH=%CLASSPATH%;lib\xalan-2.0.1.jar;

> Objectives: calculate or read already calculated descriptors for the molecules and also for comparison.
> (MOLCONZZ / PETRA / MOE etc.,)
That's all fine and possible.
Don't forget to add all kind of external descriptors to
extKnownResults.txt in joelib/data/plain
or JOELib will not recognize them as integer, double or fingerprint, 
when calculating a statistic or doing a fingerprint comparison or an
euclidian distance based comparison.

> sincerely yours
> M.karthikeyan

Regards, Joerg K. Wegner

> 
> 
> 
> we...@in... wrote
> Hello,
> 
> can i forward this message to the help mailing list.
> This facilitate other users using JOELib, when occuring analogous problems
> ?
> 
> Regards, Joerg
> 
> On Wed, 9 Apr 2003, Joerg Wegner wrote:
> 
> 
>>Hello,
>> 
>>
>>>I got the message:
>>>C:\JOELib>java -cp . joelib.test.Convert +d example.smi example.sdf
>>>12:13:44 [INFO ] joelib.io.IOTypeHolder  -0 input/output types loaded.
>>>Input type of example.smi could not be estimated..
>>
>>That's not what i suggested. I suggested sh convert.sh.
>>You command line 'java -cp .' is not able to locate the joelib.properties
>>file in the classpath or directory structure.
>>IOTypes are defined in the joelib.properties file so the occuring error is 
>>clear.  
>>sh convert.sh sets all libraries on it's own, which faciliates the usage.
>>Under windows the classpath-extensions are hard coded in the convert.bat
>>file.
>> 
>>
>>>in the second attempt I tried on one halogen molecule in SDF format
>>>wondering whether I am making any mistake?
>>
>>Same mistake.
>>0 IOType definitions.
>>0 descriptor informations.
>>
>>The biggest advantage of JOELib id the dynamic definition of IO-types and
>>descriptor calculation methods. All other required files like
>>aromatic.txt, atomtypes.txt are also required, so the correct classpath
>>and the correct files are really important.
>>By the way you can use JOELib with programs like Corina and Petra which is
>>a little bit more difficult, but every flexibility and transparency
>>requires more parameters !;-)
>>
>>I recommend always the source code distribution, because modifications
>>and bug fixing is really easy with the 'apache ant' makefile mechanism.
>>
>>Please have a look in the tutorial. I you use sh convert.sh (Cygwin under 
>>Windows!?) don't forget to set the JOElib base path.
>>setenv JOELIBDIR /cygdrive/d/workingAt/joelib
>>also (for ant)
>>setenv JAVA_HOME c:/Programme/j2sdk1.4.1
>>setenv ANTHOME c:/Programme/Java/lib/ant1.5.1
>>(or was it ANT_HOME !?:-)
>>
>>
>>
>>>Sincerely
>>>M.Karthikeyan
>>>---
>>>
>>>
>>>java joelib.test.Convert -iSDF halogen.sdf
>>>
>>>
>>>halogen.sdf
>>>C11H20
>>>DAtclserve04070319043D 0   0.00000     0.00000
>>> 
>>> 31 32  0  0  0  0  0  0  0  0999 V2000
>>>   -2.6432   -0.0309    0.6774 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -2.2036   -1.1790   -0.2172 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.7991   -1.6331    0.1160 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>    0.3241   -0.7775   -0.4343 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>    1.6331   -1.4058    0.0509 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>    2.8306   -0.5087   -0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>    2.6352    0.7988    0.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>    1.3912    1.4864   -0.0064 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>    0.1356    0.6360    0.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.9531    1.3045   -0.6792 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -2.3079    1.3025   -0.0163 C   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -3.7179   -0.0927    0.8485 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -2.1170   -0.0887    1.6301 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -2.8894   -2.0160   -0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -2.2357   -0.8533   -1.2569 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.7009   -1.6662    1.2011 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.6708   -2.6472   -0.2626 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    0.2900   -0.7412   -1.5232 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    1.5678   -1.5781    1.1252 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    1.7765   -2.3618   -0.4528 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    3.7467   -0.9999    0.0916 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    2.8860   -0.2978   -1.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    2.5000    0.5811    1.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    3.5037    1.4431    0.4047 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    1.2584    2.4399    0.5048 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>    1.5290    1.6728   -1.0715 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.1504    0.5775    1.2421 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -0.6604    2.3351   -0.8794 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -1.0237    0.7700   -1.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -3.0673    1.5048   -0.7716 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>   -2.3353    2.1000    0.7263 H   0  0  0  0  0  0  0  0  0  0  0  0
>>>  1  2  1  0  0  0  0
>>>  2  3  1  0  0  0  0
>>>  3  4  1  0  0  0  0
>>>  4  5  1  0  0  0  0
>>>  5  6  1  0  0  0  0
>>>  6  7  1  0  0  0  0
>>>  7  8  1  0  0  0  0
>>>  8  9  1  0  0  0  0
>>>  4  9  1  0  0  0  0
>>>  9 10  1  0  0  0  0
>>> 10 11  1  0  0  0  0
>>>  1 11  1  0  0  0  0
>>>  1 12  1  0  0  0  0
>>>  1 13  1  0  0  0  0
>>>  2 14  1  0  0  0  0
>>>  2 15  1  0  0  0  0
>>>  3 16  1  0  0  0  0
>>>  3 17  1  0  0  0  0
>>>  4 18  1  0  0  0  0
>>>  5 19  1  0  0  0  0
>>>  5 20  1  0  0  0  0
>>>  6 21  1  0  0  0  0
>>>  6 22  1  0  0  0  0
>>>  7 23  1  0  0  0  0
>>>  7 24  1  0  0  0  0
>>>  8 25  1  0  0  0  0
>>>  8 26  1  0  0  0  0
>>>  9 27  1  0  0  0  0
>>> 10 28  1  0  0  0  0
>>> 10 29  1  0  0  0  0
>>> 11 30  1  0  0  0  0
>>> 11 31  1  0  0  0  0
>>>M  END
>>>$$$$
>>>=============
>>>Output:
>>>
>>>
>>>
>>>12:08:35 [INFO ] joelib.io.IOTypeHolder                   - 0 input/output types loaded.
>>>12:08:35 [ERROR] joelib.test.Convert                      - Input type 'SDF' not defined.
>>>12:08:35 [INFO ] joelib.desc.DescriptorHelper             - 0 descriptor informations loaded.
>>>Usage is :
>>>java -cp . joelib.test.Convert [options] <input file> [<output file>]
>>>
>>>Options:
>>> [-i<inputFormat>]       - Format of the input file
>>> [-o<outputFormat>]      - Format of the output file
>>> [-h]                    - Removes all hydrogens from molecule
>>> [+h]                    - Adds hydrogens to molecule
>>> [+p]                    - Adds only polar hydrogens (+h implicit)
>>> [-e]                    - Converts only non-empty molecules
>>> [-d]                    - Removes all descriptors from the molecule
>>> [+d]                    - Adds all available descriptors to the molecule
>>> [+v]                    - Switch verbosity ON
>>> [+snd]                  - Shows all available native value descriptors
>>> [+sad]                  - Shows all available atom property descriptors
>>> [+sall]                 - Shows all available descriptors
>>> [+x<descriptor name>]   - Converts only molecules where <descriptor name> exists
>>> [-r<skip  desc. rule>]  - Skips molecules, if rule fits
>>> [+r<conv. desc. rule>]  - Converts only molecules where rule fits
>>> [+f<lineStructure>]     - Required if you use FLAT output format which other input format
>>> [+s<lineStructure>]     - Can be used for an alternate SMILES entry line structure
>>> [-m<SMARTS rule>]       - Skips molecules, if SMARTS rule fits
>>> [+m<SMARTS rule>]       - Converts only molecules where SMARTS rule fits
>>> [-um<SMARTS rule>]      - Skips molecules, if unique SMARTS rule fits
>>> [+um<SMARTS rule>]      - Converts only molecules where unique SMARTS rule fits
>>> [-?][--help]            - Shows this message
>>>
>>>If no output file is defined, all molecules will be written to stdout.
>>>
>>>Filter rules have the form:
>>><native value descriptor><relation><value>
>>>where <relation> is <, <=, ==, >, >= or !=
>>>Example:
>>>"+rNumber_of_halogen_atoms==2"
>>>
>>>SMARTS filter rules have the form:
>>><SMARTS pattern><relation><value>
>>>where <relation> is <, <=, ==, >, >= or !=
>>>Example:
>>>"+umaNC=O==1"
>>>Converts all molecules, where the molecule contains ONE NC=O group connected to an aromatic atom (aNC=O).
>>>
>>>Supported molecule types:
>>>     Name          Readable      Writeable     Description
>>>----------------------------------------------------------
>>>   0 UNDEFINED     false         false         Undefined                                          
>>>
>>>Native value descriptors: 
>>>
>>>----------------------
>>>we...@in... wrote
>>>Hello,
>>>
>>>SMILES file: example.smi
>>>
>>>c1ccccc1 benzene
>>>CCC      propane
>>>
>>>then try
>>>sh convert.sh +d example.smi example.sdf
>>>
>>>
>>>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
>>
>>
>>
> 
> 
> 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
> 
> 

-- 
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

Thread: [Joelib-devel] Re: JOELib

joelib-devel