Command syntax incorrect - ChemAxon Forum Archive

User dba550fffe

12-02-2009 10:32:58

Hi,

I have some problens when use the screenmd, in the exemple "Pharmacophore similarity" http://www.chemaxon.com/jchem/examples/screen/index.html#screen_pharma; I obtain this error "The command syntax is incorrect." I don't know what is the problem.

Conditions:

jchem-5_1_04-windows_with_jre.exe

Windows Xp

Microsoft Access

Freddy Rodrigues

ChemAxon efa1591b5a

12-02-2009 10:38:30

Hi,

can you copy the exact command you typed and the full error message as well? If copy/paste is not working in your command/terminal window, a screen snapshot is also fine.

Apologies for any inconvenience this problem might cause...

Regards,

Miklos

User dba550fffe

12-02-2009 11:37:11

Hi,

Command: pmapper nci1000.sdf -c pharma-frag.xml -o nci1000-pmap.sdf -S -t PMAP-FRAG

Can you help

Freddy Rodrigues

ChemAxon efa1591b5a

12-02-2009 11:47:21

Please check this document first: http://www.chemaxon.com/jchem/doc/admin/prepscripts.html

Does this help?

Miklos

User dba550fffe

12-02-2009 14:12:34

Hi;

This are my environment Variables:

PATH - D:\Programas\OpenBabel-2.2.0;D:\Programas\ChemAxon\JChem\bin

CHEMAXON_LICENSE_URL - D:\Programas\ChemAxon\license.cxl

CLASSPATH - sun.jdbc.odbc.JdbcOdbcDriver;D:\Programas\ChemAxon\JChem\lib\jchem.jar

JAVA_HEAP_SIZE - 700m

JAVA_HOME - D:\Programas\Java\jre1.6.0_07

JCHEMHOME - D:\Programas\ChemAxon\JChem

Path - D:\Programas\ChemAxon\JChem\.\.install4j;d:\programas\java\jre1.6.0_03\bin\client;D:\PROGRA~1\Java\JRE16~3.0_0\bin;D:\PROGRA~1\Java\JRE16~3.0_0\bin;D:\Programas\Mozilla Firefox;D:\WINDOWS\system32;D:\WINDOWS;D:\WINDOWS\system32\WBEM;D:\Programas\ATI Technologies\ATI.ACE\;D:\Programas\Ficheiros comuns\MDL SHARED\ISIS;D:\Programas\Microsoft SQL Server\80\Tools\Binn\;D:\Programas\OpenBabel-2.1.1;D:\PROGRA~1\FICHEI~1\MUVEET~1\030625;.;D:\programas\java\jre1.6.0_03\bin;D:\Programas\Microsoft SQL Server\90\Tools\binn\;D:\Programas\OpenBabel-2.2.0;D:\PROGRA~1\FICHEI~1\MUVEET~1\030625;d:\programas\chemaxon\jchem\jre\bin;D:\Programas\ChemAxon\JChem\bin

jchemManager

JDBC driver: sun.jdbc.odbc.JdbcOdbcDriver

URL of database: jdbc:odbc:myAccess

Property table: JChemProperties

When execute the command line.

pmapper nci1000.sdf -c pharma-frag.xml -o nci1000-pmap.sdf -S -t PMAP-FRAG

I obtain the same error.

User dba550fffe

17-02-2009 09:44:43

Some days I placed in this forum some information about the program like environmental

variables and other thinks, because a have the same problem "The syntax

command is incorrect".

Can help me

Freddy Rodrigues

ChemAxon efa1591b5a

17-02-2009 10:23:11

Hi,

I don't quite understand your last post. I reckon the long word document in XML has little relevance. If so, could you please remove it?

Regarding your environment, setting looks good. However, the PATH and Path are a bit odd. Try to add all access paths to PATH rather than Path.

It appears to me the jcman command does work, is that right?

Please obtain a list of command in your jchem\bin folder and copy in a message in this forum. Try to execute some commands that you find in that directory. You can try all that have .bat extension.

You can try pmapper without any parameter. What happens?

HTH

Miklos

User dba550fffe

17-02-2009 11:33:08

Hi;

list of command in the jchen/bin folder:

compr, config, count, crview, cxcalc, enumerate, evaluate, fragment, fragstat, generatemd, generfp, hitstatistics, jarp, jchem2actx, jcman, jcsearch, libmcs, license, mcs, molconvert, moledit, molfragment, msketch, mspade, mview, nneib, optimizemetrics, pca, pmapper, react, reactionTester, regactx, rgdecomp, rmap, rtest, screeningoptimizer, screenmd, setup, standardize, standedit, synthesisbrowser, synthesize, toxiccalc, toxicophore, ward.

When execute the command pmapper the result is in the attach file.

The command jcman work well, I created a database.

I do this add all access paths to PATH rather than Path.

When I put in the command line same .bat extension, I don't obtain error.

Other problem, is when make this command line.

D:\Programas\ChemAxon\JChem\bin>pmapper -h

I obtain the same error: "The syntax command is incorrect"

Freddy Rodrigues

ChemAxon efa1591b5a

18-02-2009 09:20:48

Thanks for all the information. It's quite puzzling though.

Your command in jchem/bin are just fine, nothing is missing, your installation is complete.

It appears, that all commands, including pmapper works, though you cannot pass any parameters in the command line, is that correct?

Did you try other applications?

Could you try something like this: java -cp lib\jchem.jar chemaxon.pharmacophore.PMapper -h

Does this work at all?

regards

Miklos

User dba550fffe

18-02-2009 09:57:44

Hi,

Sorry again, is true when I try to place some parameters the mistake is the same:

Examples:

screenmd -h

The syntax command is incorrect

screemd -s

The syntax command is incorrect

screenmd -x

The syntax command is incorrect

When I try the line command.

java -cp lib\jchem.jar chemaxon.pharmacophore.PMapper -h

Exception in thread "main" java.lang.NoClassDefFoundError: chemaxon/pharmacophore/PMapper

Regards,

Freddy Rdodrigues

ChemAxon efa1591b5a

09-03-2009 09:39:31

<span style="font-family: Times; font-size: 16px;">

Hi,

Is the folder "Utilizador" your JChem installation directory? Because, the command I suggested 'java -cp ... ' only works in that directory. The error message you received indicates, that lib\jchem.jar is not under Utilizador.

Regarding the pmapper command (and apparently, all other commands you tried), it's strange that no command line parameters can be passed. Could you try this short experiement

1. Open a command window.

2. Type this:

Code:

copy con: dd.bat

Code:

dir %1

Code:

Ctrl Z

3. Now you created a command, dd, which is a .bat (batch) file. It executes the dir command (list the content of the directory (folder) passed as a command line parameters).

So try this, for instance:

Code:

dd .

It should work and produce a list of file names in your current working directory. Did it work?

Regards

Miklos

User dba550fffe

10-03-2009 13:26:44

Hi

Sorry again, the command "java -cp ...", work well and I make the experiment and work well.

So I going in the directory Bin and make the fallow command.

D:\Programas\ChemAxon\JChem\bin>pmapper -h

The sintax error is incorrect.

Obtain the same error.

Whem I make the command we obtain

D:\Programas\ChemAxon\JChem\bin>pmapper

PMapper 5.1.4, (C) 1999-2008 ChemAxon Ltd.

Determination of pharmacophore properties.

Usage:

pmapper [options] [input files]

Options:

-h, --help                    this help message

-c, --config        path of the XML configuration file

-o, --output

       output file path (default: stdout)

-t, --tag                     name of the SDFile tag to store the

                                Pharmacophore Map (default: PMAP)

-S, --sdf-output              SDF output (otherwise only PMAP list)

-g, --ignore-error                  continue with next molecule on error

-v, --verbose                 print calculation warnings to the console

Examples:

pmapper -c Pharmacophores.xml m.mol

pmapper -S -t PHARMACOPHORES -c Pharmacophores.xml m.mol -o o.sdf

I thing is the .bat files doesn't work.

Regards

Freddy Rodrigues

ChemAxon efa1591b5a

10-03-2009 13:34:36

Yes, I agree with you, I also suspect that .bat files are not o.k.

Can you attach the pmapper.bat file?

thanks

Miklos

User dba550fffe

10-03-2009 13:43:44

Hi,

The .bat file.

Regards

Freddy Rodrigues

ChemAxon efa1591b5a

19-03-2009 13:20:52

Hi,

The batch files are ok. thanks for sending.

We managed to reproduce the problem, the reason is not yet identified. The strange fact is that it is only version 5.1.4 that suffers from this odd behaviour. All .bat files in that release produce the same error. The good new is that the most recent version of JChem, release 5.2 works all right.

Please download the new version and upgrade your old JChem installiation.

We apologise for any inconvenience.

Regards

Miklos