JChem Fragmenter 5.8 Error While Running Example Files

 

Dear All,

I'm a new user for this software Fragmenter (in Jchem 5.8 version). I have installed it on Windows Vista system. I had followed all the instructions for installation and it went okay!

When i gave "fragment -c Fragmenter.xml input.mol -f sdf:-a -o fragments1.sdf" windows command line.... the output file gives errror of access denied to file fragments1.sdf...

but when i give "fragment -c Fragmenter.xml input.mol" i can see the results... there is some conflict happening in windows. Can any one please help me with his?

I'm also attaching the screenshot of this error message.

Regards,

Ankit

 

Try to start the windows command prompt in Administrator mode; or try the give another output file location (you can write on), e.g.:

-o d:\fragmenter1.sdf

"Access is denied" means that ,in a nutshell, you do not have the right to write to your C:\Program Files\folder.

Since the command, you copied, would like to create an output file named: fragments1.sdf to the same location (C:\Program Files\Chemaxon\JChem\examples\fragmenter folder.) you need to have "administrator" rights to make it possible.

BR,

Viktoria

vpalfi wrote:

Try to start the windows command prompt in Administrator mode; or try the give another output file location (you can write on), e.g.: -o d:\fragmenter1.sdf "Access is denied" means that ,in a nutshell, you do not have the right to write to your C:\Program Files\folder. Since the command, you copied, would like to create an output file named: fragments1.sdf to the same location (C:\Program Files\Chemaxon\JChem\examples\fragmenter folder.) you need to have "administrator" rights to make it possible. BR, Viktoria

Thanks very much I got it solved now :)

I was working with fragmenterstatistics for that i need to insert a table of structures with its activity to command prompt in windows (my OS)

Now to create that table of structures and activity i need to use JChem Manger and create a local data base... for configuring this tool I need to have oracle or msql data bases installed in my system.

I'm a chemist and trying to work with this computational stuff.... so I wanted to ask you do I have to carry out following steps?

1) creating database with tables in MySQL work bench 

2) And then giving its URL to JChem manager?

or if I have wrongly interpreted this then kindly tell me the most simplest way to configure Manager so that I can easily make table for structures and start my analysis.

Waiting for your reply

Regards,

Ankit

Hi Ankit,

JChemManager can handle more type of databases: http://www.chemaxon.com/jchem/doc/admin/JChemBaseFAQ.html#JCMAN_X_host. />The simplest is the use of Derby. If you have installed JChem on your machine, then Derby must work.

Start JChemManager
Fill connection window:
JDBC driver: org.apache.derby.jdbc.EmbeddedDriver
URL of database: jdbc:derby:c:\derby;create=true
Property Table: JChemProperties
Login name
Password

In the URL of database the c:\derby is only a suggestion, it depends on you to dedicate a place in your filesystem. Do not create this folder before starting jcman.
Login name and password are optional.

The use of the other type of databases needs them to be created before starting JChemManager (possible by a system administrator).

With JChemManager you will be able to create different kind of tables, then insert, modify, delete, export data, etc., that is not necessary to create tables with any other tools before using JChemManager.

This documentations may help you:
http://www.chemaxon.com/jchem/doc/admin/

Best reagrds

Krisztina

Thnx it worked.... I will get back if i have some questions regarding creating table and fragmentstats :)

anrochani wrote:

Thnx it worked.... I will get back if i have some questions regarding creating table and fragmentstats :)

Dear all,

I had been trying to make table in .sdf format ( using Jchem Manager) like beta2_adrenoreceptor_antagonist for carrying out my fragmentstat analysis... using command line example given as

 

fragment -c FragmenterAll.xml beta2_adrenoceptor_antagonists.sdf -s ACTIVITY -o fragments.cxsmiles

Actually i want to make table with fields as activity and structures in it..

Can you tell me how do I to do this. I have now Jchem manager working... please guide me what should i do? 

 

So if you want to create a table containing your structures and the activity data of each structure there are two ways inJChem to execute this. Starting from and sdf file containing the structures:

1 Using JCMan GUI

1a Create a „Molecules” type table, import the structures.sdf, then Modify this table (Add column: Activity, Type: float)
1b. Open the same database  (as used with JCMan GUI) with another database handling software and enter the data into the Activity column.
1c. Open JCMan GUI again and export the table into new sdf file

 

2 Using JChem for Excel

2a. Install JChem for Excel http://www.chemaxon.com/download/jchem-for-excel/ />2b. Run MS Excel (32 bit version)
2c. Select JChem on Excel menubar, import structures.sdf
2d. Add new Column for Activity values, enter the values
2e. Export into new sdf file

 

Best Regards,

Krisztina