how to let structures in sdf be searchable over the internet

I am trying to let chemical structures in sdf file be searchable over the internet, like in the attahced picture.

I am trying to follow the instruction for example for 'inserting and modifing compounds and performing searches over the internet' http://www.chemaxon.com/jchem/examples/db_search/index.jsp,

This is the link for the instruction. http://www.chemaxon.com/jchem/examples/db_search/setup.html. At step 4, which database I should choose?  Do I have to have database server?

Thanks.

Hi,

Yes, you have to have a database server instance running that the web application can connect to.

The JChem Administration Guide lists the supported databases:

http://www.chemaxon.com/jchem/doc/admin/index.html

Please note that some of the supported databases are free.

I suggest to choose a database that is the easiest to install and administer for you.

MySQL and PostgreSQL mat be good choices, they are free and have windows installers if that helps.

Best regards,

Szilard 

 

 

Szilard,

Thank you for your reply.I have downloaded and installed MySQL to my computer.  I have another question as I do not know much about computer. How to fill the URL of database?  Thanks

Hi,

Please follow the Administration guide, section 4 "Connecting to Databases" privides a list of links for the URL format for each supported database. (below the screenshot):

http://www.chemaxon.com/jchem/doc/admin/#connect

For example for MySQL:

http://www.chemaxon.com/jchem/doc/admin/JChemBaseFAQ.html#mysql

When you install a MySQL database, usually a database called "test" is created by default.

You may need to create a user if you do not want to connect as root.

Please see the MySQL documentation on how to manage users and security.

Best regards,

Szilard

 

Szilard,

Sorry for the elementary question. I tried the URL of database for MySQL listed in Administration guide, but I was told the database URL is invalid.  I installed MySQL by default.

Thank you for your help.

 

Hi,

I do not see any obvious error in your connection string.

Could you let us know your JChem version ?

Best regards,

Szilard

 

Hi Szilard,

The Jchem version I am using is Version 5.11.3 Jchem for endusers and java developers. And I used 64bit windows installers for windows platform.

Thank you.

Hi,

My coleagues will try to reproduce this error - I could not.

A random tip until then: maybe something went wrong when you have copy/pasted the URL from a browser, and it's not visually apparent in the screenshot.

In that case it may worth to try to type in the URL.

Please note that the default database in MySQL is "test", if you want to use "mydb" you have to explicitly create it in MySQL.

Best regards,

Szilard

Hi, Szilard,

Thank you for your reply. I really appreciate it. But error message still shows up after I type the URL into that box.

I installed the MySQL by default. Either 'test' or 'mydb' in URL can not be connected.

For the login, I tried login name'root' with no password, and tried no login name with no password. Database still can not be connected.

Hi,

Your URL seems to be fine now in the screenshot.

Please note that the error message is different, the only remaining problem is authentication.

All you have to do now is to provide appropriate user credentails/ password to connect.

Please see the MySQL doumnetation on how to create user accounts:

http://dev.mysql.com/doc/refman/5.6/en/adding-users.html

Szilard