Periodic Boundary Conditions

Hello

Is it possible to store and search molecules in the database with Periodic Boundary Conditions?

Thank you

Joan,

Can you please explain more fully the context of your question?  How would storing and searching be affected?

 

Thanks,

Jon

Hello

The intention should be to load the atomic Cartesian coordinates together with the lattice parameters of the unit cell, in whitch the atoms are placed (VASP code input/output files).

Thank you,

Joan

MarvinSpace can display atoms within a surrounding box,
but it is a question whether we are supporting the VASP data.

Also, the JChem Base database technology does not have any tools for this kind of modelling work.

Thank you any way.

Best regards,

Joan

Dear Joan,

I am sorry, I can see that there remained some questions here.

 

Unfortunately, we do not support VASP files. You may consider converting them to another supported format:

http://www.chemaxon.com/marvin/help/formats/formats.html

 

And if you can extract the periodic boundary information from the files (e.g. from a Java program), you can store it in the same record as additional fields in a JChem table.

 

See more information here:

http://www.chemaxon.com/jchem/doc/dev/dbconcepts/index.html#tablestructure

 

Structure tables contain chemical structures and associated data, including both those used by the JChem system internally and custom, user defined data. (User defined data may be any information related to the chemical structure: name, external id, physico-chemical properties, etc. Any number and type of user defined data can be added to JChem tables (within the limits of the underlying RDBMS) and can be standard (static) or calculated columns). ... User defined columns can be added at table creation or any other time later.

 

Best regards,

Szabolcs

Thank you.

Best regards,

Joan