new mols.smart file &OR defining jep.script

I want to add more alias (names instead of SMARTS) which i could access using reactor. I learned that i could replace either mols.smarts file or define additional molecule sets in the user-defined initial script. The mols.smarts file in my computer is located in ..\MarvinBeans\help\chemicalterms\Evaluator_files or ..\JChem\marvin\help\chemicalterms\Evaluator_files. Am i suppose to replace this file with new mol.smarts file. If so how can SMARTS text file (newly defined) or SD file be converted to this file-type.

I strongly prefer to go for second option of using jep.script but i am not able to locate this file. Its not in the folder suggested or hidden. Is it present only for Developer version only? I have End-User version. If no where can i locate this file. Also How should i be able to create such JavaEmbeddedPython file, all i have is SMARTS. I am not computer savvy but if detailed well i could get some help from my partners. 

I am using Marvin 5.3.3 and Jchem 3.0.0 for windows. thanks a bunch.

Any news, comments, suggestions!!

bhhataba wrote:

I want to add more alias (names instead of SMARTS) which i could access using reactor. I learned that i could replace either mols.smarts file or define additional molecule sets in the user-defined initial script. The mols.smarts file in my computer is located in ..\MarvinBeans\help\chemicalterms\Evaluator_files or ..\JChem\marvin\help\chemicalterms\Evaluator_files. Am i suppose to replace this file with new mol.smarts file. If so how can SMARTS text file (newly defined) or SD file be converted to this file-type. I strongly prefer to go for second option of using jep.script but i am not able to locate this file. Its not in the folder suggested or hidden. Is it present only for Developer version only? I have End-User version. If no where can i locate this file. Also How should i be able to create such JavaEmbeddedPython file, all i have is SMARTS. I am not computer savvy but if detailed well i could get some help from my partners.

The location and the format of mols.smarts and jep.scripts is described in Evaluator help, in  Predefined Molecules and Molecule Sets section, please read it. The "..\MarvinBeans\help\chemicalterms\Evaluator_files" is the location of the help files, where we have a copy of mols.smarts for reference.

If you have an SDfile with names in "NAME" SDF field, then you can convert it to SMARTS with molconverter command line application using the following command:

$ molconvert smarts:TNAME test.sdf

There is no predefined jep.scripts included in Marvin or JChem, you should create it (in all versions) if you need it. If you use Marvin 5.3.3, then - on Windows - you should create the "<user home directory>/chemaxon/5.3/jep.script" file, where "<user home directory>" refers to your home directory.

Note: mols.smarts will be replaced with an other file in Marvin 5.4, which has different file format.

bhhataba wrote:

I am using Marvin 5.3.3 and Jchem 3.0.0 for windows. thanks a bunch.

Are you sure it's JChem 3.0.0? It's a quite old version, and we do not support it any more.

Zsolt

thanks a bunch. I am wondering if there is a format for the jep.script file such that i could modify it, a template as such.

Also, is it possible to define the path for the mol file in a different location using commands rather than replacing the existing mols.smarts file with a new one.

Thanks I am able to modify the sdf to smarts. The Jchem version i am using is 5.3.7 and updated to 5.3.8 recently, sorry for the confusion.

bhhataba wrote:

thanks a bunch. I am wondering if there is a format for the jep.script file such that i could modify it, a template as such.

The format is very simple: valid Chemical Terms expressions separated with semicolon. Semicolon may be omitted as long as you write each assignment in a separate line. See examples here, in the "Initial scripts" section.

bhhataba wrote:

Also, is it possible to define the path for the mol file in a different location using commands rather than replacing the existing mols.smarts file with a new one.

The built-in mols.smarts is located in C:\Program Files (x86)\ChemAxon\MarvinBeans\lib\MarvinBeans-jep.jar JAR file (if the default installation is followed). You don't have to modify it, just create an other one in "<user home directory>/chemaxon/5.3/" directory. The contents of the newly created file will be added to the built-in.

I hope this helps.

Zsolt

Hi there,

In functionalgroups.cxsmi it is the 'representations' or the 'query' that is the actual representation of 'names'. How are 'representations' generated? Thank you.

The "query" column constaints SMARTS that can be used as a query
structure to find the corresponding functional groups by substructure
searching. We use these SMARTS queries in Chemical Terms expressions like match(nitro).

The "representations" column contains structures in a visualizable form (having R-atoms) in extended SMILES format. If you move the mouse over the word "nitro" in the chemicla terms editor, you will see a picture created from the "representations column".