generating iupac and tradional name

what is the syntax to generate iupac and traditional names from an sd file of structures and store them in a new iupac and tradional name field?





Is there any functionality to generate the above using jchem manager whilst importing an sd file into a database table. e.g. like when it generates the smile strings, formula and mol weights?

ob4ect wrote:

what is the syntax to generate iupac and traditional names from an sd file of structures and store them in a new iupac and traditional name field?

Generate preferred IUPAC names and store them in "iupac" SD field (input file: test.sdf, output file: names.sdf):

Code:

cxcalc -S -t "iupac" -o names.sdf name test.sdf

Generate traditional names and store them in "traditional name" SD field (input file: the previously generated names.sdf, output file: names2.sdf):

Code:

cxcalc -S -t "traditional name" -o names2.sdf name -t traditional names.sdf

After these two steps the output will contain a "iupac" field with preferred IUPAC name and a "traditional name" field with traditional name.





Using pipelining capabilities of Unix/Linux systems these two steps can be executed in one step:

Code:

cxcalc -S -t "iupac" name test.sdf | cxcalc -S -t "traditional name" -o names2.sdf name -t traditional

Store both names in one field, named "iupac and traditional names":

Code:

cxcalc -S -t "iupac and traditional names" -o bothnames.sdf name -t preferred,traditional test.sdf

Quote:

Is there any functionality to generate the above using jchem manager whilst importing an sd file into a database table. e.g. like when it generates the smile strings, formula and mol weights?

Yes, you can add a Chemical Terms field to JChem table, that generates the preferred IUPAC name or traditional name.





Chemical Terms expression for generating preferred IUPAC name:

Code:

name()

Chemical Terms expression for generating traditional name:

Code:

traditionalName()

Adding a Chemical Terms field to a JChem table using JChemManager: http://www.chemaxon.com/jchem/doc/admin/index.html#tableTypes


(See the screenshot, and the description below screenshot.)





Adding a Chemical Terms field to a JChem table using Instant JChem application: http://www.chemaxon.com/instantjchem/webPages/htmlFiles/chemical_terms_fields.html





I have attached the result file of the command line example (names2.sdf).





Best regards,


Zsolt

why does the iupac naming plugin require a license yet marvin sketch will generate the iupac name wihtout a license?

ob4ect wrote:

why does the iupac naming plugin require a license yet marvin sketch will generate the iupac name wihtout a license?

In single mode IUPAC Naming plugin does not require a license, but in batch mode license is required.





Batch mode:


- cxcalc ("name" calculation),


- Chemical Terms ("name()" and "taditionalName()" functions),


- API,


- molconvert (converting to "name" format),


- saving more than one molecule in name format from MarvinView.





Note: In Instant JChem Chemical Terms is used for calculation, so license is required.





Best regards,


Zsolt

so how does one go about acquiring a license to use these features in batch mode if you are a student and using it for academic purpose?

ob4ect wrote:

so how does one go about acquiring a license to use these features in batch mode if you are a student and using it for academic purpose?

Hi,





Follow this link. You will need an active forum registration to apply.





Zsolt